ORCID Profile
0000-0002-7429-1846
Current Organisations
University of Western Australia
,
Seqera
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Publisher: Springer Science and Business Media LLC
Date: 29-01-2018
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
Publisher: Springer Science and Business Media LLC
Date: 30-07-2019
Publisher: American Meteorological Society
Date: 02-1998
Publisher: AIP Publishing
Date: 04-01-2013
DOI: 10.1063/1.4772960
Abstract: The vibrational properties of CaCO3 aragonite have been investigated both theoretically, by using a quantum mechanical approach (all electron Gaussian type basis set and B3LYP HF-DFT hybrid functional, as implemented in the CRYSTAL code) and experimentally, by collecting polarized infrared (IR) reflectance and Raman spectra. The combined use of theory and experiment permits on the one hand to analyze the many subtle features of the measured spectra, on the other hand to evidentiate limits and deficiencies of both approaches. The full set of TO and LO IR active modes, their intensities, the dielectric tensor (in its static and high frequency components), and the optical indices have been determined, as well as the Raman frequencies. Tools such as isotopic substitution and graphical animation of the modes are available, that complement the analysis of the spectrum.
Publisher: American Chemical Society (ACS)
Date: 22-01-2014
DOI: 10.1021/JP409837D
Publisher: Springer Science and Business Media LLC
Date: 03-2019
Publisher: Ubiquity Press, Ltd.
Date: 2023
DOI: 10.5334/JORS.451
Publisher: Mineralogical Society of America
Date: 05-2014
DOI: 10.2138/AM.2014.4772
Publisher: Wiley
Date: 04-04-2013
DOI: 10.1002/JCC.23283
Abstract: It is shown that ab initio simulation can be used as a powerful complementary tool in the interpretation of the experimental reflectance spectra R(ν) of crystalline compounds. Experimental frequencies and intensities are obtained from a best fit of R(ν) with a set of d ed harmonic oscillators, whose number and initial position in frequency can dramatically influence the final results, as the parameters are strongly correlated. Computed ab initio values for frequencies and intensities are accurate enough to represent an excellent starting point for the best fit process. Moreover, at variance with respect to experiment, simulation permits to identify all the symmetry allowed modes, also when characterized by low intensity or when close to a very intense peak. Overall, simulation-aided analysis of experimental spectra prevents from classifying combination modes as fundamental modes and permits to discard artifacts due to superposition of bands, background, and noise. Finally, it allows to (almost) completely characterize the set of fundamental modes.
Publisher: Wiley
Date: 05-04-2011
DOI: 10.1002/JCC.21750
Abstract: The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all-electron Gaussian-type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high-frequency dielectric tensor ϵ(∞) . These quantities are essential to compute the dielectric function ϵ(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general that B3LYP overperforms WC1LYP and, in turn, PBE0 that PBESOL is better than PBE that LDA is the worst performing functional among the six under study.
Publisher: American Chemical Society (ACS)
Date: 17-11-2014
DOI: 10.1021/JP509958D
Publisher: Elsevier
Date: 2015
Publisher: CERN
Date: 2017
Publisher: Wiley
Date: 13-04-2017
Publisher: American Chemical Society (ACS)
Date: 18-04-2018
Publisher: Elsevier BV
Date: 04-2010
Publisher: American Chemical Society (ACS)
Date: 23-01-2013
DOI: 10.1021/JP3103436
Publisher: Mineralogical Society of America
Date: 2016
DOI: 10.2138/AM-2016-5382
Publisher: Mineralogical Society of America
Date: 11-2011
DOI: 10.2138/AM.2011.3804
Publisher: Wiley
Date: 11-03-2014
DOI: 10.1002/QUA.24658
Publisher: IOP Publishing
Date: 02-08-2013
DOI: 10.1088/0953-8984/25/35/355401
Abstract: A symmetry-adapted algorithm producing uniformly at random the set of symmetry independent configurations (SICs) in disordered crystalline systems or solid solutions is presented here. Starting from Pólya's formula, the role of the conjugacy classes of the symmetry group in uniform random s ling is shown. SICs can be obtained for all the possible compositions or for a chosen one, and symmetry constraints can be applied. The approach yields the multiplicity of the SICs and allows us to operate configurational statistics in the reduced space of the SICs. The present low-memory demanding implementation is briefly sketched. The probability of finding a given SIC or a subset of SICs is discussed as a function of the number of draws and their precise estimate is given. The method is illustrated by application to a binary series of carbonates and to the binary spinel solid solution Mg(Al,Fe)2O4.
Publisher: The Shodor Education Foundation, Inc.
Date: 02-2021
Publisher: AIP Publishing
Date: 11-09-2014
DOI: 10.1063/1.4895113
Abstract: Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative ex les, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.
Publisher: IOP Publishing
Date: 04-03-2009
Publisher: Wiley
Date: 14-05-2015
DOI: 10.1002/JCC.23941
Abstract: The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface.
Publisher: Wiley
Date: 24-06-2014
DOI: 10.1002/JRS.4527
Publisher: Informa UK Limited
Date: 06-09-2013
Publisher: Mineralogical Society of America
Date: 05-2013
DOI: 10.2138/AM.2013.4156
Publisher: AIP Publishing
Date: 25-04-2014
DOI: 10.1063/1.4871900
Abstract: Powder and single crystal Raman spectra of the two most common phases of calcium carbonate are calculated with ab initio techniques (using a “hybrid” functional and a Gaussian-type basis set) and measured both at 80 K and room temperature. Frequencies of the Raman modes are in very good agreement between calculations and experiments: the mean absolute deviation at 80 K is 4 and 8 cm−1 for calcite and aragonite, respectively. As regards intensities, the agreement is in general good, although the computed values overestimate the measured ones in many cases. The combined analysis permits to identify almost all the fundamental experimental Raman peaks of the two compounds, with the exception of either modes with zero computed intensity or modes overlapping with more intense peaks. Additional peaks have been identified in both calcite and aragonite, which have been assigned to 18O satellite modes or overtones. The agreement between the computed and measured spectra is quite satisfactory in particular, simulation permits to clearly distinguish between calcite and aragonite in the case of powder spectra, and among different polarization directions of each compound in the case of single crystal spectra.
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6CE00190D
Abstract: Ab initio calculations measure strain energy, curling and lattice misfit of single-walled chrysotile nanotubes.
Publisher: Elsevier BV
Date: 08-2013
Publisher: AIP Publishing
Date: 27-05-2020
DOI: 10.1063/5.0004892
Abstract: CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions). The use of atom-centered basis functions allows treating 3D (crystals), 2D (slabs), 1D (polymers), and 0D (molecules) systems on the same grounds. In turn, all-electron calculations are inherently permitted along with pseudopotential strategies. A variety of density functionals are implemented, including global and range-separated hybrids of various natures and, as an extreme case, Hartree–Fock (HF). The cost for HF or hybrids is only about 3–5 times higher than when using the local density approximation or the generalized gradient approximation. Symmetry is fully exploited at all steps of the calculation. Many tools are available to modify the structure as given in input and simplify the construction of complicated objects, such as slabs, nanotubes, molecules, and clusters. Many tensorial properties can be evaluated by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, first and second hyperpolarizabilities, etc. The calculation of infrared and Raman spectra is available, and the intensities are computed analytically. Automated tools are available for the generation of the relevant configurations of solid solutions and/or disordered systems. Three versions of the code exist: serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated on each core, whereas in the third one, the Fock matrix is distributed for diagonalization. All the relevant vectors are dynamically allocated and deallocated after use, making the code very agile. CRYSTAL can be used efficiently on high performance computing machines up to thousands of cores.
Publisher: Wiley
Date: 09-03-2021
Abstract: Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way bio ersity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state‐of‐the‐art applications to process eDNA data from raw sequences (single‐end or paired‐end) to generation of curated and noncurated zero‐radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high‐performance computing (HPC) clusters. Finally, we present an in‐house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an ex le of a published coral ersity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 s les. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data scalability and reproducibility.
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.
Publisher: Wiley
Date: 11-08-2011
DOI: 10.1002/QUA.23195
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4CP01442A
Abstract: An accurate and detailed electronic structure study of giant carbon fullerenes, benefitting from improved symmetry exploitation in the CRYSTAL14 code.
Publisher: Springer Science and Business Media LLC
Date: 2020
DOI: 10.1007/S11906-019-1010-3
Abstract: Artificial Intelligence (AI), although well established in many areas of everyday life, has only recently been trialed in the diagnosis and management of common clinical conditions. This editorial review highlights progress to date and suggests further improvements in and trials of AI in the management of conditions such as hypertension.
Publisher: Wiley
Date: 16-06-2016
Publisher: Elsevier
Date: 2013
Publisher: American Chemical Society (ACS)
Date: 11-05-2017
Publisher: AIP Publishing
Date: 28-05-2015
DOI: 10.1063/1.4921781
Abstract: We report accurate ab initio theoretical predictions of the elastic, seismic, and structural anisotropy of the orthorhombic Mg2SiO4 forsterite crystal at high pressures (up to 20 GPa) and temperatures (up to its melting point, 2163 K), which constitute earth’s upper mantle conditions. Single-crystal elastic stiffness constants are evaluated up to 20 GPa and their first- and second-order pressure derivatives reported. Christoffel’s equation is solved at several pressures: directional seismic wave velocities and related properties (azimuthal and polarization seismic anisotropies) discussed. Thermal structural and average elastic properties, as computed within the quasi-harmonic approximation of the lattice potential, are predicted at high pressures and temperatures: directional thermal expansion coefficients, first- and second-order pressure derivatives of the isothermal bulk modulus, and P-V-T equation-of-state. The effect on computed properties of five different functionals, belonging to three different classes of approximations, of the density functional theory is explicitly investigated.
Publisher: IEEE
Date: 05-2023
Publisher: American Chemical Society (ACS)
Date: 25-08-2016
Publisher: AIP
Date: 2012
DOI: 10.1063/1.4730666
Publisher: AIP Publishing
Date: 27-07-2023
DOI: 10.1063/5.0156399
Abstract: Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree–Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency.
Publisher: Springer Science and Business Media LLC
Date: 20-08-2014
Publisher: IOP Publishing
Date: 06-02-2013
DOI: 10.1088/0953-8984/25/10/105401
Abstract: The starting point for a quantum mechanical investigation of disordered systems usually implies calculations on a limited subset of configurations, generated by defining either the composition of interest or a set of compositions ranging from one end member to another, within an appropriate supercell of the primitive cell of the pure compound. The way in which symmetry can be used in the identification of symmetry independent configurations (SICs) is discussed here. First, Pólya's enumeration theory is adopted to determine the number of SICs, in the case of both varying and fixed composition, for colors numbering two or higher. Then, De Bruijn's generalization is presented, which allows analysis of the case where the colors are symmetry related, e.g. spin up and down in magnetic systems. In spite of their efficiency in counting SICs, neither Pólya's nor De Bruijn's theory helps in solving the difficult problem of identifying the complete list of SICs. Representative SICs are obtained by adopting an orderly generation approach, based on lexicographic ordering, which offers the advantage of avoiding the (computationally expensive) analysis and storage of all the possible configurations. When the number of colors increases, this strategy can be combined with the surjective resolution principle, which permits the efficient generation of SICs of a problem in |R| colors starting from the ones obtained for the (|R| - 1)-colors case. The whole scheme is documented by means of three ex les: the abstract case of a square with C(4v) symmetry and the real cases of the garnet and olivine mineral families.
Publisher: American Chemical Society (ACS)
Date: 05-07-2023
No related grants have been discovered for Marco De La Pierre.