ORCID Profile
0000-0002-2881-5477
Current Organisation
James Cook University
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Publisher: AIP Publishing
Date: 28-07-2018
DOI: 10.1063/1.5028333
Abstract: We present quantum electron transport theory that incorporates dynamical effects of motion of atoms on electrode-molecule interfaces in the calculations of the electric current. The theory is based on non-equilibrium Green’s functions. We separate time scales in the Green’s functions as fast relative time and slow central time. The derivative with respect to the central time serves as a small parameter in the theory. We solve the real-time Kadanoff-Baym equations for molecular Green’s functions using Wigner representation and keep terms up to the second order with respect to the central time derivatives. Molecular Green’s functions and consequently the electric current are expressed as functions of molecular junction coordinates as well as velocities and accelerations of molecule-electrode interface nuclei. We apply the theory to model a molecular system and study the effects of non-adiabatic nuclear motion on molecular junction conductivity.
Publisher: AIP Publishing
Date: 18-06-2003
DOI: 10.1063/1.1584661
Abstract: The paper describes the derivation of the Kohn–Sham equations for a nanowire with direct current. A value of the electron current enters the problem as an input via a subsidiary condition imposed by pointwise Lagrange multiplier. Using the constrained minimization of the Hohenberg–Kohn energy functional, we derive a set of self-consistent equations for current carrying orbitals of the molecular wire.
Publisher: AIP Publishing
Date: 03-11-2009
DOI: 10.1063/1.3262519
Abstract: Based on the formalism of thermofield dynamics we propose a concept of nonequilibrium Fock space and nonequilibrium quasiparticles for quantum many-body system in nonequilibrium steady state. We develop a general theory as well as demonstrate the utility of the approach on the ex le of electron transport through the interacting region. The proposed approach is compatible with advanced quantum chemical methods of electronic structure calculations such as coupled cluster theory and configuration interaction.
Publisher: American Physical Society (APS)
Date: 11-08-2009
Publisher: AIP Publishing
Date: 22-01-2015
DOI: 10.1063/1.4906151
Abstract: We study the adsorption and ring-opening of lactide on the naturally chiral metal surface Pt(321)S. Lactide is a precursor for polylactic acid ring-opening polymerization, and Pt is a well known catalyst surface. We study, here, the energetics of the ring-opening of lactide on a surface that has a high density of kink atoms. These sites are expected to be present on a realistic Pt surface and show enhanced catalytic activity. The use of a naturally chiral surface also enables us to study potential chiral selectivity effects of the reaction at the same time. Using density functional theory with a functional that includes the van der Waals forces in a first-principles manner, we find modest adsorption energies of around 1.4 eV for the pristine molecule and different ring-opened states. The energy barrier to be overcome in the ring-opening reaction is found to be very small at 0.32 eV and 0.30 eV for LL- and its chiral partner DD-lactide, respectively. These energies are much smaller than the activation energy for a dehydrogenation reaction of 0.78 eV. Our results thus indicate that (a) ring-opening reactions of lactide on Pt(321) can be expected already at very low temperatures, and Pt might be a very effective catalyst for this reaction (b) the ring-opening reaction rate shows noticeable enantioselectivity.
Publisher: AIP Publishing
Date: 12-12-2006
DOI: 10.1063/1.2401609
Abstract: It has recently been shown that relaxation of the rotational energy of hot nonequilibrium photofragments (i) slows down significantly with the increase of their initial rotational temperature and (ii) differs dramatically from the relaxation of the equilibrium rotational energy correlation function, manifesting thereby the breakdown of the linear response description [A. C. Moskun et al., Science 311, 1907 (2006)]. We demonstrate that this phenomenon may be caused by the angular momentum dependence of rotational friction. We have developed the generalized Fokker–Planck equation whose rotational friction depends upon angular momentum algebraically. The calculated rotational correlation functions correspond well to their counterparts obtained via molecular dynamics simulations in a broad range of initial nonequilibrium conditions. It is suggested that the angular momentum dependence of friction should be taken into account while describing rotational relaxation far from equilibrium.
Publisher: AIP Publishing
Date: 08-06-2023
DOI: 10.1063/5.0153000
Abstract: We propose a model for a molecular motor in a molecular electronic junction driven by a natural manifestation of Landauer’s blowtorch effect. The effect emerges via the interplay of electronic friction and diffusion coefficients, each calculated quantum mechanically using nonequilibrium Green’s functions, within a semiclassical Langevin description of the rotational dynamics. The motor functionality is analyzed through numerical simulations where the rotations exhibit a directional preference according to the intrinsic geometry of the molecular configuration. The proposed mechanism for motor function is expected to be ubiquitous for a range of molecular geometries beyond the one examined here.
Publisher: IOP Publishing
Date: 21-10-2011
Publisher: AIP Publishing
Date: 08-06-2005
DOI: 10.1063/1.1898215
Abstract: Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting “glycine dipeptide” (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (ϕ,ψ) maps of the local-mode frequencies and couplings. Performing conformational averages of the (ϕ,ψ) maps with respect to the most important peptide conformational states in solution (α,β,PII, and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.
Publisher: American Physical Society (APS)
Date: 16-04-2020
Publisher: Elsevier BV
Date: 05-2008
Publisher: AIP Publishing
Date: 15-10-2020
DOI: 10.1063/5.0023275
Abstract: The molecular junction geometry is modeled in terms of nuclear degrees of freedom that are embedded in a stochastic quantum environment of non-equilibrium electrons. The time-evolution of the molecular geometry is governed via a mean force, a frictional force, and a stochastic force, forces arising from many electrons tunneling across the junction for a given nuclear vibration. Conversely, the current-driven nuclear dynamics feed back to the electronic current, which can be captured according to the extended expressions for the current that have explicit dependences on classical nuclear velocities and accelerations. Current-induced nuclear forces and the non-adiabatic electric current are computed using non-equilibrium Green’s functions via a timescale separation solution of Keldysh–Kadanoff–Baym equations in the Wigner space. Applying the theory to molecular junctions demonstrated that non-adiabatic corrections play an important role when nuclear motion is considered non-equilibrium and, in particular, showed that non-equilibrium and equilibrium descriptions of nuclear motion produce significantly different current characteristics. It is observed that non-equilibrium descriptions generally produce heightened conductance profiles relative to the equilibrium descriptions and provide evidence that the effective temperature is an effective measure of the steady-state characteristics. Finally, we observe that the non-equilibrium descriptions of nuclear motion can give rise to the Landauer blowtorch effect via the emergence of multi-minima potential energy surfaces in conjunction with non-uniform temperature profiles. The Landauer blowtorch effect and its impact on the current characteristics, waiting times, and the Fano factor are explored for an effective adiabatic potential that morphs between a single, double, and triple potential as a function of voltage.
Publisher: American Physical Society (APS)
Date: 25-02-2008
Publisher: AIP Publishing
Date: 13-12-2017
DOI: 10.1063/1.5007071
Abstract: We develop nonequilibrium Green’s function-based transport theory, which includes effects of nonadiabatic nuclear motion in the calculation of the electric current in molecular junctions. Our approach is based on the separation of slow and fast time scales in the equations of motion for Green’s functions by means of the Wigner representation. Time derivatives with respect to central time serve as a small parameter in the perturbative expansion enabling the computation of nonadiabatic corrections to molecular Green’s functions. Consequently, we produce a series of analytic expressions for non-adiabatic electronic Green’s functions (up to the second order in the central time derivatives), which depend not solely on the instantaneous molecular geometry but likewise on nuclear velocities and accelerations. An extended formula for electric current is derived which accounts for the non-adiabatic corrections. This theory is concisely illustrated by the calculations on a model molecular junction.
Publisher: Elsevier BV
Date: 1998
Publisher: Springer Science and Business Media LLC
Date: 12-1996
Publisher: American Chemical Society (ACS)
Date: 18-11-190728635
Publisher: American Physical Society (APS)
Date: 12-01-2023
Publisher: AIP Publishing
Date: 27-01-2011
DOI: 10.1063/1.3548065
Abstract: We discuss the use of super-fermion formalism to represent and solve quantum kinetic equations for the electron transport problem. Starting with the Lindblad master equation for the molecule connected to two metal electrodes, we convert the problem of finding the nonequilibrium steady state to the many-body problem with non-Hermitian Liouvillian in super-Fock space. We transform the Liouvillian to the normal ordered form, introduce nonequilibrium quasiparticles by a set of canonical nonunitary transformations and develop general many-body theory for the electron transport through the interacting region. The approach is applied to the electron transport through a single level. We consider a minimal basis hydrogen atom attached to two metal leads in Coulomb blockade regime (out of equilibrium Anderson model) within the nonequilibrium Hartree–Fock approximation as an ex le of the system with electron interaction. Our approach agrees with exact results given by the Landauer theory for the considered models.
Publisher: AIP Publishing
Date: 27-01-2021
DOI: 10.1063/5.0039328
Abstract: Experimental measurements of electron transport properties of molecular junctions are often performed in solvents. Solvent–molecule coupling and physical properties of the solvent can be used as the external stimulus to control the electric current through a molecule. In this paper, we propose a model that includes dynamical effects of solvent–molecule interaction in non-equilibrium Green’s function calculations of the electric current. The solvent is considered as a macroscopic dipole moment that reorients stochastically and interacts with the electrons tunneling through the molecular junction. The Keldysh–Kadanoff–Baym equations for electronic Green’s functions are solved in the time domain with subsequent averaging over random realizations of rotational variables using the Furutsu–Novikov method for the exact closure of infinite hierarchy of stochastic correlation functions. The developed theory requires the use of wideband approximation as well as classical treatment of solvent degrees of freedom. The theory is applied to a model molecular junction. It is demonstrated that not only electrostatic interaction between molecular junction and solvent but also solvent viscosity can be used to control electrical properties of the junction. Alignment of the rotating dipole moment breaks the particle–hole symmetry of the transmission favoring either hole or electron transport channels depending upon the aligning potential.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0SC01073A
Abstract: Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.
Publisher: IOP Publishing
Date: 13-01-2006
Publisher: AIP Publishing
Date: 02-08-2006
DOI: 10.1063/1.2227395
Abstract: We have developed a general approach for the calculation of the single molecule polarization correlation function C(t), which delivers a correlation of the emission dichroisms at time 0 and t. The approach is model independent and valid for general asymmetric top molecules. The key dynamic quantities of our analysis are the even-rank orientational correlation functions, the weighted sum of which yields C(t). We have demonstrated that the use of nonorthogonal schemes for the detection of the single molecule polarization responses makes it possible to manipulate the weighting coefficients in the expansion of C(t). Thus valuable information about the orientational correlation functions of the rank higher than the second can be extracted from C(t).
Publisher: AIP Publishing
Date: 25-02-2013
DOI: 10.1063/1.4792441
Abstract: The adsorption of the chiral molecule lactic acid on chiral Pt surfaces is studied by density functional theory calculations. First, we study the adsorption of L-lactic acid on the flat Pt(111) surface. Using the optimed PBE - van der Waals (oPBE-vdW) functional, which includes van der Waals forces on an ab initio level, it is shown that the molecule has two binding sites, a carboxyl and the hydroxyl oxygen atoms. Since real chiral surfaces are (i) known to undergo thermal roughening that alters the distribution of kinks and step edges but not the overall chirality and (ii) kink sites and edge sites are usually the energetically most favored adsorption sites, we focus on two surfaces that allow qualitative s ling of the most probable adsorption sites. We hereby consider chiral surfaces exhibiting (111) facets, in particular, Pt(321) and Pt(643). The binding sites are either both on kink sites—which is the case for Pt(321) or on one kink site—as on Pt(643). The binding energy of the molecule on the chiral surfaces is much higher than on the Pt(111) surface. We show that the carboxyl group interacts more strongly than the hydroxyl group with the kink sites. The results indicate the possible existence of very small chiral selectivities of the order of 20 meV for the Pt(321) and Pt(643) surfaces. L-lactic acid is more stable on Pt(321)S than D-lactic acid, while the chiral selectivity is inverted on Pt(643)S. The most stable adsorption configurations of L- and D-lactic acid are similar for Pt(321) but differ for Pt(643). We explore the impact of the different adsorption geometries on the work function, which is important for field ion microscopy.
Publisher: American Physical Society (APS)
Date: 17-12-2019
Publisher: AIP Publishing
Date: 13-12-2013
DOI: 10.1063/1.4839755
Abstract: The adsorption of the chiral molecule lactate on the intrinsically chiral noble metal surfaces Pt(321), Au(321), and Ag(321) is studied by density functional theory calculations. We use the oPBE-vdW functional which includes van der Waals forces on an ab initio level. It is shown that the molecule binds via its carboxyl and the hydroxyl oxygen atoms to the surface. The binding energy is larger on Pt(321) and Ag(321) than on Au(321). An analysis of the contributions to the binding energy of the different molecular functional groups reveals that the deprotonated carboxyl group contributes most to the binding energy, with a much smaller contribution of the hydroxyl group. The Pt(321) surface shows considerable enantioselectivity of 0.06 eV. On Au(321) and Ag(321) it is much smaller if not vanishing. The chiral selectivity of the Pt(321) surface can be explained by two factors. First, it derives from the difference in van der Waals attraction of L- and D-lactate to the surface that we trace to differences in the binding energy of the methyl group. Second, the multi-point binding pattern for lactate on the Pt(321) surface is sterically more sensitive to surface chirality and also leads to large binding energy contributions of the hydroxyl group. We also calculate the charge transfer to the molecule and the work function to gauge changes in electronic structure of the adsorbed molecule. The work function is lowered by 0.8 eV on Pt(321) with much smaller changes on Au(321) and Ag(321).
Publisher: American Physical Society (APS)
Date: 04-12-2018
Publisher: American Physical Society (APS)
Date: 02-1998
Publisher: AIP Publishing
Date: 04-2009
DOI: 10.1063/1.3103263
Abstract: The present paper is aimed at studying the microscopic origin of the jump diffusion. Starting from the N-body Liouville equation and making only the assumption that molecular reorientation is overd ed, we derive and solve the new (hereafter generalized diffusion) equation. This is the most general equation which governs orientational relaxation of an equilibrium molecular ensemble in the hindered rotation limit and in the long time limit. The generalized diffusion equation is an extension of the small-angle diffusion equation beyond the impact approximation. We establish the conditions under which the generalized diffusion equation can be identified with the jump diffusion equation, and also discuss the similarities and differences between the two approaches.
Publisher: AIP Publishing
Date: 23-09-2020
DOI: 10.1063/5.0019178
Abstract: Electronic current flowing in a molecular electronic junction dissipates significant amounts of energy to vibrational degrees of freedom, straining and rupturing chemical bonds and often quickly destroying the integrity of the molecular device. The infamous mechanical instability of molecular electronic junctions critically limits performance and lifespan and raises questions as to the technological viability of single-molecule electronics. Here, we propose a practical scheme for cooling the molecular vibrational temperature via application of an AC voltage over a large, static operational DC voltage bias. Using nonequilibrium Green’s functions, we computed the viscosity and diffusion coefficient experienced by nuclei surrounded by a nonequilibrium ”sea” of periodically driven, current-carrying electrons. The effective molecular junction temperature is deduced by balancing the viscosity and diffusion coefficients. Our calculations show the opportunity of achieving in excess of 40% cooling of the molecular junction temperature while maintaining the same average current.
Publisher: American Physical Society (APS)
Date: 19-03-2019
Publisher: AIP Publishing
Date: 30-03-2004
DOI: 10.1063/1.1687316
Abstract: We discuss how the Lagrange multiplier method of nonequilibrium steady state statistical mechanics can be applied to describe the electronic transport in a quantum wire. We describe the theoretical scheme using a tight-binding model. The Hamiltonian of the wire is extended via a Lagrange multiplier to “open” the quantum system and to drive current through it. The diagonalization of the extended Hamiltonian yields the transport properties of wire. We show that the Lagrange multiplier method is equivalent to the Landauer approach within the considered model.
Publisher: AIP Publishing
Date: 26-09-2002
DOI: 10.1063/1.1506151
Abstract: Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band of the small peptide trialanine with that of N-methylacetamide, a commonly used model system for the peptide bond. In contrast to N-methylacetamide, the amide I band of trialanine is significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined with density-functional-theory calculations, the origin of the spectral inhomogeneity is investigated. While both systems exhibit similar hydrogen-bonding dynamics, it is found that the conformational dynamics of trialanine causes a significant additional spectral broadening. In particular, transitions between the poly(Gly)II and the αR conformations are identified as the main source of the additional spectral inhomogeneity of trialanine. The experimental and computational results suggest that trialanine adopts essentially two conformations: poly(Gly)II (80%) and αR (20%). The potential of the joint experimental and computational approach to explore conformational dynamics of peptides is discussed.
Publisher: AIP Publishing
Date: 17-02-2017
DOI: 10.1063/1.4976561
Abstract: On the elementary level, electronic current consists of in idual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time t+τ given that an electron was detected in the same electrode at an earlier time t. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain the master equation and compute the distribution of waiting times for electron transport. The details of waiting time distributions are used to elucidate microscopic mechanism of electron transport and the role of electron-vibration interactions. We find that as nonequilibrium develops in the molecular junction, the skewness and dispersion of the waiting time distribution experience stepwise drops with the increase of the electric current. These steps are associated with the excitations of vibrational states by tunnelling electrons. In the strong electron-vibration coupling regime, the dispersion decrease dominates over all other changes in the waiting time distribution as the molecular junction departs far away from the equilibrium.
Publisher: AIP Publishing
Date: 25-10-2018
DOI: 10.1063/1.5049770
Abstract: When electric current flows through a molecular junction, the molecule constantly charges and discharges by tunneling electrons. These charging and discharging events occur at specific but random times and are separated by stochastic time intervals. These time intervals can be associated with the dwelling time for a charge (electron or hole) to reside on the molecule. In this paper, the statistical properties of these time intervals are studied and a general formula for their distribution is derived. The theory is based on the Markovian master equation which takes into account transitions between the vibrational states of charged and neutral molecules in the junction. Two quantum jump operators are identified from the Liouvillian of the master equation—one corresponds to charging of the molecule and the other discharges the molecule back to the neutral state. The quantum jump operators define the conditional probability that given that the molecule was charged by a tunneling electron at time t, the molecule becomes neutral at a later time t + τ discharging the electron to the drain electrode. Statistical properties of these time intervals τ are studied with the use of this distribution.
Publisher: AIP Publishing
Date: 23-03-2016
DOI: 10.1063/1.4944493
Abstract: In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.
Publisher: American Chemical Society (ACS)
Date: 14-09-2006
DOI: 10.1021/JP065120T
Abstract: We study computationally the electron transport properties of dithiocarboxylate terminated molecular junctions. Transport properties are computed self-consistently within density functional theory and nonequilibrium Green's functions formalism. A microscopic origin of the experimentally observed current lification by dithiocarboxylate anchoring groups is established. For the 4,4'-biphenyl bis(dithiocarboxylate) junction, we find that the interaction of the lowest unoccupied molecular orbital (LUMO) of the dithiocarboxylate anchoring group with LUMO and highest occupied molecular orbital (HOMO) of the biphenyl part results in bonding and antibonding resonances in the transmission spectrum in the vicinity of the electrode Fermi energy. A new microscopic mechanism of rectification is predicted based on the electronic structure of asymmetrical anchoring groups. We show that the peaks in the transmission spectra of 4'-thiolato-biphenyl-4-dithiocarboxylate junction respond differently to the applied voltage. Depending upon the origin of a transmission resonance in the orbital interaction picture, its energy can be shifted along with the chemical potential of the electrode to which the molecule is more strongly or more weakly coupled.
Publisher: IOP Publishing
Date: 15-05-2012
DOI: 10.1088/0953-8984/24/22/225304
Abstract: We use a superoperator representation of the quantum kinetic equation to develop nonequilibrium perturbation theory for an inelastic electron current through a quantum dot. We derive a Lindblad-type kinetic equation for an embedded quantum dot (i.e. a quantum dot connected to Lindblad dissipators through a buffer zone). The kinetic equation is converted to non-Hermitian field theory in Liouville-Fock space. The general nonequilibrium many-body perturbation theory is developed and applied to the quantum dot with electron-vibronic and electron-electron interactions. Our perturbation theory becomes equivalent to a Keldysh nonequilibrium Green's function perturbative treatment provided that the buffer zone is large enough to alleviate the problems associated with approximations of the Lindblad kinetic equation.
Publisher: IOP Publishing
Date: 04-12-2015
Publisher: AIP Publishing
Date: 08-09-2000
DOI: 10.1063/1.1288384
Abstract: The exact atomic electrostatic potential (AEP) and atomic multipole moments are calculated using the topological partitioning of the electron density. High rank (l⩽20) spherical tensor multipole moments are used to examine the convergence properties of the multipole expansion. We vary independently the maximum multipole rank, lmax, and the radius of the spherical grid around an atom in a molecule where we measure the discrepancy between the exact AEP and the one obtained via multipole expansion. The root mean square values are between 0.1 and 1.6 kJ/mol for four atoms (C, N, O, S) on a spherical grid with the ρ=0.001 a.u. convergence radius and for lmax=4. Our calculations demonstrate that this fast convergence is due to the decay of the electron density. We show that multipole moments generated by finite atoms are adequate for use in the multipole expansion of the electrostatic potential, contrary to some claims made in the literature. Moreover they can be used to model intermolecular and in principle intramolecular interactions as well.
Publisher: American Chemical Society (ACS)
Date: 11-08-2001
DOI: 10.1021/JP011511Q
Publisher: IOP Publishing
Date: 22-01-2013
DOI: 10.1088/0953-8984/25/7/075702
Abstract: We present a derivation of the Markovian master equation for an out-of-equilibrium quantum dot connected to two superconducting reservoirs, which are described by the Bogoliubov-de Gennes Hamiltonians and have the chemical potentials, the temperatures, and the complex order parameters as the relevant quantities. We consider a specific ex le in which the quantum dot is represented by the Anderson impurity model and study the transport properties, proximity effect and Andreev bound states in equilibrium as well as far-from-equilibrium setups.
Publisher: AIP Publishing
Date: 10-10-2007
DOI: 10.1063/1.2779037
Abstract: In order to adequately describe molecular rotation far from equilibrium, we have generalized the J-diffusion model by allowing the rotational relaxation rate to be angular momentum dependent. The calculated nonequilibrium rotational correlation functions (CFs) are shown to decay much slower than their equilibrium counterparts, and orientational CFs of hot molecules exhibit coherent behavior, which persists for several rotational periods. As distinct from the results of standard theories, rotational and orientational CFs are found to dependent strongly on the nonequilibrium preparation of the molecular ensemble. We predict the Arrhenius energy dependence of rotational relaxation times and violation of the Hubbard relations for orientational relaxation times. The standard and generalized J-diffusion models are shown to be almost indistinguishable under equilibrium conditions. Far from equilibrium, their predictions may differ dramatically.
Publisher: Springer Science and Business Media LLC
Date: 21-09-0008
Publisher: Springer Science and Business Media LLC
Date: 09-02-2011
Publisher: AIP
Date: 2008
DOI: 10.1063/1.2915576
Publisher: Elsevier BV
Date: 08-1998
Publisher: AIP Publishing
Date: 27-03-2002
DOI: 10.1063/1.1460857
Abstract: Schrödinger equation with given, a priori known current is formulated. A nonzero current density is maintained in the quantum system via a subsidiary condition imposed by vector, local Lagrange multiplier. Constrained minimization of the total energy on the manifold of an arbitrary current density topology results into a nonlinear self-consistent Schrödinger equation. The applications to electronic transport in two-terminal molecular devices are developed and new macroscopic definition of a molecular current–voltage characteristic is proposed. The Landauer formula for the conductance of an ideal one-dimensional lead is obtained within the approach. The method is examined by modeling of current carrying states of one-dimensional harmonic oscillator.
Publisher: AIP Publishing
Date: 10-05-2018
DOI: 10.1063/1.5033354
Abstract: We present a theoretical approach to solve the Markovian master equation for quantum transport with stochastic telegraph noise. Considering probabilities as functionals of a random telegraph process, we use Novikov’s functional method to convert the stochastic master equation to a set of deterministic differential equations. The equations are then solved in the Laplace space, and the expression for the probability vector averaged over the ensemble of realisations of the stochastic process is obtained. We apply the theory to study the manifestations of telegraph noise in the transport properties of molecular junctions. We consider the quantum electron transport in a resonant-level molecule as well as polaronic regime transport in a molecular junction with electron-vibration interaction.
Publisher: AIP Publishing
Date: 28-10-2009
DOI: 10.1063/1.3253799
Abstract: We have derived several relations, which allow the evaluation of the system free energy changes in the leading order in ℏ2 along classically generated trajectories. The results are formulated in terms of purely classical Hamiltonians and trajectories, so that semiclassical partition functions can be computed, e.g., via classical molecular dynamics simulations. The Hamiltonians, however, contain additional potential-energy terms, which are proportional to ℏ2 and are temperature-dependent. We discuss the influence of quantum interference on the nonequilibrium work and problems with unambiguous definition of the semiclassical work operator.
Publisher: American Physical Society (APS)
Date: 08-1997
Publisher: Elsevier BV
Date: 07-2005
Publisher: AIP Publishing
Date: 14-09-2017
DOI: 10.1063/1.4991038
Abstract: Quantum transport of electrons through a molecule is a series of in idual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ1 and τ2 means that the density matrix of the molecule is not fully renewed after time τ1 and the probability of observing waiting time τ2 for the second electron transfer depends on the previous electron waiting time τ1. The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.
Publisher: Elsevier BV
Date: 11-2001
Publisher: Springer Science and Business Media LLC
Date: 05-1997
DOI: 10.1007/BF02634272
Publisher: American Physical Society (APS)
Date: 18-07-2008
Publisher: American Physical Society (APS)
Date: 15-01-2008
Publisher: IOP Publishing
Date: 17-02-2014
Publisher: American Physical Society (APS)
Date: 19-12-2019
Publisher: AIP Publishing
Date: 16-03-2021
DOI: 10.1063/5.0045652
Abstract: Confined nanoscale spaces, electric fields, and tunneling currents make the molecular electronic junction an experimental device for the discovery of new out-of-equilibrium chemical reactions. Reaction-rate theory for current-activated chemical reactions is developed by combining the Keldysh nonequilibrium Green’s function treatment of electrons, Fokker–Planck description of the reaction coordinate, and Kramers first-passage time calculations. The nonequilibrium Green’s functions (NEGF) provide an adiabatic potential as well as a diffusion coefficient and temperature with local dependence on the reaction coordinate. Van K en’s Fokker–Planck equation, which describes a Brownian particle moving in an external potential in an inhomogeneous medium with a position-dependent friction and diffusion coefficient, is used to obtain an analytic expression for the first-passage time. The theory is applied to several transport scenarios: a molecular junction with a single reaction coordinate dependent molecular orbital and a model diatomic molecular junction. We demonstrate the natural emergence of Landauer’s blowtorch effect as a result of the interplay between the configuration dependent viscosity and diffusion coefficients. The resultant localized heating in conjunction with the bond-deformation due to current-induced forces is shown to be the determining factors when considering chemical reaction rates, each of which results from highly tunable parameters within the system.
Publisher: Springer Science and Business Media LLC
Date: 27-02-2013
DOI: 10.1007/S00894-013-1794-Z
Abstract: Ab initio molecular dynamics simulations have been performed of a gold-1,4-benzenedithiol (BDT)-gold nanojunction under mechanical stress. For three different pulling rates between 10 and 40 m s(-1), it is found that the nanowire always ruptures between the second and third Au atom from the thiol sulfur. Larger rupture forces and longer extensions are required at higher pulling rates and vice versa. The electrical conductance was calculated along a pulling trajectory using the DFT-NEGF method to study the effect of thermal and stress-induced structural changes on the electrical transport properties. While the mechanically induced stretching of the junction is seen to lower the time-averaged conductance, thermal conformational changes are capable of altering the conductance by one order of magnitude. No single geometric quantity could be identified as the main contributor to the conductance fluctuations. Small modulations, however, can be explained in terms of C=C double bond vibrations in the BDT molecule. The dependence of the conductance on different geometric variables has further been investigated systematically by performing constrained geometry optimizations along a number of angle and dihedral coordinates. The largest changes in the conductance are observed when the Au-S-C angle and the Au-S-C-C dihedral are simultaneously constrained.
Publisher: AIP Publishing
Date: 18-04-2011
DOI: 10.1063/1.3581098
Abstract: Based on the super-fermion representation of quantum kinetic equations we develop nonequilibrium, post-Hartree–Fock many-body perturbation theory for the current through a region of interacting electrons. We apply the theory to out of equilibrium Anderson model and discuss practical implementation of the approach. Our calculations show that nonequilibrium electronic correlations may produce significant quantitative and qualitative corrections to mean-field electronic transport properties.
Publisher: AIP Publishing
Date: 15-04-2001
DOI: 10.1063/1.1356013
Abstract: An atom–atom partitioning of the (super)molecular Coulomb energy is proposed on the basis of the topological partitioning of the electron density. Atom–atom contributions to the molecular intra- and intermolecular Coulomb energy are computed exactly, i.e., via a double integration over atomic basins, and by means of the spherical tensor multipole expansion, up to rank L=lA+lB+1=5. The convergence of the multipole expansion is able to reproduce the exact interaction energy with an accuracy of 0.1–2.3 kJ/mol at L=5 for atom pairs, each atom belonging to a different molecule constituting a van der Waals complex, and for nonbonded atom–atom interactions in single molecules. The atom–atom contributions do not show a significant basis set dependence (3%) provided electron correlation and polarization basis functions are included. The proposed atom–atom Coulomb interaction energy can be used both with post-Hartree–Fock wave functions and experimental charge densities in principle. The Coulomb interaction energy between two molecules in a van der Waals complex can be computed by summing the additive atom–atom contributions between the molecules. Our method is able to extract from the supermolecule wave function an estimate of the molecular interaction energy in a complex, without invoking the reference state of free noninteracting molecules. We provide computational details of this method and apply it to (C2H2)2 (HF)2 (H2O)2 butane 1,3,5-hexatriene acrolein and urocanic acid, thereby covering a cross section of hydrogen bonds, and covalent bonds with and without charge transfer.
Publisher: American Physical Society (APS)
Date: 16-07-2007
Publisher: AIP Publishing
Date: 10-03-2006
DOI: 10.1063/1.2174959
Abstract: We demonstrate that the single-channel transmission in the resonance tunneling regime exhibits self-similarity as a function of the nanowire length and the energy of incident electrons. The self-similarity is used to design the nonlinear transformation of the nanowire length and energy which, on the basis of known values of transmission for a certain region on the energy-length plane, yields transmissions for other regions on this plane. Test calculations with a one-dimensional tight-binding model illustrate the described transformations. Density function theory based transport calculations of Na atomic wires confirm the existence of the self-similarity in the transmission.
Publisher: Elsevier BV
Date: 1998
Publisher: AIP Publishing
Date: 15-02-2019
DOI: 10.1063/1.5058735
Abstract: Non-equilibrium Green’s function theory for non-adiabatic effects in quantum transport [Kershaw and Kosov, J. Chem. Phys. 147, 224109 (2017) and J. Chem. Phys. 149, 044121 (2018)] is extended to the case of interacting electrons. We consider a general problem of quantum transport of interacting electrons through a central region with dynamically changing geometry. The approach is based on the separation of time scales in the non-equilibrium Green’s functions and the use of the Wigner transformation to solve the Kadanoff-Baym equations. The Green’s functions and correlation self-energy are non-adiabatically expanded up to the second order central time derivatives. We produce expressions for Green’s functions with non-adiabatic corrections and a modified formula for electric current both depend not only on instantaneous molecular junction geometry but also on nuclear velocities and accelerations. The theory is illustrated by the study of electron transport through a model single-resonant level molecular junction with local electron-electron repulsion and a dynamically changing geometry.
Publisher: American Physical Society (APS)
Date: 16-07-2013
Publisher: AIP Publishing
Date: 14-04-2006
DOI: 10.1063/1.2191058
Abstract: We present a model for the description of orientational relaxation in hydrogen-bonding liquids. The model contains two relaxation parameters which regulate the intensity and efficiency of dissipation, as well as the memory function which is responsible for the short-time relaxation effects. It is shown that the librational portion of the orientational relaxation is described by an algebraic ∼t−3∕2 contribution, on top of which more rapid and nonmonotonous decays caused by the memory effects are superimposed. The long-time behavior of the orientational relaxation is exponential, although nondiffusional. It is governed by the rotational energy relaxation. We apply the model to interpret recent molecular dynamic simulations and polarization pump-probe experiments on HOD in liquid D2O [C. J. Fecko et al., J. Chem. Phys. 122, 054506 (2005)].
Publisher: American Physical Society (APS)
Date: 11-05-2016
Publisher: American Chemical Society (ACS)
Date: 05-2003
DOI: 10.1021/JP022445A
Publisher: American Chemical Society (ACS)
Date: 05-2006
DOI: 10.1021/JP0610665
Abstract: Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups.
Publisher: Elsevier BV
Date: 03-1998
Publisher: AIP Publishing
Date: 06-02-2016
DOI: 10.1063/1.4907276
Abstract: We study the binding pattern of the amino acid alanine on the naturally chiral Pt surfaces Pt(531), Pt(321), and Pt(643). These surfaces are all vicinal to the {111} direction but have different local environments of their kink sites and are thus a model for realistic roughened Pt surfaces. Alanine has only a single methyl group attached to its chiral center, which makes the number of possible binding conformations computationally tractable. Additionally, only the amine and carboxyl group are expected to interact strongly with the Pt substrate. On Pt(531), we study the molecule in its pristine as well as its deprotonated form and find that the deprotonated one is more stable by 0.47 eV. Therefore, we study the molecule in its deprotonated form on Pt(321) and Pt(643). As expected, the oxygen and nitrogen atoms of the deprotonated molecule provide a local binding “tripod” and the most stable adsorption configurations optimize the interaction of this “tripod” with undercoordinated surface atoms. However, the interaction of the methyl group plays an important role: it induces significant chiral selectivity of about 60 meV on all surfaces. Hereby, the L-enantiomer adsorbs preferentially to the Pt(321)S and Pt(643)S surfaces, while the D-enantiomer is more stable on Pt(531)S. The binding energies increase with increasing surface density of kink sites, i.e., they are largest for Pt(531)S and smallest for Pt(643)S.
Publisher: Springer Science and Business Media LLC
Date: 02-2019
Publisher: AIP Publishing
Date: 04-2013
DOI: 10.1063/1.4797495
Abstract: We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Green's functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an ex le, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e., the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.
Publisher: AIP Publishing
Date: 08-04-2005
DOI: 10.1063/1.1872812
Abstract: This work presents the formalism and implementation of excited state nuclear forces within density functional linear response theory using a plane wave basis set. An implicit differentiation technique is developed for computing nonadiabatic coupling between Kohn–Sham molecular orbital wave functions as well as gradients of orbital energies which are then used to calculate excited state nuclear forces. The algorithm has been implemented in a plane wave seudopotential code taking into account only a reduced active subspace of molecular orbitals. It is demonstrated for the H2 and N2 molecules that the analytical gradients rapidly converge to the exact forces when the active subspace of molecular orbitals approaches completeness.
Publisher: World Scientific Pub Co Pte Lt
Date: 28-03-1996
DOI: 10.1142/S0217732396000850
Abstract: A method taking account of a deviation of state occupation numbers from the thermal RPA prescriptions is elaborated to study collective excitations in hot nuclei. This thermal renormalized random phase approximation (TRRPA) is from Ken-Ji Hara and D.J. Rowe. In developing the TRRPA, a formalism of the thermofield dynamics (TFD) is used. Some numerical results are given for the SU(2) model.
Publisher: American Physical Society (APS)
Date: 25-01-2012
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1SC04943G
Abstract: Single-molecule circuits using silicon contacts are robust, conductive, controllable, and highly reproducible in blinking experiments, with enhanced conductance in break-junctions owing to residual dangling bonds.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2009
Publisher: American Physical Society (APS)
Date: 24-11-1997
Publisher: AIP Publishing
Date: 02-2017
DOI: 10.1063/1.4974985
Abstract: We developed a method for computing matrix elements of single-particle operators in the correlated random phase approximation ground state. Working with the explicit random phase approximation ground state wavefunction, we derived a practically useful and simple expression for a molecular property in terms of random phase approximation litudes. The theory is illustrated by the calculation of molecular dipole moments for a set of representative molecules.
Publisher: AIP Publishing
Date: 22-06-2007
DOI: 10.1063/1.2740257
Abstract: We study the influence of the velocity dependence of friction on the escape rate of a Brownian particle from the deep potential well (Eb≫kBT, Eb is the barrier height, kB is the Boltzmann constant, and T is the bath temperature). The bath-induced relaxation is treated within the Rayleigh model (a heavy particle of mass M in the bath of light particles of mass m≪M) up to the terms of the order of O(λ4), λ2=m∕M≪1. The term ∼1 is equivalent to the Fokker-Planck dissipative operator, and the term ∼λ2 is responsible for the velocity dependence of friction. As expected, the correction to the Kramers escape rate in the overd ed limit is proportional to λ2 and is small. The corresponding correction in the underd ed limit is proportional to λ2Eb∕(kBT) and is not necessarily small. We thus suggest that the effects due to the velocity-dependent friction may be of considerable importance in determining the rate of escape of an under- and moderately d ed Brownian particle from a deep potential well, while they are of minor importance for an overd ed particle.
Publisher: AIP Publishing
Date: 15-07-2019
DOI: 10.1063/1.5108518
Abstract: In quantum transport through nanoscale devices, fluctuations arise from various sources: the discreteness of charge carriers, the statistical nonequilibrium that is required for device operation, and unavoidable quantum uncertainty. As experimental techniques have improved over the last decade, measurements of these fluctuations have become available. They have been accompanied by a plethora of theoretical literature using many different fluctuation statistics to describe the quantum transport. In this paper, we overview three prominent fluctuation statistics: full counting, waiting time, and first-passage time statistics. We discuss their weaknesses and strengths and explain connections between them in terms of renewal theory. In particular, we discuss how different information can be encoded in different statistics when the transport is nonrenewal and how this behavior manifests in the measured physical quantities of open quantum systems. All theoretical results are illustrated via a demonstrative transport scenario, a Markovian master equation for a molecular electronic junction with electron-phonon interactions. We demonstrate that to obtain nonrenewal behavior, and thus to have temporal correlations between successive electron tunneling events, there must be a strong coupling between tunneling electrons and out-of-equilibrium quantized molecular vibrations.
Publisher: Springer Science and Business Media LLC
Date: 17-05-2008
Publisher: American Physical Society (APS)
Date: 06-11-2020
Publisher: American Chemical Society (ACS)
Date: 18-07-2000
DOI: 10.1021/JP0003407
Publisher: World Scientific Pub Co Pte Lt
Date: 21-06-1994
DOI: 10.1142/S0217732394001581
Abstract: The coupling of elementary excitation modes in hot nuclei is studied. For this aim the quasiparticle-phonon nuclear model (QPM) is extended to a finite temperature by using the formalism of the thermofield dynamics. First the energies and structures of one-phonon states are calculated in the thermal random phase approximation and then the thermal QPM Hamiltonian H QPM is expressed in terms of thermal quasiparticles and thermal RPA-phonons. The equation for the energies taking into account mixing of one-and two-thermal phonon states is derived. The expression of the coupling matrix element between thermal phonons is given.
Publisher: AIP Publishing
Date: 17-08-2011
DOI: 10.1063/1.3626521
Abstract: We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ Langevin equation for a reaction coordinate. The Langevin equation contains nonconservative current-induced forces and gives nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once a nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.
Publisher: AIP Publishing
Date: 08-04-1999
DOI: 10.1063/1.478572
Abstract: This paper describes a method to do ab initio molecular dynamics in electronically excited systems within the random phase approximation (RPA). Using a dynamical variational treatment of the RPA frequency, which corresponds to the electronic excitation energy of the system, we derive coupled equations of motion for the RPA litudes, the single particle orbitals, and the nuclear coordinates. These equations scale linearly with basis size and can be implemented with only a single holonomic constraint. Test calculations on a model two level system give exact agreement with analytical results. Furthermore, we examined the computational efficiency of the method by modeling the excited state dynamics of a one-dimensional polyene lattice. Our results indicate that the present method offers a considerable decrease in computational effort over a straight-forward configuration interaction (singles) plus gradient calculation performed at each nuclear configuration.
Publisher: American Physical Society (APS)
Date: 10-1998
Publisher: American Physical Society (APS)
Date: 07-11-2022
Publisher: AIP Publishing
Date: 04-11-2011
DOI: 10.1063/1.3658736
Abstract: We present a method to perform stability analysis of nonequilibrium fixed points appearing in self-consistent electron transport calculations. The nonequilibrium fixed points are given by the self-consistent solution of stationary, nonlinear kinetic equation for single-particle density matrix. We obtain the stability matrix by linearizing the kinetic equation around the fixed points and analyze the real part of its spectrum to assess the asymptotic time behavior of the fixed points. We derive expressions for the stability matrices within Hartree-Fock and linear response adiabatic time-dependent density functional theory. The stability analysis of multiple fixed points is performed within the nonequilibrium Hartree-Fock approximation for the electron transport through a molecule with a spin-degenerate single level with local Coulomb interaction.
Publisher: American Physical Society (APS)
Date: 06-05-2021
Publisher: Elsevier BV
Date: 12-2017
Publisher: American Physical Society (APS)
Date: 26-10-2016
No related grants have been discovered for Daniel Kosov.