ORCID Profile
0000-0001-9587-9457
Current Organisation
Curtin University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Theoretical and Computational Chemistry | Physical Chemistry (Incl. Structural) | Nanotechnology | Nanotechnology | Condensed Matter Physics—Structural Properties | Solid State Chemistry | Structural Chemistry | Chemical Spectroscopy | Colloid And Surface Chemistry | Condensed Matter Physics | Mineralogy And Crystallography | Biomaterials | Quantum Chemistry | Theory Of Materials | Theoretical and Computational Chemistry not elsewhere classified | Theoretical And Computational Chemistry Not Elsewhere Classified | Chemical Thermodynamics And Energetics | Biological And Medical Chemistry | Organic Chemical Synthesis | Chemistry Of Catalysis | Resources Engineering Not Elsewhere Classified | Chemical Sciences Not Elsewhere Classified | Computation Theory and Mathematics | Alloy Materials | Instruments And Techniques | Petroleum Geology | Biophysics | Physical Chemistry not elsewhere classified | Membrane Biology | Resources Engineering and Extractive Metallurgy | Materials Engineering | Environmental Engineering Not Elsewhere Classified | Other Information, Computing And Communication Sciences | Condensed Matter Physics—Other | Computation Theory And Mathematics Not Elsewhere Classified | Simulation And Modelling | Bioinorganic Chemistry | Organic Chemistry | Engineering And Technology Not Elsewhere Classified | Macromolecular and Materials Chemistry | Inorganic Chemistry | Transition Metal Chemistry | Statistical Mechanics | Electrochemistry | Inorganic Geochemistry | Nanoscale Characterisation | Industrial Chemistry | Supramolecular Chemistry | Materials Engineering Not Elsewhere Classified | Surfaces and Structural Properties of Condensed Matter | Molecular and Organic Electronics | Condensed Matter Imaging
ANZSRC Socio-Economic Objective (SEO)
Chemical sciences | Physical sciences | Manufactured products not elsewhere classified | Expanding Knowledge in the Chemical Sciences | Biological sciences | Earth sciences | Energy storage | Energy transformation not elsewhere classified | Computer software and services not elsewhere classified | Application packages | Materials performance and processes | Alumina production | Ceramics, glass and industrial mineral products not elsewhere classified | Diagnostics | Computer hardware and electronic equipment not elsewhere classified | Inorganic industrial chemicals | Organic industrial chemicals not classified elsewhere | Other | Conservation and efficiency | Energy transformation | Gas—conversion to liquid fuels | Land and water management | Industrial chemicals and related products | Expanding Knowledge in the Earth Sciences | Expanding Knowledge in the Physical Sciences | Treatments (e.g. chemicals, antibiotics) |
Related Links
Publications
Atomistic simulation of Mg2SiO4 and Mg2GeO4 spinels: a new model
Publisher: Springer Science and Business Media LLC
Date: 22-07-2005
Computational study of LnGaO3(Ln = La–Gd) perovskites
Publisher: IOP Publishing
Date: 15-09-2005
Uncovering the Atomistic Mechanism for Calcite Step Growth
Publisher: Wiley
Date: 13-04-2017
Abstract: Determining a complete atomic-level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO
Introducing the crystalline phase of dicalcium phosphate monohydrate
Publisher: Springer Science and Business Media LLC
Date: 24-03-2020
DOI: 10.1038/S41467-020-15333-6
Abstract: Calcium orthophosphates (CaPs) are important in geology, biomineralization, animal metabolism and biomedicine, and constitute a structurally and chemically erse class of minerals. In the case of dicalcium phosphates, ever since brushite (CaHPO 4 ·2H 2 O, dicalcium phosphate dihydrate, DCPD) and monetite (CaHPO 4 , dicalcium phosphate, DCP) were first described in 19 th century, the form with intermediary chemical formula CaHPO 4 ·H 2 O (dicalcium phosphate monohydrate, DCPM) has remained elusive. Here, we report the synthesis and crystal structure determination of DCPM. This form of CaP is found to crystallize from amorphous calcium hydrogen phosphate (ACHP) in water-poor environments. The crystal structure of DCPM is determined to show a layered structure with a monoclinic symmetry. DCPM is metastable in water, but can be stabilized by organics, and has a higher alkalinity than DCP and DCPD. This study serves as an inspiration for the future exploration of DCPM’s potential role in biomineralization, or biomedical applications.
Reactive force field simulation of proton diffusion in BaZrO3using an empirical valence bond approach
Publisher: IOP Publishing
Date: 03-08-2011
DOI: 10.1088/0953-8984/23/33/334213
Abstract: A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO(3) has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO(3) have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.
Defects and dislocations in MgO: atomic scale models of impurity segregation and fast pipe diffusion
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0JM01550D
A first principles study of the distribution of iron in sphalerite
Publisher: Elsevier BV
Date: 06-2010
CrystalGrower: a generic computer program for Monte Carlo modelling of crystal growth
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0SC05017B
Abstract: Generic in silico methodology – CrystalGrower – for simulating crystal habit and nanoscopic surface topology to determine crystallisation free energies.
Predicting crystal growth via a unified kinetic three-dimensional partition model
Publisher: Springer Science and Business Media LLC
Date: 04-2017
DOI: 10.1038/NATURE21684
Abstract: Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails iding the structure into 'natural tiles' or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a erse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and l-cystine.
The SIESTA method; developments and applicability
Publisher: IOP Publishing
Date: 24-01-2008
DOI: 10.1088/0953-8984/20/6/064208
Abstract: Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.
Structure and Surface Complexation at the Calcite(104)–Water Interface
Publisher: American Chemical Society (ACS)
Date: 03-09-2021
Climate change frames debate over the extinction of megafauna in Sahul (Pleistocene Australia-New Guinea)
Publisher: Proceedings of the National Academy of Sciences
Date: 06-05-2013
Abstract: Around 88 large vertebrate taxa disappeared from Sahul sometime during the Pleistocene, with the majority of losses (54 taxa) clearly taking place within the last 400,000 years. The largest was the 2.8-ton browsing Diprotodon optatum , whereas the ∼100- to 130-kg marsupial lion, Thylacoleo carnifex , the world’s most specialized mammalian carnivore, and Varanus priscus , the largest lizard known, were formidable predators. Explanations for these extinctions have centered on climatic change or human activities. Here, we review the evidence and arguments for both. Human involvement in the disappearance of some species remains possible but unproven. Mounting evidence points to the loss of most species before the peopling of Sahul (circa 50–45 ka) and a significant role for climate change in the disappearance of the continent’s megafauna.
From fused aromatics to graphene-like nanoribbons: The effects of multiple terminal groups, length and symmetric pathways on charge transport
Publisher: American Physical Society (APS)
Date: 17-11-2011
Molecular dynamics simulations of liquid–liquid interfaces in an electric field: The water–1,2-dichloroethane interface
Publisher: AIP Publishing
Date: 28-10-2020
DOI: 10.1063/5.0027876
Abstract: The polarized interface between two immiscible liquids plays a central role in many technological processes. In particular, for electroanalytical and ion extraction applications, an external electric field is typically used to selectively induce the transfer of ionic species across the interfaces. Given that it is experimentally challenging to obtain an atomistic insight into the ion transfer process and the structure of liquid–liquid interfaces, atomistic simulations have often been used to fill this knowledge gap. However, due to the long-range nature of the electrostatic interactions and the use of 3D periodic boundary conditions, the use of external electric fields in molecular dynamics simulations requires special care. Here, we show how the simulation setup affects the dielectric response of the materials and demonstrate how by a careful design of the system it is possible to obtain the correct electric field on both sides of a liquid–liquid interface when using standard 3D Ewald summation methods. In order to prove the robustness of our approach, we ran extensive molecular dynamics simulations with a rigid-ion and polarizable force field of the water/1,2-dichloroethane interface in the presence of weak external electric fields.
Defect properties of albite
Publisher: Springer Science and Business Media LLC
Date: 05-12-2007
Extraordinary diphyodonty-related change in dental function for a tooth of the extinct marsupial Ekaltadeta ima (Propleopinae, Hypsiprymnodontidae)
Publisher: Elsevier BV
Date: 07-1995
Lattice Dynamics from Force-Fields as a Technique for Mineral Physics
Publisher: Mineralogical Society of America
Date: 2010
Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability.
Publisher: American Chemical Society (ACS)
Date: 08-09-2022
Abstract: Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative ex le. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for in idual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na
Short-Range Structure of Amorphous Calcium Hydrogen Phosphate
Publisher: American Chemical Society (ACS)
Date: 02-04-2019
Amino acid inspired microscale organization of metallic nanocrystals
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3TA13540C
A First Principles Study of Palladium Clusters in Gmelinite and Their Interaction with CO
Publisher: American Chemical Society (ACS)
Date: 09-06-2001
DOI: 10.1021/JP004219B
Interleukin-17 contributes to Ross River virus-induced arthritis and myositis
Publisher: Public Library of Science (PLoS)
Date: 10-02-2022
DOI: 10.1371/JOURNAL.PPAT.1010185
Abstract: Arthritogenic alphaviruses are mosquito-borne viruses that are a major cause of infectious arthropathies worldwide, and recent outbreaks of chikungunya virus and Ross River virus (RRV) infections highlight the need for robust intervention strategies. Alphaviral arthritis can persist for months after the initial acute disease, and is mediated by cellular immune responses. A common strategy to limit inflammation and pathology is to d en the overwhelming inflammatory responses by modulating proinflammatory cytokine pathways. Here, we investigate the contribution of interleukin-17 (IL-17), a cytokine involved in arthropathies such as rheumatoid arthritis, in the development RRV-induced arthritis and myositis. IL-17 was quantified in serum from RRV-infected patients, and mice were infected with RRV and joints and muscle tissues collected to analyse cellular infiltrates, tissue mRNA, cytokine expression, and joint and muscle histopathology. IL-17 expression was increased in musculoskeletal tissues and serum of RRV-infected mice and humans, respectively. IL-17–producing T cells and neutrophils contributed to the cellular infiltrate in the joint and muscle tissue during acute RRV disease in mice. Blockade of IL-17A/F using a monoclonal antibody (mAb) reduced disease severity in RRV-infected mice and led to decreased proinflammatory proteins, cellular infiltration in synovial tissues and cartilage damage, without affecting viral titers in inflamed tissues. IL-17A/F blockade triggered a shift in transcriptional profile of both leukocyte infiltrates and musculoskeletal stromal cells by downregulating proinflammatory genes. This study highlights a previously uncharacterized role for an effector cytokine in alphaviral pathology and points towards potential therapeutic benefit in targeting IL-17 to treat patients presenting with RRV-induced arthropathy.
Derivation of an Interatomic Potential for Fluoride-Containing Microporous Silicates and Germanates
Publisher: American Chemical Society (ACS)
Date: 19-01-2005
DOI: 10.1021/CM048406O
Infectious clones produce sars-cov-2 that causes severe pulmonary disease in infected k18-human ace2 mice
Publisher: American Society for Microbiology
Date: 27-04-2021
Abstract: To develop COVID-19 countermeasures, powerful research tools are essential. We produced a SARS-COV-2 reverse genetic (RG) infectious clone toolkit that will benefit a variety of investigations.
A computational study of the high voltage LixCoyMn4-yO8 cathode material
Publisher: Royal Society of Chemistry (RSC)
Date: 2000
DOI: 10.1039/B003636F
The Structure of CaSO4 Nanorods: The Precursor of Gypsum
Publisher: American Chemical Society (ACS)
Date: 06-06-2019
Molecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1JM13230J
Calcium Carbonate Polyamorphism and Its Role in Biomineralization: How Many Amorphous Calcium Carbonates Are There?
Publisher: Wiley
Date: 04-11-2012
Abstract: Although the polymorphism of calcium carbonate is well known, and its polymorphs--calcite, aragonite, and vaterite--have been highly studied in the context of biomineralization, polyamorphism is a much more recently discovered phenomenon, and the existence of more than one amorphous phase of calcium carbonate in biominerals has only very recently been understood. Here we summarize what is known about polyamorphism in calcium carbonate as well as what is understood about the role of amorphous calcium carbonate in biominerals. We show that consideration of the amorphous forms of calcium carbonate within the physical notion of polyamorphism leads to new insights when it comes to the mechanisms by which polymorphic structures can evolve in the first place. This not only has implications for our understanding of biomineralization, but also of the means by which crystallization may be controlled in medical, pharmaceutical, and industrial contexts.
Atomistic modeling and experimental studies of radiation damage in monazite-type LaPO4 ceramics
Publisher: Elsevier BV
Date: 02-2017
Simulation of Calcium Phosphate Species in Aqueous Solution: Force Field Derivation
Publisher: American Chemical Society (ACS)
Date: 19-01-2018
Abstract: A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO
An interatomic potential model for carbonates allowing for polarization effects
Publisher: Springer Science and Business Media LLC
Date: 08-2003
A Quantum Mechanically Derived Force Field To Predict CO2 Adsorption on Calcite {10.4} in an Aqueous Environment
Publisher: American Chemical Society (ACS)
Date: 20-10-2017
Prediction of inorganic crystal framework structures
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B315066F
Wetting Properties of the CO
Publisher: American Chemical Society (ACS)
Date: 12-11-2019
DOI: 10.1021/ACS.LANGMUIR.9B02881
Abstract: Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO
Crocetane: A potential marker of photic zone euxinia in thermally mature sediments and crude oils of Devonian age
Publisher: Elsevier BV
Date: 2009
Interatomic potential parameters for potassium tetrachlorozincate and their application to modelling its phase transformations
Publisher: International Union of Crystallography (IUCr)
Date: 27-04-2001
DOI: 10.1107/S0108767300017955
Abstract: An empirical fitting procedure is applied to derive interatomic potential parameters for a model phase transition system, namely potassium tetrachlorozincate (K(2)ZnCl(4)). The derived potential is found to reliably model the known crystallographic structure for the ferroelectric and paraelectric phases of this compound. Potential transferability is demonstrated by applying the parameters derived to the optimization of the known molecular structure for a similar inorganic system (rubidium tetrachlorozincate).
An ab initio study of methanol adsorption in zeolites
Publisher: Elsevier BV
Date: 12-1993
An analytical model for the thermal conductivity of silicon nanostructures
Publisher: AIP Publishing
Date: 06-05-2005
DOI: 10.1063/1.1898437
Abstract: A simple model of thermal conductivity, based on the harmonic theory of solids, is used to study the heat transfer in nanostructures. The thermal conductivity is obtained by summing the contribution of all the vibration modes of the system. All the vibrational properties (dispersion curves and relaxation time) that are used in the model are obtained using the data for bulk s les. The size effect is taken into account through the s ling of the Brillouin zone and the distance that a wave vector can travel between two boundaries in the structure. The model is used to predict the thermal conductivity of silicon nanowires and nanofilms, and demonstrates a good agreement with experimental results. Finally, using this model, the quality of the silicon interatomic potential, used for molecular-dynamics simulations of heat transfer, is evaluated.
Entropy Drives Calcium Carbonate Ion Association
Publisher: Wiley
Date: 14-09-2016
Abstract: The understanding of the molecular mechanisms underlying the early stages of crystallisation is still incomplete. In the case of calcium carbonate, experimental and computational evidence suggests that phase separation relies on so-called pre-nucleation clusters (PNCs). A thorough thermodynamic analysis of the enthalpic and entropic contributions to the overall free energy of PNC formation derived from three independent methods demonstrates that solute clustering is driven by entropy. This can be quantitatively rationalised by the release of water molecules from ion hydration layers, explaining why ion association is not limited to simple ion pairing. The key role of water release in this process suggests that PNC formation should be a common phenomenon in aqueous solutions.
A simulation study of the adsorption of nitrogen in Ca-chabazite
Publisher: Elsevier BV
Date: 08-2002
Parameterization of a potential function for the Ca 2+ -Ne and Ca 2+ -N 2 interactions using high-level ab initio data
Publisher: Informa UK Limited
Date: 20-10-2000
Reply to Brook et al: No empirical evidence for human overkill of megafauna in Sahul
Publisher: Proceedings of the National Academy of Sciences
Date: 25-07-2013
First-Principles Design of Well-Ordered Silica Nanotubes from Silica Monolayers and Nanorings
Publisher: American Chemical Society (ACS)
Date: 13-06-2007
DOI: 10.1021/JP070032+
Surface modification induced enhanced CO2 sorption in cucurbit[6]uril, an organic porous material
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7CP03866F
Abstract: Theoretical and experimental studies on CO 2 sorption of the organic macrocycle cucurbit[6]uril (CB[6]).
Simulations of minerals using density-functional theory based on atomic orbitals for linear scaling
Publisher: Springer Science and Business Media LLC
Date: 02-2004
Simulation of Crystallization of Biominerals
Publisher: Annual Reviews
Date: 07-2018
DOI: 10.1146/ANNUREV-MATSCI-070317-124327
Abstract: Biominerals are crucial materials that play a vital role in many forms of life. Understanding the various steps through which ions in aqueous environment associate to form increasingly structured particles that eventually transform into the final crystalline or amorphous poly(a)morph in the presence of biologically active molecules is therefore of great significance. In this context, computer modeling is now able to provide an accurate atomistic picture of the dynamics and thermodynamics of possible association events in solution, as well as to make predictions as to particle stability and possible alternative nucleation pathways, as a complement to experiment. This review provides a general overview of the most significant computational methods and of their achievements in this field, with a focus on calcium carbonate as the most abundant biomineral.
Many-Body Potential for Point Defect Clusters in Fe-C Alloys
Publisher: American Physical Society (APS)
Date: 21-05-2007
A new class of self-assembled monolayers on gold using an alkynyl group as a linker
Publisher: IEEE
Date: 2006
The interaction of methanol with Brønsted acid sites in ZSM-5
Publisher: Royal Society of Chemistry (RSC)
Date: 1991
DOI: 10.1039/C39910000178
A theoretical study of lithium intercalation into V6O13—a combined classical, quantum mechanical approach
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B103928H
Examining the Accuracy of Density Functional Theory for Predicting the Thermodynamics of Water Incorporation into Minerals: The Hydrates of Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 14-08-2013
DOI: 10.1021/JP4048105
Synthesis, characterisation and catalytic performance of the solid acid DAF-1
Publisher: Royal Society of Chemistry (RSC)
Date: 1995
DOI: 10.1039/FT9959103537
Stable prenucleation mineral clusters are liquid-like ionic polymers
Publisher: Springer Science and Business Media LLC
Date: 20-12-2011
DOI: 10.1038/NCOMMS1604
Attenuation and stability of chikv-nols, a live-attenuated chikungunya virus vaccine candidate
Publisher: MDPI AG
Date: 22-12-2019
Abstract: Our previous investigation of the nucleolar localisation sequence (NoLS) of chikungunya virus (CHIKV) capsid protein demonstrated the role of capsid in CHIKV virulence. Mutating the NoLS of capsid in CHIKV led to the development of a unique live-attenuated CHIKV vaccine candidate, termed CHIKV-NoLS. CHIKV-NoLS-immunised mice developed long-term immunity from CHIKV infection after a single dose. To further evaluate CHIKV-NoLS attenuation and suitability as a vaccine, we examined the footpad of inoculated mice for underlying CHIKV-NoLS-induced immunopathology by histological and flow cytometric analysis. In comparison to CHIKV-WT-infected mice, CHIKV-NoLS-inoculated mice exhibited minimal inflammation and tissue damage. To examine the stability of attenuation, the plaque phenotype and replication kinetics of CHIKV-NoLS were determined following extended in vitro passage. The average plaque size of CHIKV-NoLS remained notably smaller than CHIKV-WT after extended passage and attenuated replication was maintained. To examine thermostability, CHIKV-NoLS was stored at 21 °C, 4 °C, −20 °C and −80 °C and infectious CHIKV-NoLS quantified up to 84 days. The infectious titre of CHIKV-NoLS remains stable after 56 days when stored at either −20 °C or −80 °C. Interestingly, unlike CHIKV-WT, the infectious titre of CHIKV-NoLS is not sensitive to freeze thaw cycles. These data further demonstrate preclinical safety and stability of CHIKV-NoLS.
Interatomic potentials for the simulation of the zinc-blende and wurtzite forms ofZnS
Publisher:
American Physical Society (APS)
Date:
28-07-2004
Publisher: American Physical Society (APS)
Date: 28-07-2004
Atomistic theory and simulation of the morphology and structure of ionic nanoparticles
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1NR11106J
Abstract: Computational techniques are widely used to explore the structure and properties of nanomaterials. This review surveys the application of both quantum mechanical and force field based atomistic simulation methods to nanoparticles, with a particular focus on the methodologies available and the ways in which they can be utilised to study structure, phase stability and morphology. The main focus of this article is on partially ionic materials, from binary semiconductors through to mineral nanoparticles, with more detailed considered of three ex les, namely titania, zinc sulphide and calcium carbonate.
Does the Structural Water within Gypsum Remain Crystalline at the Aqueous Interface?
Publisher: American Chemical Society (ACS)
Date: 27-09-2021
Simulating the binding of key organic functional groups to aqueous calcium carbonate species
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1CP04226B
Abstract: The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing.
Computational-chemical assessments of well characterised uniform catalysts
Publisher: Royal Society of Chemistry (RSC)
Date: 1989
DOI: 10.1039/DC9898700079
The influence of pressure on the structure and dynamics of hydrogen bonds in zoisite and clinozoisite
Publisher: Springer Science and Business Media LLC
Date: 19-10-2007
Virtual reconstruction and prey size preference in the mid cenozoic thylacinid, Nimbacinus dicksoni (Thylacinidae, Marsupialia)
Publisher: Public Library of Science (PLoS)
Date: 09-04-2014
Vibrational Analysis of Brucite Surfaces and the Development of an Improved Force Field for Molecular Simulation of Interfaces
Publisher: American Chemical Society (ACS)
Date: 08-04-2014
DOI: 10.1021/JP411092B
Effects of cation disorder on oxygen vacancy migration in Gd2 Ti2 O7
Publisher: Springer Science and Business Media LLC
Date: 1999
Atomic scale modelling of the cores of dislocations in complex materials part 2: applications
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B505716G
Abstract: In an accompanying article, we have described a methodology for the simulation of dislocations in structurally complex materials. We illustrate the applicability of this method through studies of screw dislocations in a structurally simple ionic ceramic (MgO), a molecular ionic mineral (forsterite, Mg2SiO4), a semi-ionic zeolite (siliceous zeolite A) and a covalent molecular crystalline material (the pharmaceutical, orthorhombic paracetamol-II). We focus on the extent of relaxation and the structure of the dislocation cores and comment on similarities and points of disparity between these materials. It is found that the magnitude of the relaxation varies from material to material and does not simply correlate with the magnitude of the principal elastic constants in an easily predictable fashion, or with the size of the cohesive lattice energy or length of the Burgers vector, which emphasises the need to model the non-linear forces and atomic structure of the core.
Erratum: Magnetic properties of polymerizedC 60 Publisher:
American Physical Society (APS)
Date:
07-01-2005
Publisher: American Physical Society (APS)
Date: 07-01-2005
Can Point Defects in Surfaces in Solution be Atomically Resolved by Atomic Force Microscopy?
Publisher: American Physical Society (APS)
Date: 23-11-2016
Incorporation of Y and REEs in aluminosilicate garnet: Energetics from atomistic simulation
Publisher: Mineralogical Society of America
Date: 05-2014
DOI: 10.2138/AM.2014.4720
Thermodynamics of pyrope–majorite, Mg3Al2Si3O12–Mg4Si4O12, solid solution from atomistic model calculations
Publisher: Informa UK Limited
Date: 02-2006
The structure and dynamics of crystalline durene by neutron scattering and numerical modelling using density functional methods
Publisher: Elsevier BV
Date: 11-2000
A theoretical study of native acceptors in
Publisher: IOP Publishing
Date: 29-06-1998
Multilevel Computational Analysis of Fluorocarbon Polyatomic Deposition on Diamond
Publisher: American Chemical Society (ACS)
Date: 30-06-2010
DOI: 10.1021/JP100667N
Ground state structure ofBaZrO 3 Publisher:
American Physical Society (APS)
Date:
07-05-2009
Publisher: American Physical Society (APS)
Date: 07-05-2009
Calculation of the energetics of water incorporation in majorite garnet
Publisher: Mineralogical Society of America
Date: 05-2015
DOI: 10.2138/AM-2015-5063
Carbon-Based Metal-Free Catalysts for Electrocatalytic Reduction of Nitrogen for Synthesis of Ammonia at Ambient Conditions
Publisher: Wiley
Date: 16-01-2019
Abstract: The electrocatalytic nitrogen reduction reaction (NRR) is a promising catalytic system for N
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 02-04-2020
DOI: 10.26434/CHEMRXIV.11879805.V2
Abstract: The speciation of calcium carbonate in water is important to the geochemistry of the world’s oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we have derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid-ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 21-02-2020
DOI: 10.26434/CHEMRXIV.11879805.V1
Abstract: The speciation of calcium carbonate in water is important to the geochemistry of the world’s oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we have derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid-ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Monitoring the Dissolution and Hydrolysis of Pyrosulfate by Electrochemistry at a Liquid‐Liquid Microinterface Array
Publisher: Wiley
Date: 11-11-2022
Abstract: Dissolution and hydrolysis processes are important in a variety of settings, including industrial and environmental applications. In this work, the hydrolysis of pyrosulfate (disulfate) was investigated by ion‐transfer electrochemistry at an array of microinterfaces between two immiscible electrolyte solutions (μITIES). Current associated with pyrosulfate transfer was observed, but it decreased with time. This is due to the hydrolysis of pyrosulfate to hydrogen sulfate and sulfate. Corroborating data for the hydrolysis was obtained from pH measurements (acidification of the aqueous solution) and Raman spectroscopy (formation of sulfate and hydrogen sulfate). Measurement of the ion‐transfer potential from the voltammograms enabled estimation of pyrosulfate's Gibbs energy of transfer between the phases. Quantum mechanical calculations were employed to estimate the thermodynamics for the reactions of pyrosulfate, hydrogen sulfate and sulfate, which supported the experimentally observed trends. Altogether, these results illustrate the use of electrochemistry at the μITIES to characterise dissolution and hydrolysis processes.
Adsorption energetics of potassium sulfate dye inclusion crystals
Publisher: Elsevier BV
Date: 02-2003
Periodic ab initio determination of interatomic potentials for alumina
Publisher: IOP Publishing
Date: 10-1992
Water Is the Key to Nonclassical Nucleation of Amorphous Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 19-11-2010
DOI: 10.1021/JA108508K
Abstract: Calcium carbonate is a ubiquitous mineral that represents one of the most significant biominerals, a major contributor to carbon sequestration through geological deposits, and a technological hindrance as a result of scale formation. Amorphous calcium carbonate is intimately involved in the nucleation and growth of this material, yet much remains undiscovered regarding the atomic detail. Through dynamical simulation we demonstrate that nucleation of amorphous calcium carbonate follows a nonclassical pathway. This arises from the addition of ion pairs to clusters exhibiting a consistently exothermic free energy that persists with increasing particle size. Furthermore, the disruption of the surrounding water of solvation by the atomically rough surface reduces the barrier to growth to the order of ambient thermal energy, thereby allowing the amorphous phase to grow faster than crystalline polymorphs. Amorphous calcium carbonate nanoparticles are also found to exploit size-dependent water content to render itself more stable than the favored bulk phase, calcite, below a critical diameter of close to 4 nm.
A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies
Publisher: Springer Science and Business Media LLC
Date: 25-10-2007
Quasi-static deformation simulations of molecular crystals
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2CE01426B
Abstract: This research employs two computational methods to simulate shear deformation of molecular crystals it calculates slip barriers, finds rotational twinning, and predicts polymorphic transitions.
Chemical and Thermal Expansion of Calcium-Doped Lanthanum Chromite
Publisher: Elsevier BV
Date: 02-2000
Catalysis of nanotube plasticity under tensile strain
Publisher: American Physical Society (APS)
Date: 08-11-2002
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 07-04-2020
Simulation of proton diffusion in In-doped CaZrO3
Publisher: Elsevier BV
Date: 15-09-2008
Elastic stiffness coefficients of thenardite and their pressure and temperature dependence
Publisher: Walter de Gruyter GmbH
Date: 16-07-2012
Abstract: The elastic stiffness coefficients, c ij , of orthorhombic Na 2 SO 4 thenardite (space group Fddd) were measäured with an ultrasonic plane wave technique at ambient temperature as a function of hydrostatic pressure in the range of 0.1–70 MPa. The variation of the c ij in the range of 1–5000 MPa was studied with density functional theory (DFT) based calculations. The experimental results and the DFT calculations were used to derive a force-field model, which was then employed to compute lattice parameters and elastic stiffness tensors of thenardite and of two other Na 2 SO 4 polymorphs as functions of the temperature based on quasi-harmonic lattice dynamics. The structural parameters of the three polymorphs measured at high temperatures are reproduced to within 1.7% by the present calculations. Phases II (space group Pbnm ) and III ( Cmcm ) appear to have significantly higher entropies than thenardite in agreement with their metastable formation at higher temperatures.
Probing the Multiple Structures of Vaterite through Combined Computational and Experimental Raman Spectroscopy
Publisher: American Chemical Society (ACS)
Date: 17-11-2014
DOI: 10.1021/JP509958D
Prediction of novel alloy phases of Al with Sc or Ta
Publisher: Springer Science and Business Media LLC
Date: 07-05-2015
DOI: 10.1038/SREP09909
Abstract: Using the evolutionary optimization algorithm, as implemented in the USPEX crystal predictor program and first principles total energy calculations, the compositional phase diagrams for Al-Sc and Al-Ta alloy systems at zero temperature and pressure have been calculated. In addition to the known binary intermetallic phases, new potentially stable alloys, AlSc 3 and AlTa 7 , have been identified in the Al-poor region of the phase diagram. The dynamic and thermal stability of their lattices has been confirmed from the calculated vibrational normal mode spectra in the harmonic approximation.
Structural and Electronic Properties of the Layered LiNi0.5Mn0.5O2 Lithium Battery Material
Publisher: American Chemical Society (ACS)
Date: 09-10-2003
DOI: 10.1021/CM031098U
A new structural model for disorder in vaterite from first-principles calculations
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1CE05976A
Determination of the structure ofγ
Publisher: American Physical Society (APS)
Date: 28-06-2005
Atomistic model of diopside-K-jadeite (CaMgSi2O6-KAlSi2O6) solid solution
Publisher: Pleiades Publishing Ltd
Date: 07-2010
Assisted Desolvation as a Key Kinetic Step for Crystal Growth
Publisher: American Chemical Society (ACS)
Date: 21-09-2006
DOI: 10.1021/JA064706Q
Abstract: The crystallization of materials from a supersaturated solution is a fundamental chemical process. Although several very successful models that provide a qualitative understanding of the crystal growth process exist, in most cases the atomistic detail of crystal growth is not fully understood. In this work, molecular dynamics simulations of the morphologically most important surfaces of barite in contact with a supersaturated solution have been performed. The simulations show that an ordered and tightly bound layer of water molecules is present on the crystal surface. The approach of an ion to the surface requires desolvation of both the surface and the ion itself leading to an activated process that is rate limiting for two-dimensional nucleation to occur. However, desolvation on specific surfaces can be assisted by anions adsorbed on the crystal surface. This hypothesis, corroborated by crystallization and scanning electron microscopy studies, allows the rationalization of the morphology of barite crystals grown at different supersaturations.
Density functional theory study of the relative stability of the iron disulfide polymorphs pyrite and marcasite
Publisher: American Physical Society (APS)
Date: 12-03-2010
Development of a New Interatomic Potential for the Modeling of Ligand Field Effects
Publisher: American Chemical Society (ACS)
Date: 29-06-2001
DOI: 10.1021/JP010742U
GULP: A computer program for the symmetry-adapted simulation of solids
Publisher: Royal Society of Chemistry (RSC)
Date: 1997
DOI: 10.1039/A606455H
Corrigendum to “Crocetane: A potential marker of photic zone euxinia in thermally mature sediments and crude oils of Devonian age” [Org. Geochem. 40 (2009) 1–11]
Publisher: Elsevier BV
Date: 08-2011
Aufdeckung der Rolle von Hydrogencarbonat‐Ionen bei der Bildung von Calciumcarbonat im nahezu neutralen pH‐Bereich
Publisher: Wiley
Date: 18-06-2021
Abstract: Die Grundlagen der Mineralisation und die entsprechenden Mechanismen sind noch nicht ausreichend verstanden. Dies ist insbesondere für biologische und geologische Systeme der Fall. In dieser Studie konnte die Beteiligung von HCO 3 − ‐Ionen an der Nukleation von CaCO 3 durch quantitative Untersuchungen der Ionenassoziationen im nahezu neutralen pH‐Bereich nachgewiesen werden. Der strukturelle Einbau von HCO 3 − ‐Ionen in amorphe Intermediate konnte mittels ssNMR belegt werden und wird des Weiteren durch quantenmechanische Berechnungen sowie Simulationen der Moleküldynamik gestützt. Der Einfluss von HCO 3 − ‐Ionen erstreckt sich dabei auf 1) eine konkurrierende Rolle in Gleichgewichten bezüglich der Bildung von Ionenpaaren und Ionenclustern vor der Nukleation sowie auf 2) den Einbau in amorphe Mineralpartikel als wichtige strukturelle Komponente. Der Einfluss dieser aktiv beteiligten löslichen Spezies auf die Bildung von Calciumcarbonat ist von fundamentaler Bedeutung, um die physiologische und geologische Mineralisation in ihren Grundsätzen besser zu verstehen.
Proton Mobility in the In-Doped CaZrO3 Perovskite Oxide
Publisher: American Chemical Society (ACS)
Date: 05-2007
DOI: 10.1021/CM070291B
Theoretical and Experimental Investigations on the Morphology of Pharmaceutical Crystals
Publisher: Elsevier BV
Date: 07-2002
DOI: 10.1002/JPS.10148
A reactive force field for aqueous-calcium carbonate systems
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1CP21034C
Abstract: A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water.
Oxygen Spectroscopy and Polarization-Dependent Imaging Contrast (PIC)-Mapping of Calcium Carbonate Minerals and Biominerals
Publisher: American Chemical Society (ACS)
Date: 10-06-2014
DOI: 10.1021/JP503700G
Abstract: X-ray absorption near-edge structure (XANES) spectroscopy and spectromicroscopy have been extensively used to characterize biominerals. Using either Ca or C spectra, unique information has been obtained regarding amorphous biominerals and nanocrystal orientations. Building on these results, we demonstrate that recording XANES spectra of calcium carbonate at the oxygen K-edge enables polarization-dependent imaging contrast (PIC) mapping with unprecedented contrast, signal-to-noise ratio, and magnification. O and Ca spectra are presented for six calcium carbonate minerals: aragonite, calcite, vaterite, monohydrocalcite, and both hydrated and anhydrous amorphous calcium carbonate. The crystalline minerals reveal excellent agreement of the extent and direction of polarization dependences in simulated and experimental XANES spectra due to X-ray linear dichroism. This effect is particularly strong for aragonite, calcite, and vaterite. In natural biominerals, oxygen PIC-mapping generated high-magnification maps of unprecedented clarity from nacre and prismatic structures and their interface in Mytilus californianus shells. These maps revealed blocky aragonite crystals at the nacre-prismatic boundary and the narrowest calcite needle-prisms. In the tunic spicules of Herdmania momus, O PIC-mapping revealed the size and arrangement of some of the largest vaterite single crystals known. O spectroscopy therefore enables the simultaneous measurement of chemical and orientational information in CaCO3 biominerals and is thus a powerful means for analyzing these and other complex materials. As described here, PIC-mapping and spectroscopy at the O K-edge are methods for gathering valuable data that can be carried out using spectromicroscopy beamlines at most synchrotrons without the expense of additional equipment.
Conductance of a phenylene-vinylene molecular wire: Contact gap and tilt angle dependence
Publisher: American Physical Society (APS)
Date: 02-04-2010
Solubility-consistent force field simulations for aqueous metal carbonate systems using GPUs
Publisher: American Chemical Society (ACS)
Date: 30-01-2023
DOI: 10.26434/CHEMRXIV-2023-NRTBD-V2
Abstract: Crystallisation of alkaline earth metal carbonates from water is important for biomineralisation and environmental geochemistry. Here large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of in idual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to s le complex systems. Here we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on GPUs thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallisation, including ion-pairing and mineral-water interfacial structure and dynamics.
Understanding the Catalytic Behavior of Zeolites: A First-Principles Study of the Adsorption of Methanol
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-03-1996
Virtual Probes of Mineral-Water Interfaces: The More Flops, the Better!
Publisher: Mineralogical Society of America
Date: 06-2013
Computational Insight into Calcium–Sulfate Ion Pair Formation
Publisher: American Chemical Society (ACS)
Date: 14-11-2017
trans-1,2-Dicyano-cyclopropane and other cyano-cyclopropane derivatives
Publisher: Springer Science and Business Media LLC
Date: 17-10-2007
A Computational Investigation into the Suitability of Purely Siliceous Zeolites as Reverse Osmosis Membranes
Publisher: American Chemical Society (ACS)
Date: 23-02-2011
DOI: 10.1021/JP109591F
Where Is the Most Hydrophobic Region? Benzopurpurine Self-Assembly at the Calcite–Water Interface
Publisher: American Chemical Society (ACS)
Date: 24-10-2017
Computer-Simulation Study of the Orthorhombic−Hexagonal Phase Change in Lanthanide Manganates (LnMnO3)
Publisher: American Chemical Society (ACS)
Date: 29-03-2003
DOI: 10.1021/CM021324K
Development of Accurate Force Fields for the Simulation of Biomineralization
Publisher: Elsevier
Date: 2013
Calcite (104) Surface–Electrolyte Structure: A 3D Comparison of Surface X-ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 28-07-2020
Atomistic simulation of the crystal structures and bulk moduli of TiO 2 polymorphs
Publisher: Elsevier BV
Date: 04-2001
Thermodynamics of Catalytic Formation of Dimethyl Ether from Methanol in Acidic Zeolites
Publisher: Wiley
Date: 18-06-2001
DOI: 10.1002/1521-3765(20010618)7:12<2521::AID-CHEM25210>3.0.CO;2-N
Abstract: We present a theoretical study of the formation of the first intermediate, dimethyl ether, in the methanol to gasoline conversion within the framework of an ab initio molecular dynamics approach. The study is performed under conditions that closely resemble the reaction conditions in the zeolite catalyst including the full topology of the framework. The use of the method of thermodynamic integration allows us to extract the free-energy profile along the reaction coordinate. We find that the entropic contribution qualitatively alters the free-energy profile relative to the total energy profile. Different transition states are found from the internal and free energy profiles. The entropy contribution varies significantly along the reaction coordinate and is responsible for stabilizing the products and for lowering the energy barrier. The hugely inhomogeneous variation of the entropy can be understood in terms of elementary processes that take place during the chemical reaction. Our simulations provide new insights into the complex nature of this chemical reaction.
Determining the Adsorption Free Energies of Small Organic Molecules and Intrinsic Ions at the Terrace and Steps of Calcite
Publisher: American Chemical Society (ACS)
Date: 18-01-2022
Uncovering the Role of Bicarbonate in Calcium Carbonate Formation at Near‐Neutral pH
Publisher: Wiley
Date: 18-06-2021
Abstract: Mechanistic pathways relevant to mineralization are not well‐understood fundamentally, let alone in the context of their biological and geological environments. Through quantitative analysis of ion association at near‐neutral pH, we identify the involvement of HCO 3 − ions in CaCO 3 nucleation. Incorporation of HCO 3 − ions into the structure of amorphous intermediates is corroborated by solid‐state nuclear magnetic resonance spectroscopy, complemented by quantum mechanical calculations and molecular dynamics simulations. We identify the roles of HCO 3 − ions as being through (i) competition for ion association during the formation of ion pairs and ion clusters prior to nucleation and (ii) incorporation as a significant structural component of amorphous mineral particles. The roles of HCO 3 − ions as active soluble species and structural constituents in CaCO 3 formation are of fundamental importance and provide a basis for a better understanding of physiological and geological mineralization.
Computer simulation of defects and oxygen transport in yttria-stabilized zirconia
Publisher: Elsevier BV
Date: 15-06-2006
Modulation of monocyte-driven myositis in alphavirus infection reveals a role for CX3 CR1+ macrophages in tissue repair
Publisher: American Society for Microbiology
Date: 28-04-2020
Abstract: Arthritogenic alphaviruses cause debilitating inflammatory disease, and current therapies are restricted to palliative approaches. Here, we show that following monocyte-driven muscle inflammation, tissue recovery is associated with the accumulation of CX 3 CR1 + macrophages in the muscle. Modulating inflammatory monocyte infiltration using immune-modifying microparticles (IMP) reduced tissue damage and inflammation and enhanced the formation of tissue repair-associated CX 3 CR1 + macrophages in the muscle. This shows that modulating key effectors of viral inflammation using microparticles can alter the outcome of disease by facilitating the accumulation of macrophage subsets associated with tissue repair.
Theoretical simulation of localized holes in MgO
Publisher: IOP Publishing
Date: 29-06-1992
Ab Initio Simulations of the (101) Surfaces of Potassium Dihydrogenphosphate (KDP)
Publisher: American Chemical Society (ACS)
Date: 06-04-2006
DOI: 10.1021/CT060012W
Abstract: We have used density functional calculations to examine the (101) surfaces of KDP, under vacuum, nitrogen, and aqueous conditions, and these simulations are found to agree well with nanoscale experimental studies demonstrating that the density functional calculations are providing a good description of the surfaces of this complex inorganic salt.
Simulating the Dissolution and Growth of Zeolite Beta C
Publisher: Wiley
Date: 04-02-2005
Siesta : Recent developments and applications
Publisher: AIP Publishing
Date: 27-05-2020
DOI: 10.1063/5.0005077
Abstract: A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents ex les of application of the capabilities of the code, as well as a view of on-going and future developments.
ZeoTsites: a code for topological and crystallographic tetrahedral sites analysis in zeolites and zeotypes
Publisher: Elsevier BV
Date: 03-2001
Simulating micrometre-scale crystal growth from solution
Publisher: Springer Science and Business Media LLC
Date: 11-2005
DOI: 10.1038/NATURE04173
Abstract: Understanding crystal growth is essential for controlling the crystallization used in industrial separation and purification processes. Because solids interact through their surfaces, crystal shape can influence both chemical and physical properties. The thermodynamic morphology can readily be predicted, but most particle shapes are actually controlled by the kinetics of the atomic growth processes through which assembly occurs. Here we study the urea-solvent interface at the nanometre scale and report kinetic Monte Carlo simulations of the micrometre-scale three-dimensional growth of urea crystals. These simulations accurately reproduce experimentally observed crystal growth. Unlike previous models of crystal growth, no assumption is made that the morphology can be constructed from the results for independently growing surfaces or from an a priori specification of surface defect concentration. This approach offers insights into the role of the solvent, the degree of supersaturation, and the contribution that extended defects (such as screw dislocations) make to crystal growth. It also connects observations made at the nanometre scale, through in situ atomic force microscopy, with those made at the macroscopic level. If extended to include additives, the technique could lead to the computer-aided design of crystals.
Erratum: From fused aromatics to graphene-like nanoribbons: The effects of multiple terminal groups, length and symmetric pathways on charge transport [Phys. Rev. B84, 205436 (2011)]
Publisher: American Physical Society (APS)
Date: 16-07-2012
SIESTA: A Linear‐Scaling Method for Density Functional Calculations
Publisher: Wiley
Date: 05-07-2011
Magnetic properties of polymerizedC 60
Publisher:
American Physical Society (APS)
Date:
15-07-2004
Publisher: American Physical Society (APS)
Date: 15-07-2004
Subsolidus phase relations in Ca2Mo2O8–NaEuMo2O8-powellite solid solution predicted from static lattice energy calculations and Monte Carlo simulations
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B801912F
Abstract: Thermodynamic mixing properties and subsolidus phase relations of Ca2Mo2O8-NaEuMo2O8 powellites were modelled in the temperature range of 423-1773 K with static lattice energy calculations based on empirically constrained interatomic potentials. Relaxed static lattice energies (SLE) of a large set of randomly varied structures in a 4 x 4 x 2 supercell of I4(1)/a powellite (a = 5.226 A, c = 11.433 A) containing 128 exchangeable (Ca, Na and Eu) atoms were calculated using the general utility lattice program (GULP). These energies were cluster expanded in the basis set of 69 pair-wise effective interactions and three configuration-independent parameters. Temperature-dependent enthalpies of mixing were calculated using the Monte Carlo method. Free energies of mixing were obtained by thermodynamic integration of the Monte Carlo results. The simulations suggest that the NaEuMo2O8 end-member is nearly fully ordered and has I4[combining macron] symmetry. The calculated subsolidus temperature-composition phase diagram is dominated by three miscibility gaps which are separated by narrow fields of stability of two ordered phases with the compositions of x = 4/9 and x = 2/3, where x is the mole fraction of the NaEuMo2O8 end-member.
Molecular properties of the magnesia surface
Publisher: American Chemical Society (ACS)
Date: 12-1992
DOI: 10.1021/J100204A052
Defect interactions and ionic transport in scandia stabilized zirconia
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B902764E
Abstract: Classical molecular dynamics simulation has been used to study ionic transport in scandia-stabilized zirconia, as well as scandia and yttria-co-doped zirconia, as a function of temperature and composition. The oxygen diffusion coefficient shows a peak at a composition of 6 mol% Sc(2)O(3). At 1125 K and higher temperatures, oxygen vacancies prefer to be second nearest neighbours to yttrium ions and first neighbours to scandium ions, because the defect interactions in scandia-stabilized zirconia are governed mainly by electrostatic effects. Oxygen migration between cation tetrahedra is impeded less effectively by Sc-Sc edges than by Y-Y edges. The formation of neutral dopant-anion vacancy clusters is favoured, in agreement with recent nuclear magnetic resonance observations.
Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories
Publisher: American Chemical Society (ACS)
Date: 18-07-2011
DOI: 10.1021/JA204714K
Abstract: Mineral growth and dissolution are often treated as occurring via a single reversible process that governs the rate of reaction. We show that multiple distinct intermediate states can occur during both growth and dissolution. Specifically, we used metadynamics, a method for efficiently exploring the free-energy landscape of a system, coupled to umbrella s ling and reactive flux calculations to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped barite (BaSO(4)) surface. The activation energies calculated for the rate-limiting reactions, which are different for attachment and detachment, precisely match those measured experimentally during both growth and dissolution. These results can potentially explain anomalous non-steady-state mineral reaction rates observed experimentally and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.
Atomistic models of carbonate minerals: Bulk and surface structures, defects, and diffusion
Publisher: Informa UK Limited
Date: 06-2002
Thermodynamics of mixing and ordering in pyrope — grossular solid solution
Publisher: Mineralogical Society
Date: 02-2004
Abstract: Static lattice energy calculations have been combined with cluster expansion formalism to predict pairwise ordering interactions in the pyrope–grossular solid solution. The ordering interactions, the Js, have been then used to calculate the activity-composition relations over a wide temperature range with the help of the Cluster Variation Method. It is shown that short-range ordering in the system is driven by size mismatch. The prediction of the right signs and magnitudes of the ordering interaction energies requires separation of the mixing enthalpy into the configuration-dependent (chemical) and the configuration-independent (elastic) components. The study predicts the existence of a miscibility gap below 500°C.
Solubility-consistent force field simulations for aqueous metal carbonate systems using graphical processing units
Publisher: The Royal Society
Date: 22-05-2023
Abstract: Crystallization of alkaline earth metal carbonates from water is important for biomineralization and environmental geochemistry. Here, large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of in idual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to s le complex systems. Here, we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on graphical processing units thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallization, including ion-pairing and mineral–water interfacial structure and dynamics. This article is part of a discussion meeting issue ‘Supercomputing simulations of advanced materials’.
Atomistic modelling of gibbsite: surface structure and morphology
Publisher: Elsevier BV
Date: 2000
Anhydrous Calcium Oxalate Polymorphism: A Combined Computational and Synchrotron X-ray Diffraction Study
Publisher: American Chemical Society (ACS)
Date: 15-09-2016
Derivation of an Accurate Force-Field for Simulating the Growth of Calcium Carbonate from Aqueous Solution: A New Model for the Calcite−Water Interface
Publisher: American Chemical Society (ACS)
Date: 18-02-2010
DOI: 10.1021/JP910977A
A comparative simulation study of the adsorption of nitrogen and methane in siliceous heulandite and chabazite
Publisher: Elsevier BV
Date: 11-2001
Prediction of relapse in paediatric pre‐B acute lymphoblastic leukaemia using a three‐gene risk index
Publisher: Wiley
Date: 21-02-2008
DOI: 10.1111/J.1365-2141.2008.06981.X
Abstract: Despite high cure rates 25% of children with acute lymphoblastic leukaemia (ALL) relapse and have dismal outcome. Crucially, many are currently stratified as standard risk (SR) and additional markers to improve patient stratification are required. Here we have used diagnostic bone marrow specimens from 101 children with pre-B ALL to examine the use of gene expression profiles (GEP) as predictors of long-term clinical outcome. Patients were ided into two cohorts for model development and validation based on availability of specimen material. Initially, GEP from 55 patients with sufficient material were analysed using HG-U133A microarrays, identifying an 18-gene classifier (GC) that was more predictive of outcome than conventional prognostic parameters. After feature selection and validation of expression levels by quantitative reverse transcription polymerase chain reaction (qRT-PCR), a three-gene qRT-PCR risk index [glutamine synthetase (GLUL), ornithine decarboxylase antizyme inhibitor (AZIN), immunoglobulin J chain (IGJ)] was developed that predicted outcome with an accuracy of 89% in the array cohort and 87% in the independent validation cohort. The data demonstrate the feasibility of using GEP to improve risk stratification in childhood ALL. This is particularly important for the identification of patients destined to relapse despite their current stratification as SR, as more intensive front-line treatment options for these in iduals are already available.
The controlled disassembly of mesostructured perovskites as an avenue to fabricating high performance nanohybrid catalysts
Publisher: Springer Science and Business Media LLC
Date: 25-05-2017
DOI: 10.1038/NCOMMS15553
Abstract: Versatile superstructures composed of nanoparticles have recently been prepared using various disassembly methods. However, little information is known on how the structural disassembly influences the catalytic performance of the materials. Here we show how the disassembly of an ordered porous La 0.6 Sr 0.4 MnO 3 perovskite array, to give hexapod mesostructured nanoparticles, exposes a new crystal facet which is more active for catalytic methane combustion. On fragmenting three-dimensionally ordered macroporous (3DOM) structures in a controlled manner, via a process that has been likened to retrosynthesis, hexapod-shaped building blocks can be harvested which possess a mesostructured architecture. The hexapod-shaped perovskite catalyst exhibits excellent low temperature methane oxidation activity ( T 90% =438 °C reaction rate=4.84 × 10 −7 mol m −2 s −1 ). First principle calculations suggest the fractures, which occur at weak joints within the 3DOM architecture, afford a large area of (001) surface that displays a reduced energy barrier for hydrogen abstraction, thereby facilitating methane oxidation.
A quantum chemical study of LIX63 hydroxyoxime syn/anti isomerisation
Publisher: Informa UK Limited
Date: 08-12-2020
Coupled Al/Si and O/N order/disorder in BaYb[Si4–x Al x O x
Publisher: Walter de Gruyter GmbH
Date: 07-2007
DOI: 10.1524/ZKRI.2007.222.8.402
Abstract: The fractions of aluminium, [Al]/[Al + Si], and oxygen, [O]/[O + N], in crystallographically distinct sites of BaYb[Si 4– x Al x O x N 7– x ] oxonitridoaluminosilicate (space group P 6 3 mc , No. 186) were refined based on the results of neutron powder diffraction for a synthetic s le with the composition of x = 2.2(2) and simulated as functions of temperature for the compositions x = 2 and x = 2.3 using a combination of static lattice energy calculations (SLEC) and Monte Carlo simulations. The SLEC calcu lations have been performed on a set of 800 structures differing in the distribution of Al/Si and O/N within the 2 × 2 × 2 supercell containing 36 formula units of BaYb[Si 4– x Al x O x N 7– x ]. The SLEC were based on a transferable set of empirical interatomic potentials developed within the present study. The static lattice energies of these structures have been expanded in the basis set of pair-wise ordering energies and on-site chemical potentials. The ordering energies and the chemical potentials have been used to calculate the configuration energies of the oxonitridoaluminosilicates (so-called sialons) using a Monte Carlo algorithm. The simulations suggest that Al and O are distributed unevenly over two non-equivalent T(Si/Al) and three L(N/O) sites, respectively, and the distribution shows strong dependence both on the temperature and the composition. Both simulated s les exhibit order/disorder transitions in the temperature range 500–1000 K to phases with partial long-range order below these temperatures. Above the transition temperatures the Si/Al and N/O distributions are affected by short-range ordering. The predicted site occupancies are in a qualitative agreement with the neutron diffraction results.
A thermodynamic adsorption/entrapment model for selenium(IV) coprecipitation with calcite
Publisher: Elsevier BV
Date: 06-2014
Exploring the role of ions and amino acids in directing the growth of minerals from solution
Publisher: Mineralogical Society
Date: 02-2008
DOI: 10.1180/MINMAG.2008.072.1.273
Abstract: The influence of both sulphate ions and aspartic acid on directing the growth of baryte has been explored using computer simulation. Both species are found to significantly reduce the activation free-energy to growth under appropriate conditions, with the influence of sulphate being surface specific. This offers the potential for a new approach to morphology control without inhibition that may have implications for biomineralization.
Pre-nucleation clusters as solute precursors in crystallisation
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3CS60451A
Abstract: We review evidence for phase separation via pre-nucleation clusters of the most common biominerals, as well as amino acids.
Crystal Nucleation and Growth of Inorganic Ionic Materials from Aqueous Solution: Selected Recent Developments, and Implications
Publisher: Wiley
Date: 09-06-2022
Abstract: In this review article, selected, latest theoretical, and experimental developments in the field of nucleation and crystal growth of inorganic materials from aqueous solution are highlighted, with a focus on literature after 2015 and on non‐classical pathways. A key point is to emphasize the so far underappreciated role of water and solvent entropy in crystallization at all stages from solution speciation through to the final crystal. While drawing on ex les from current inorganic materials where non‐classical behavior has been proposed, the potential of these approaches to be adapted to a wide‐range of systems is also discussed, while considering the broader implications of the current re‐assessment of pathways for crystallization. Various techniques that are suitable for the exploration of crystallization pathways in aqueous solution, from nucleation to crystal growth are summarized, and a flow chart for the assignment of specific theories based on experimental observations is proposed.
Topological and geometrical characterization of zeotypes with a free software code called zeotsites: The case study of germanium location in octadecasil
Publisher: Elsevier
Date: 2004
Flexibility in a Metal-Organic Framework Material Controlled by Weak Dispersion Forces: The Bistability of MIL-53(Al)
Publisher: Wiley
Date: 03-09-2010
The SIESTA method forab initioorder-Nmaterials simulation
Publisher: IOP Publishing
Date: 08-03-2002
Chemisorption of Molecular Hydrogen on Carbon Nanotubes: A Route to Effective Hydrogen Storage?
Publisher: American Chemical Society (ACS)
Date: 18-07-2008
DOI: 10.1021/JP802104N
Atomic scale modelling of the cores of dislocations in complex materials part 1: methodology
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B505612H
Abstract: Dislocations influence many properties of crystalline solids, including plastic deformation, growth and dissolution, diffusion and the formation of polytypes. Some of these processes can be described using continuum methods but this approach fails when a description of the structure of the core is required. To progress in these types of problems, an atomic scale model is essential. So far, atomic scale modelling of the cores of dislocations has been limited to systems with rather simple crystal structures. In this article, we describe modifications to current methodology, which have been used for strongly ionic materials with simple structures. These modifications permit the study of dislocation cores in more structurally complex materials.
Exploring the influence of organic species on pre- and post-nucleation calcium carbonate
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2FD20052J
GULP: Capabilities and prospects
Publisher: Walter de Gruyter GmbH
Date: 05-2005
DOI: 10.1524/ZKRI.220.5.552.65070
Abstract: The current status and capabilities of the atomistic simulation code GULP are described. In particular, the differences between versions 1.3.2 and 3.0 are detailed, as well as a concise pointer to applications in computational crystallography.
Aspartic acid as a crystal growth catalyst
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B708260F
Understanding the Barriers to Crystal Growth: Dynamical Simulation of the Dissolution and Growth of Urea from Aqueous Solution
Publisher: American Chemical Society (ACS)
Date: 20-01-2005
DOI: 10.1021/JA043395L
Abstract: Both the dissolution and growth of a molecular crystalline material, urea, has been studied using dynamical atomistic simulation. The kinetic steps of dissolution and growth are clearly identified, and the activation energies for each possible step are calculated. Our molecular dynamics simulations indicate that crystal growth on the [001] face is characterized by a nucleation and growth mechanism. Nucleation on the [001] urea crystal face is predicted to occur at a very high rate, followed by rapid propagation of the steps. The rate-limiting step for crystallization is actually found to be the removal of surface defects, rather than the initial formation of the next surface layer. Through kinetic Monte Carlo modeling of the surface growth, it is found that this crystal face evolves via a rough surface topography, rather than a clean layer-by-layer mechanism.
The Multiple Structures of Vaterite
Publisher: American Chemical Society (ACS)
Date: 17-05-2013
DOI: 10.1021/CG4002972
Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture
Publisher: Springer Science and Business Media LLC
Date: 24-05-2019
DOI: 10.1038/S41467-019-10383-X
Abstract: Since Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid l -Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when d -Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality lification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.
Water Structure, Dynamics and Ion Adsorption at the Aqueous {010} Brushite Surface
Publisher: MDPI AG
Date: 03-08-2018
DOI: 10.3390/MIN8080334
Abstract: Understanding the growth processes of calcium phosphate minerals in aqueous environments has implications for both health and geology. Brushite, in particular, is a component of certain kidney stones and is used as a bone implant coating. Understanding the water–brushite interface at the molecular scale will help inform the control of its growth. Liquid-ordering and the rates of water exchange at the brushite–solution interface have been examined through the use of molecular dynamics simulation and the results compared to surface X-ray diffraction data. This comparison highlights discrepancies between the two sets of results, regardless of whether force field or first principles methods are used in the simulations, or the extent of water coverage. In order to probe other possible reasons for this difference, the free energies for the adsorption of several ions on brushite were computed. Given the exothermic nature found in some cases, it is possible that the discrepancy in the surface electron density may be caused by adsorption of excess ions.
On classical and non-classical views on nucleation
Publisher: American Journal of Science (AJS)
Date: 11-2018
DOI: 10.2475/09.2018.05
The interaction of dolomite surfaces with metal impurities: a computer simulation study
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B510454H
Abstract: This study investigates the behaviour of selected, morphologically important surfaces of dolomite (CaMg(CO3)2), using computational modelling techniques. Interatomic potential methods have been used to examine impurity substitution at cationic sites in these surfaces. Environmentally prevalent cations were studied to this end, namely Ni2+, Co2+, Zn2+, Fe2+, Mn2+ and Cd2+, all of which are also found as end-member carbonate minerals. Solid-solution substitution was investigated and showed that Cd and Mn will substitute from their end-member carbonate phase at either dolomite cation site. Mn is found to preferentially substitute at Mg sites, in agreement with experimental findings. For Ni2+, Co2+ and Zn2+, the magnitude of substitution energies is approximately equal for all surfaces, with the exception of the (1014) surface. However, for the larger cations, a far greater disparity in substitution energies is observed. At a stepped surface, analogous substitutions were performed and it was found that substitution energies for all impurity cations were reduced, indicating that uptake is more viable during growth. The predominant surface, the (1014), was solvated with a monolayer of water in order to investigate the influence of hydration on substitution energetics. The addition of water changes the relative preference for substitution of the different cations. Under aqueous conditions, the substitution energy is determined by three competing factors, the relative importance of which cannot be predicted without this type of computational investigation.
Understanding the Kinetics of Barium Sulfate Precipitation from Water and Water–Methanol Solutions
Publisher: American Chemical Society (ACS)
Date: 30-01-2008
DOI: 10.1021/CG070110I
Transferable variable-charge interatomic potential for atomistic simulation of titanium oxides
Publisher: American Physical Society (APS)
Date: 09-2000
Derivation of an Interatomic Potential for Germanium- and Silicon-Containing Zeolites and Its Application to the Study of the Structures of Octadecasil, ASU-7, and ASU-9 Materials
Publisher: American Chemical Society (ACS)
Date: 10-04-2003
DOI: 10.1021/CM021262Y
A software tool for the topological and geometrical characterization of three-dimensional frameworks
Publisher: Elsevier BV
Date: 10-2003
Timoshenko Bending and Eshelby Twisting Predicted in Molecular Nanocrystals
Publisher: American Chemical Society (ACS)
Date: 03-10-2018
Static lattice energy calculations of mixing and ordering enthalpy in binary carbonate solid solutions
Publisher: Elsevier BV
Date: 2006
Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing
Publisher: American Chemical Society (ACS)
Date: 10-09-2019
Is the Calcite–Water Interface Understood? Direct Comparisons of Molecular Dynamics Simulations with Specular X-ray Reflectivity Data
Publisher: American Chemical Society (ACS)
Date: 27-02-2013
DOI: 10.1021/JP310943S
A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research
Publisher: Public Library of Science (PLoS)
Date: 25-02-2021
DOI: 10.1371/JOURNAL.PBIO.3001091
Abstract: The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at mrcppu-covid.bio/ , constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.
Thermodynamically Consistent Force Field for Molecular Dynamics Simulations of Alkaline-Earth Carbonates and Their Aqueous Speciation
Publisher: American Chemical Society (ACS)
Date: 21-10-2015
An interatomic potential study of the properties of gallium nitride
Publisher: IOP Publishing
Date: 03-11-1997
Interaction of Silicon Dangling Bonds with Insulating Surfaces
Publisher: American Physical Society (APS)
Date: 22-01-2004
Adsorption and dimerisation of thiol molecules on Au(111) using aZ-matrix approach in density functional theory
Publisher: Informa UK Limited
Date: 20-12-2006
A computational investigation of the properties of a reverse osmosis membrane
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0JM01545H
Hammer-toothed 'marsupial skinks' from the Australian Cenozoic
Publisher: The Royal Society
Date: 20-04-2011
Abstract: Extinct species of Malleodectes gen. nov. from Middle to Late Miocene deposits of the Riversleigh World Heritage Area, northwestern Queensland, Australia are enigmatic, highly specialized, probably snail-eating marsupials. Dentally, they closely resemble a bizarre group of living heterodont, wet forest scincid lizards from Australia ( Cyclodomorphus ) that may well have outcompeted them as snail-eaters when the closed forests of central Australia began to decline. Although there are scincids known from the same Miocene deposits at Riversleigh, these are relatively plesiomorphic, generalized feeders. This appears to be the most striking ex le known of dental convergence and possible competition between a mammal and a lizard, which in the long run worked out better for the lizards.
Computational studies of proton migration in perovskite oxides
Publisher: Elsevier BV
Date: 04-1995
Vacancy defect configurations in the metal–organic framework UiO-66: energetics and electronic structure
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C7TA11155J
Abstract: The energetics and electronic structure of defects in the metal–organic framework UiO-66 is investigated using density functional theory.
Oxygen ion migration in orthorhombic LaMnO3−δ
Publisher: AIP Publishing
Date: 24-10-2003
DOI: 10.1063/1.1615759
Abstract: Interatomic potentials that can model ligand field effects were used to investigate the properties of vacancies in orthorhombic LaMnO3. The minimum energy structures of LaMnO3−δ (where δ=1/192) were calculated for an oxygen vacancy on either the O1 or O2 site, respectively. It is predicted that the “degenerate” activation energy (and pathway) for oxygen diffusion in cubic LaMnO3−δ is lifted after a cubic–orthorhombic phase transition. Within the orthorhombic phase, one of the once triply degenerate activation energies is lowered, indicating that there is a preferred migration pathway, while one is increased, indicating an increased activation energy for unrestricted oxygen migration (and a much closer agreement to that observed in strontium doped systems). The lowest energy pathways within the orthorhombic, as opposed to the cubic perovskite structure, are no longer symmetric. The activation energies of migration indicate a preferential vacancy migration between the O2 and O1(s) sites, where the migrating oxygen ion would simultaneously arc around the central manganese ion with a bond length, Mn–O, which varied between 1.72 and 1.77 Å. This type of pathway suggests that vacancies migrate along O2(m)–O1(s)–O2(m)–O1(s) chains.
Dopant and proton incorporation in perovskite-type zirconates
Publisher: Elsevier BV
Date: 02-11-1999
Influence of pH and temperature on alunite dissolution: Rates, products and insights on mechanisms from atomistic simulation
Publisher: Elsevier BV
Date: 12-2015
Specific inhibition of NLRP3 in chikungunya disease reveals a role for inflammasomes in alphavirus-induced inflammation
Publisher: Springer Science and Business Media LLC
Date: 28-08-2017
DOI: 10.1038/S41564-017-0015-4
Abstract: Mosquito-borne viruses can cause severe inflammatory diseases and there are limited therapeutic solutions targeted specifically at virus-induced inflammation. Chikungunya virus (CHIKV), a re-emerging alphavirus responsible for several outbreaks worldwide in the past decade, causes debilitating joint inflammation and severe pain. Here, we show that CHIKV infection activates the NLRP3 inflammasome in humans and mice. Peripheral blood mononuclear cells isolated from CHIKV-infected patients showed elevated NLRP3, caspase-1 and interleukin-18 messenger RNA expression and, using a mouse model of CHIKV infection, we found that high NLRP3 expression was associated with peak inflammatory symptoms. Inhibition of NLRP3 activation using the small-molecule inhibitor MCC950 resulted in reduced CHIKV-induced inflammation and abrogated osteoclastogenic bone loss and myositis, but did not affect in vivo viral replication. Mice treated with MCC950 displayed lower expression levels of the cytokines interleukin-6, chemokine ligand 2 and tumour necrosis factor in joint tissue. Interestingly, MCC950 treatment abrogated disease signs in mice infected with a related arthritogenic alphavirus, Ross River virus, but not in mice infected with West Nile virus-a flavivirus. Here, using mouse models of alphavirus-induced musculoskeletal disease, we demonstrate that NLRP3 inhibition in vivo can reduce inflammatory pathology and that further development of therapeutic solutions targeting inflammasome function could help treat arboviral diseases.
An ab initio study of C60 adsorption on the Si(001) surface
Publisher: Elsevier BV
Date: 10-2005
Simulation of low index rutile surfaces with a transferable variable-charge Ti–O interatomic potential and comparison with ab initio results
Publisher: Elsevier BV
Date: 04-2002
The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 12-05-2020
DOI: 10.26434/CHEMRXIV.12279911
Abstract: Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2 / and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure, / meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamics / based on both DFT and two different force field models. Additionally, the simulated structures are / used to calculate the corresponding structure factors, which in turn are compared to those obtained / from experiment, thereby avoiding the need for fitting or subjective interpretation. In general, there / is a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of the / structure of water at the interface. Of the three simulation methods examined, the DFT results were / found to agree best with the experimental structure. /
Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface
Publisher: American Chemical Society (ACS)
Date: 09-2020
DOI: 10.26434/CHEMRXIV.12899831.V1
Abstract: Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.
Radiation tolerance of ceramics—insights from atomistic simulation of damage accumulation in pyrochlores
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0EE00066C
The General Utility Lattice Program (GULP )
Publisher: Informa UK Limited
Date: 05-2003
A periodic density functional study of the location of titanium within TS-1
Publisher: Elsevier BV
Date: 03-2006
A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination
Publisher: American Chemical Society (ACS)
Date: 04-11-2021
Abstract: In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range d ing of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.
Resolving Point Defects in the Hydration Structure of Calcite (10.4) with Three-Dimensional Atomic Force Microscopy
Publisher: American Physical Society (APS)
Date: 13-03-2018
The dissociation mechanism and thermodynamic properties of HCl(aq) in hydrothermal fluids (to 700 degrees C, 60 kbar) by ab initio molecular dynamics simulations
Publisher: Elsevier BV
Date: 04-2018
Glucocorticoid resistance in T-lineage acute lymphoblastic leukaemia is associated with a proliferative metabolism
Publisher: Springer Science and Business Media LLC
Date: 12-05-2009
Adsorption of As(OH)3 on the (001) Surface of FeS2 Pyrite: A Quantum-mechanical DFT Study
Publisher: American Chemical Society (ACS)
Date: 11-07-2007
DOI: 10.1021/JP072468V
Predicting the structure of screw dislocations in nanoporous materials
Publisher: Springer Science and Business Media LLC
Date: 07-09-2004
DOI: 10.1038/NMAT1213
Hydrogen-bridge bonding on semiconductor surfaces: Density-functional calculations
Publisher: American Physical Society (APS)
Date: 16-12-2004
Chemical bonding at the metal–organic framework/metal oxide interface: simulated epitaxial growth of MOF-5 on rutile TiO2
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7TA00356K
Abstract: Thin-film deposition of metal–organic frameworks (MOFs) is now possible, but little is known regarding the microscopic nature of hybrid hetero-interfaces.
The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 12-05-2020
DOI: 10.26434/CHEMRXIV.12279911.V1
Abstract: Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure,meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamicsbased on both DFT and two different force field models. Additionally, the simulated structures areused to calculate the corresponding structure factors, which in turn are compared to those obtainedfrom experiment, thereby avoiding the need for fitting or subjective interpretation. In general, thereis a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of thestructure of water at the interface. Of the three simulation methods examined, the DFT results werefound to agree best with the experimental structure.
First principles studies of the surface of galena PbS
Publisher: Elsevier BV
Date: 03-2003
Structure and Dynamics of Water at Step Edges on the Calcite {101̅4} Surface
Publisher: American Chemical Society (ACS)
Date: 25-08-2016
Implementation of aZ-matrix approach within the SIESTA periodic boundary conditions code and its application to surface adsorption
Publisher: Informa UK Limited
Date: 07-2006
A first-principles determination of the orientation of H3O+ in hydronium alunite
Publisher: Mineralogical Society of America
Date: 23-06-2010
DOI: 10.2138/AM.2010.3537
Quantum mechanical vs. empirical potential modeling of uranium dioxide (UO2) surfaces: (111), (110), and (100)
Publisher: Mineralogical Society of America
Date: 11-2006
DOI: 10.2138/AM.2006.2180
Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO 3 Solutions
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-08-2013
Abstract: The initial transition from a disordered solution to the formation of nuclei that grow into crystals continues to be a puzzle. Recent experiments suggested the formation of stable ordered clusters that appear prior to the formation of the first nuclei. Wallace et al. (p. 885 see the Perspective by Myerson and Trout ) used molecular dynamics to look at the potential structure and dynamics of these clusters and lattice gas simulations to explore the population dynamics of the cluster populations prior to nucleation. A liquid-liquid phase separation process was observed whereby one phase becomes more concentrated in ions and becomes the precursor for nuclei to form.
Determining the Complete Stability of Calcite Kink Sites: Real vs Ideal
Publisher: American Chemical Society (ACS)
Date: 05-07-2023
CrystalClear: an open, modular protocol for predicting molecular crystal growth from solution
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2SC06761G
Abstract: We present a new protocol for the prediction of free energies that determine the growth rates of sites in molecular crystals for subsequent use in Monte Carlo simulations using tools such as CrystalGrower.
The mandible and dentition of the Early Cretaceous monotreme Teinolophos trusleri
Publisher: Informa UK Limited
Date: 23-06-2016
Themed issue: Modelling of materials
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0JM90095H
Influence of isotropic and biaxial strain on proton conduction in Y-doped BaZrO3: a reactive molecular dynamics study
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3TA12800H
Recent Computational Studies in Solid State Chemistry
Publisher: Elsevier BV
Date: 09-1993
A computational investigation of the structure of κ-alumina using interatomic potentials
Publisher: Royal Society of Chemistry (RSC)
Date: 26-10-2001
DOI: 10.1039/B105664F
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 02-04-2020
DOI: 10.26434/CHEMRXIV.11879805
Abstract: The speciation of calcium carbonate in water is important to the geochemistry of the world’s oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we have derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid-ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Calculation of Attachment Energies and Relative Volume Growth Rates As an Aid to Polymorph Prediction
Publisher: American Chemical Society (ACS)
Date: 08-04-2005
DOI: 10.1021/CG049707D
Importance of dispersion in density functional calculations of cesium chloride and its related halides
Publisher: American Physical Society (APS)
Date: 19-08-2013
Graphenylene, a unique two-dimensional carbon network with nondelocalized cyclohexatriene units
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C2TC00006G
Molecular Scale Modeling of Membrane Water Treatment Processes
Publisher: Wiley
Date: 13-02-2013
Synthesis, Structural, and Photophysical Investigation of Diimine Triscarbonyl Re(I) Tetrazolato Complexes.
Publisher: American Chemical Society (ACS)
Date: 26-01-2011
DOI: 10.1021/IC1015516
Abstract: The synthesis, structural, and photophysical properties of a novel family of neutral fac-[Re(N(∧)N)(CO)(3)(L)] complexes, where N(∧)N is either 2,2'-bipyridine or 1,10-phenanthroline and L is a para functionalized 5-aryltetrazolate [namely, 5-phenyltetrazolate (Tph(-)), 4-(tetrazolate-5-yl)benzaldehyde (Tbdz(-)), 5-(4-acetylphenyl)tetrazolate (Tacy(-)), and methyl 4-(tetrazolate-5-yl)benzoate (Tmeb(-))] are reported. The complexes were prepared by direct addition of the corresponding tetrazolate anion to the acetonitrile solvated fac-[Re(N(∧)N)(CO)(3)](+) precursor. NMR data demonstrate that the coordination of the metal fragment is regiospecific at the N2 atom of the tetrazolate ring. These conclusions are also supported by X-ray structural determinations. Photophysical data were obtained in diluted and deaerated dichloromethane solutions displaying broad and structureless profiles with emission maxima ranging from 566 to 578 nm. The absorption profiles indicate the presence of higher energy intraligand (IL) π-π* transitions and lower energies ligand-to-ligand charge transfer (LLCT) and metal-to-ligand charge transfer (MLCT). As the last two transitions are mixed, they are better described as a metal-ligand-to-ligand charge transfer (MLLCT), a result that is also supported by density functional theory (DFT) calculations. The complexes show excited state lifetime values ranging from 102 to 955 ns, with associated quantum yield between 0.012 and 0.099. Compared to the parent neutral chloro or bromo [Re(N(∧)N)(CO)(3)X], the complexes show a slightly improved performance because of the π accepting nature of the tetrazolato ligand. The metal-to-ligand backbonding is in fact depleting the Re center of electron density, thus widening the HOMO-LUMO gap and reducing the non-radiative decay mechanism in accordance with the energy gap law. Finally, the electron-withdrawing or donating nature of the substituent on the phenyltetrazolato ligand allows the fine-tuning of the photophysical properties.
First principles calculations using density matrix divide-and-conquer within the SIESTA methodology
Publisher: IOP Publishing
Date: 24-06-2008
Comparison of embedded atom method potentials for small aluminium cluster simulations
Publisher: IOP Publishing
Date: 18-03-2009
DOI: 10.1088/0953-8984/21/14/144206
Abstract: In this paper, we present a comparison of the performance of a series of embedded atom method potentials for the evaluation of bulk and small aluminium cluster geometries and relative energies, against benchmark density functional theory calculations. In general, the non-pairwise potential-B (NP-B), which was parametrized against Al cluster data, performs the best.
Titanium substitution mechanisms in forsterite
Publisher: Elsevier BV
Date: 07-2007
Calculated cell discharge curve for lithium batteries with a V2O5 cathode
Publisher: Royal Society of Chemistry (RSC)
Date: 2000
DOI: 10.1039/A908757E
The prediction of inorganic crystal structures using a genetic algorithm and energy minimisation
Publisher: Royal Society of Chemistry (RSC)
Date: 1999
DOI: 10.1039/A901227C
Uncovering the Atomistic Mechanism for Calcite Step Growth
Publisher: Wiley
Date: 13-04-2017
High expression of connective tissue growth factor in pre‐B acute lymphoblastic leukaemia
Publisher: Wiley
Date: 23-08-2007
DOI: 10.1111/J.1365-2141.2007.06739.X
Abstract: In recent years microarrays have been used extensively to characterize gene expression in acute lymphoblastic leukaemia (ALL). Few studies, however, have analysed normal haematopoietic cell populations to identify altered gene expression in ALL. We used oligonucleotide microarrays to compare the gene expression profile of paediatric precursor-B (pre-B) ALL specimens with two control cell populations, normal CD34(+) and CD19(+)IgM(-) cells, to focus on genes linked to leukemogenesis. A set of eight genes was identified with a ninefold higher average expression in ALL specimens compared with control cells. All of these genes were significantly deregulated in an independent cohort of 101 ALL specimens. One gene, connective tissue growth factor (CTGF, also known as CCN2), had exceptionally high expression, which was confirmed in three independent leukaemia studies. Further analysis of CTGF expression in ALL revealed exclusive expression in B-lineage, not T-lineage, ALL. Within B-lineage ALL approximately 75% of specimens were consistently positive for CTGF expression, however, specimens containing the E2A-PBX1 translocation showed low or no expression. Protein studies using Western blot analysis demonstrated the presence of CTGF in ALL cell-conditioned media. These findings indicate that CTGF is secreted by pre-B ALL cells and may play a role in the pathophysiology of this disease.
Planewave pseudopotential modelling studies of zeolites
Publisher: Elsevier
Date: 2004
Inhibition of Interleukin-1β Signaling by Anakinra Demonstrates a Critical Role of Bone Loss in Experimental Arthritogenic Alphavirus Infections
Publisher: Wiley
Date: 06-06-2019
DOI: 10.1002/ART.40856
Thermodynamics of mixing in diopside–jadeite, CaMgSi2O6–NaAlSi2O6, solid solution from static lattice energy calculations
Publisher: Springer Science and Business Media LLC
Date: 09-10-2007
The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium
Publisher: International Union of Crystallography (IUCr)
Date: 26-10-2013
DOI: 10.1107/S0021889813023728
Abstract: A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for ex le, by boundaries of the ( Q , ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.
Computational Study of Surface Deposition and Gas Phase Powder Formation during Spinel Chemical Vapor Deposition Processes
Publisher: American Chemical Society (ACS)
Date: 24-04-2013
DOI: 10.1021/IE400502U
Order/disorder phase transition in cordierite and its possible relationship to the development of symplectite reaction textures in granulites
Publisher: Pleiades Publishing Ltd
Date: 09-2007
Atomistic Simulation of Atomic Force Microscopy Imaging of Hydration Layers on Calcite, Dolomite, and Magnesite Surfaces
Publisher: American Chemical Society (ACS)
Date: 27-05-2019
Liposomal Delivery of the RNA Genome of a Live-Attenuated Chikungunya Virus Vaccine Candidate Provides Local, but Not Systemic Protection After One Dose
Publisher: Frontiers Media SA
Date: 05-03-2020
Derivation of Interatomic Potentials for Gallophosphates from the GaPO4−Quartz Structure: Transferability Study to Gallosilicates and Zeotype Gallophosphates
Publisher: American Chemical Society (ACS)
Date: 24-04-2001
DOI: 10.1021/CM001233S
First principles calculation of the free energy barrier for the reaction of methanol in a zeolite catalyst
Publisher: Elsevier BV
Date: 11-2001
Monte Carlo simulation of mixing in Ca3Fe2Ge3O12–Ca4Ge4O12 garnets and implications for the thermodynamic stability of pyrope–majorite solid solution
Publisher: Springer Science and Business Media LLC
Date: 17-10-2006
Why Are Some Crystals Straight?
Publisher: American Chemical Society (ACS)
Date: 23-06-2020
A general forcefield for accurate phonon properties of metal–organic frameworks
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CP05106E
Abstract: We report the development of a forcefield capable of reproducing accurate lattice dynamics of metal–organic frameworks.
Calculations of the Evolution of the Ca L23 Fine Structure in Amorphous Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 28-06-2022
Abstract: Amorphous calcium carbonate (ACC) has been found in many different organisms. Biogenic ACC is frequently a precursor in the formation of calcite and aragonite. The process of structural transformation is therefore of great interest in the study of crystallization pathways in biomineralization. Changes in the prepeak/main peak (L
Geometry and diameter dependence of the electronic and physical properties of GaN nanowires from first principles
Publisher: American Physical Society (APS)
Date: 26-03-2008
Role of the Zeolitic Environment in Catalytic Activation of Methanol
Publisher: American Chemical Society (ACS)
Date: 27-03-1999
DOI: 10.1021/JA983470Q
Computational Insights into Mg2+ Dehydration in the Presence of Carbonate
Publisher: American Chemical Society (ACS)
Date: 16-02-0002
Modelling of structure and reactivity in zeolites
Publisher: Elsevier
Date: 1995
Computational workflows for perovskites: case study for lanthanide manganites
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3CP00041A
Abstract: We propose and implement an open-source computational workflow, suitable for explorative studies of perovskites. We validate said workflow on a set of lanthanide manganites, and apply it to study the defect-induced phase transition in LaMnO 3 .
Activity–composition relations in the system CaCO3–MgCO3 predicted from static structure energy calculations and Monte Carlo simulations
Publisher: Elsevier BV
Date: 02-2007
Zinc Ions Modify Calcium Oxalate Growth by Distinct Transformation of Crystal Surface Termination
Publisher: American Chemical Society (ACS)
Date: 12-05-2021
Predicted structures for Ti8C12 and Si8C12 dodecahedron molecules
Publisher: Royal Society of Chemistry (RSC)
Date: 1992
DOI: 10.1039/C39920001222
Computing the structure of pillared Clays
Publisher: Wiley
Date: 10-1990
Framework Stability of Nanoporous Inorganic Structures upon Template Extraction and Calcination: A Theoretical Study of Gallophosphate Polymorphs
Publisher: American Chemical Society (ACS)
Date: 16-01-2002
DOI: 10.1021/JA011378F
Abstract: A systematic computational study of gallophosphates was undertaken. First, lattice energy minimization calculations using a formal-charge shell model potential have been carried out on a series of hypothetical gallium phosphates derived from their metallogallophosphate, aluminophosphate, or aluminosilicate analogues through atomic substitution. The minimized structures show the typical features in terms of bond angles and distances as expected in zeolitic gallophosphates. Second, the crystal structures of several gallophosphates in their calcined forms have been predicted, using for each compound lattice energy minimization and an initial model derived from its as-synthesized templated form. All the modified structures thus have the same GaPO(4) composition. The lattice energies of all the simulated gallophosphate structures were compared to that of GaPO(4)-quartz as a reference structure. Interestingly, among all predicted calcined structures, various zeolitic topologies were found. The study of the energetics of these zeotypic structures showed a linear dependence of lattice energy upon density. Strikingly, a few simulated structures showed unrealistic structural features, such as important framework distortions, often associated with the occurrence of a hexameric unit in the original as-synthesized structures. Also, those gallophosphates with structural faults were found in the upper part of the energy/density plot. To address the validity of our force field calculations in these special cases, first principles calculations were undertaken on ULM-4, chosen as a typical representative structure. Indeed, the qualitative agreement found between our results and those obtained with the nonlocal density functional theory demonstrates the robustness of our force field. Further minimization also showed that the inclusion of polarizability is crucial for yielding results comparable with those obtained using first principles methods.
Incorporation of impurity anions into DSP: insights into structure and stability from computer modelling
Publisher: Informa UK Limited
Date: 2006
Developing community codes for materials modeling
Publisher: Elsevier BV
Date: 12-2013
An efficient technique for the prediction of solvent-dependent morphology: the COSMIC method
Publisher: Informa UK Limited
Date: 12-2007
A computer simulation study of OH defects in Mg2SiO4 and Mg2GeO4 spinels
Publisher: Springer Science and Business Media LLC
Date: 04-11-2005
Derivation of interatomic potentials for microporous aluminophosphates from the structure and properties of berlinite
Publisher: Royal Society of Chemistry (RSC)
Date: 1994
DOI: 10.1039/FT9949003175
Anomalous heat transport in binary hard-sphere gases
Publisher: American Physical Society (APS)
Date: 29-03-2019
Structure of hydrated calcium carbonates: A first-principles study
Publisher: Elsevier BV
Date: 09-2014
Electronic structure of phosphorus and arsenicδ
Publisher: American Physical Society (APS)
Date: 06-09-2013
A first principles investigation of lithium intercalation in TiO2-B
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B902683E
Simulation of Water Transport Through Functionalized Single-Walled Carbon Nanotubes (SWCNTs)
Publisher: American Chemical Society (ACS)
Date: 15-11-2012
DOI: 10.1021/JP307679H
Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface
Publisher: American Chemical Society (ACS)
Date: 09-2020
DOI: 10.26434/CHEMRXIV.12899831
Abstract: Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields. The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed. / A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field. /
Three-dimensional kinetic Monte Carlo simulation of crystal growth from solution
Publisher: Elsevier BV
Date: 08-2006
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