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Papers in this area

24 featured work(s)

preprint2014arXiv

The role of electron localization in density functionals

We introduce a new functional for simulating ground-state and time-dependent electronic systems within density-functional theory. The functional combines an expression for the exact Kohn-Sham (KS) potential in the limit of complete electron localization with a measure of the actual localization. We find accurate self-consistent charge densities, even for systems where the exact exchange-correlation potential exhibits non-local dependence on the density, such as potential steps. We compare our results to the exact KS potential for each system. The self-interaction correction is accurately described, avoiding the need for orbital-dependent potentials.

preprint2014arXiv

Neutron diffraction of hydrogenous materials: measuring incoherent and coherent intensities separately from liquid water - a 40-year-old puzzle solved

(short version) Accurate determination of the coherent static structure factor of disordered materials containing proton nuclei is prohibitively difficult by neutron diffraction, due to the large incoherent cross section of $^1$H. This notorious problem has set severe obstacles to the structure determination of hydrogenous materials up to now, via introducing large uncertainties into neutron diffraction data processing. Here we present the first accurate separate measurements, using polarized neutron diffraction, of the coherent and incoherent contributions to the total static structure factor of 5 mixtures of light and heavy water, over an unprecedentedly wide momentum transfer range. The structure factors of H$_2$O and D$_2$O mixtures derived in this work may signify the beginning of a new era in the structure determination of hydrogenous materials, using neutron diffraction.

preprint2016arXiv

Origin of static and dynamic steps in exact Kohn-Sham potentials

Knowledge of exact properties of the exchange-correlation (xc) functional is important for improving the approximations made within density functional theory. Features such as steps in the exact xc potential are known to be necessary for yielding accurate densities, yet little is understood regarding their shape, magnitude and location. We use systems of a few electrons, where the exact electron density is known, to demonstrate general properties of steps. We find that steps occur at points in the electron density where there is a change in the `local effective ionization energy' of the electrons. We provide practical arguments, based on the electron density, for determining the position, shape and height of steps for ground-state systems, and extend the concepts to time-dependent systems. These arguments are intended to inform the development of approximate functionals, such as the mixed localization potential (MLP), which already demonstrate their capability to produce steps in the Kohn-Sham potential.

preprint2017arXiv

Size effect in the ionization energy of PAH clusters

We report the first experimental measurement of the near-threshold photo-ionization spectra of polycyclic aromatic hydrocarbon clusters made of pyrene C16H10 and coronene C24H12, obtained using imaging photoelectron photoion coincidence spectrometry with a VUV synchrotron beamline. The experimental results of the ionization energy are confronted to calculated ones obtained from simulations using dedicated electronic structure treatment for large ionized molecular clusters. Experiment and theory consistently find a decrease of the ionization energy with cluster size. The inclusion of temperature effects in the simulations leads to a lowering of this energy and to a quantitative agreement with the experiment. In the case of pyrene, both theory and experiment show a discontinuity in the IE trend for the hexamer.

preprint2017arXiv

How is the derivative discontinuity related to steps in the exact Kohn-Sham potential?

The reliability of density-functional calculations hinges on accurately approximating the unknown exchange-correlation (xc) potential. Common (semi-)local xc approximations lack the jump experienced by the exact xc potential as the number of electrons infinitesimally surpasses an integer, and the spatial steps that form in the potential as a result of the change in the decay rate of the density. These features are important for an accurate prediction of the fundamental gap and the distribution of charge in complex systems. Although well-known concepts, the exact relationship between them remained unclear. In this Letter, we establish the common fundamental origin of these two features of the exact xc potential via an analytical derivation. We support our result with an exact numerical solution of the many-electron Schroedinger equation for a single atom and a diatomic molecule in one dimension. Furthermore, we propose a way to extract the fundamental gap from the step structures in the potential.

preprint2016arXiv

Local density approximations from finite systems

The local density approximation (LDA) constructed through quantum Monte Carlo calculations of the homogeneous electron gas (HEG) is the most common approximation to the exchange-correlation functional in density functional theory. We introduce an alternative set of LDAs constructed from slablike systems of one, two and three electrons that resemble the HEG within a finite region, and illustrate the concept in one dimension. Comparing with the exact densities and Kohn-Sham potentials for various test systems, we find that the LDAs give a good account of the self-interaction correction, but are less reliable when correlation is stronger or currents flow.

preprint2017arXiv

Near-Infrared Emitting Single Squaraine Dye Aggregate with large Stokes shift

The study of supramolecular interactions and aggregation behaviour of functional materials is of great importance to tune and extend their spectral sensitivity and, hence, improve the optoelectronic response of related devices. In this study, we resolve spatially and spectrally the absorption and emission features of a squaraine aggregate by means of confocal microscopy and absorption/photoluminescence spectroscopy. We observe that the aggregate affords both a broad absorption spectrum (centred at 670 nm), likely originated by a dyes configuration with allowed J- and H- arrangements, and a strong and relatively narrow emission in the near-infrared (NIR) part of the spectrum (centred at 780 nm), with a remarkable Stokes shift of 110 nm that is among the largest exhibited by squaraine dyes. These peculiarities would be beneficial for extending the spectral sensitivity of bot photovoltaic and light-emitting diodes, and extremely appealing for possible applications of these aggregates as NIR fluorescent probes in biomedical applications.

preprint2019arXiv

GuacaMol: Benchmarking Models for De Novo Molecular Design

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

preprint2019arXiv

Generalized Kasha's Scheme for Classifying Two-Dimensional Excitonic Molecular Aggregates: Temperature Dependent Absorption Peak Frequency Shift

We propose a generalized theoretical framework for classifying two-dimensional (2D) excitonic molecular aggregates based on an analysis of temperature dependent spectra. In addition to the monomer-aggregate absorption peak shift, which defines the conventional J- and H-aggregates, we incorporate the peak shift associated with increasing temperature as a measure to characterize the exciton band structure. First we show that there is a one-to-one correspondence between the monomer-aggregate and the T-dependent peak shifts for Kasha's well-established model of 1D aggregates, where J-aggregates exhibit further redshift upon increasing temperature and H-aggregates exhibit further blueshift. On the contrary, 2D aggregate structures are capable of supporting the two other combinations: blueshifting J-aggregates and redshifting H-aggregates, owing to their more complex exciton band structures. Secondly, using spectral lineshape theory, the T-dependent shift is associated with the relative abundance of states on each side of the bright state. We further establish that the density of states can be connected to the microscopic packing condition leading to these four classes of aggregates by separately considering the short and long-range contribution to the excitonic couplings. In particular the T-dependent shift is shown to be an unambiguous signature for the sign of net short-range couplings: Aggregates with net negative (positive) short-range couplings redshift (blueshift) with increasing temperature. Lastly, comparison with experiments shows that our theory can be utilized to quantitatively account for the observed but previously unexplained T-dependent absorption lineshapes. Thus, our work provides a firm ground for elucidating the structure-function relationships for molecular aggregates and is fully compatible with existing experimental and theoretical structure characterization tools.

preprint2018arXiv

Advantageous nearsightedness of many-body perturbation theory contrasted with Kohn-Sham density functional theory

For properties of interacting electron systems, Kohn-Sham (KS) theory is often favored over many-body perturbation theory (MBPT) owing to its low computational cost. However, the exact KS potential can be challenging to approximate, for example in the presence of localized subsystems where the exact potential is known to exhibit pathological features such as spatial steps. By modeling two electrons, each localized in a distinct potential well, we illustrate that the step feature has no counterpart in MBPTs (including Hartree-Fock and GW) or hybrid methods involving Fock exchange because the spatial non-locality of the self-energy renders such pathological behavior unnecessary. We present a quantitative illustration of the orbital-dependent nature of the non-local potential, and a numerical demonstration of Kohn's concept of the nearsightedness for self energies, when two distant subsystems are combined, in contrast to the KS potential. These properties emphasize the value of self-energy-based approximations in developing future approaches within KS-like theories.

preprint2019arXiv

Quasi-linear buildup of Coulomb integrals via the coupling strength parameter in the non-relativistic electronic Schrodinger equation

The non-relativistic electronic Hamiltonian, Hkin + Hne + aHee, is linear in coupling strength parameter (a), but its eigenvalues (electronic energies) have only quasi-linear dependence on it. Detailed analysis is given on the participation of electron-electron repulsion energy (Vee) in total electronic energy (Etotal electr,k) in addition to the well-known virial theorem and standard algorithm for vee(a=1)=Vee calculated during the standard- and post HF-SCF routines. Using a particular modification in the SCF part of the Gaussian package, we have analyzed the ground state solutions via the parameter a. Technically, with a single line in the SCF algorithm, operator was changed as 1/rij-> a/rij with input a. The most important findings are, 1, vee(a) is quasi-linear function of a, 2, the extension of 1st Hohenberg-Kohn theorem (PSI0(a=1)<=>Hne<=>Y0(a=0)) and its consequences in relation to a. The latter allows an algebraic transfer from the simpler solution of case a=0 (where the single Slater determinant Y0 is the accurate form) to the physical case a=1. Moreover, we have generalized the emblematic Hund rule, virial-, Hohenberg-Kohn- and Koopmans theorems in relation to the coupling strength parameter.

preprint2019arXiv

Path-accelerated molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to MD timesteps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a non-equilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

preprint2019arXiv

Feature Optimization for Atomistic Machine Learning Yields A Data-Driven Construction of the Periodic Table of the Elements

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes it possible to improve the accuracy of the model for a given amount of reference data. When using a description of the structures that is transparent and well-principled, optimizing the representation might reveal insights into the chemistry of the data set. Here we show how one can generalize the SOAP kernel to introduce a distance-dependent weight that accounts for the multi-scale nature of the interactions, and a description of correlations between chemical species. We show that this improves substantially the performance of ML models of molecular and materials stability, while making it easier to work with complex, multi-component systems and to extend SOAP to coarse-grained intermolecular potentials. The element correlations that give the best performing model show striking similarities with the conventional periodic table of the elements, providing an inspiring example of how machine learning can rediscover, and generalize, intuitive concepts that constitute the foundations of chemistry.

preprint2019arXiv

Computational Investigations of the Lithium Superoxide Dimer Rearrangement on Noisy Quantum Devices

Currently available noisy intermediate-scale quantum (NISQ) devices are limited by the number of qubits that can be used for quantum chemistry calculations on molecules. We show herein that the number of qubits required for simulations on a quantum computer can be reduced by limiting the number of orbitals in the active space. Thus, we have utilized ansätze that approximate exact classical matrix eigenvalue decomposition methods (Full Configuration Interaction). Such methods are appropriate for computations with the Variational Quantum Eigensolver algorithm to perform computational investigations on the rearrangement of the lithium superoxide dimer with both quantum simulators and quantum devices. These results demonstrate that, even with a limited orbital active space, quantum simulators are capable of obtaining energy values that are similar to the exact ones. However, calculations on quantum hardware underestimate energies even after the application of readout error mitigation.

preprint2019arXiv

Stochastic Simulation of Nonequilibrium Heat Conduction in Extended Molecule Junctions

Understanding phononic heat transport processes in molecular junctions is a central issue in the developing field of nanoscale heat conduction and manipulation. Here we present a Stochastic Nonequlibrium Molecular Dynamics simulation framework to investigate heat transport processes in molecular junctions in and beyond the linear response regime. We use extended molecular models which filter Markovian heat reservoirs through an intermediate substrate region, to provide a realistic and controllable effective bath spectral density. The results obtained for alkanedithol molecules connecting gold substrates agree with previous nonequilibrium Green&#39;s function calculations in frequency domain, and match recent experimental measurements (e.g. thermal conductance around 20 pW/K for alkanedithiols in single molecular junctions) Classical MD simulations using the full molecular forcefield and quantum Landauer-type calculations based on the harmonic part of the same forcefield are compared, and the similarity of the results indicate that heat transport is dominated by modes in the lower frequency range. Heat conductance simulations on polyynes of different lengths illuminates the effects of molecular conjugation on thermal transport.

preprint2019arXiv

Semi-analytic Evaluation of 1, 2 and 3-Electron Coulomb Integrals with Gaussian expansion of Distance Operators W= R$_{C1}^{-n}$R$_{D1}^{-m}$, R$_{C1}^{-n}$r$_{12}^{-m}$, r$_{12}^{-n}$r$_{13}^{-m}$

The equations derived help to evaluate semi-analytically (mostly for k=1,2 or 3) the important Coulomb integrals Int rho(r1)...rho(rk) W(r1,...,rk) dr1...drk, where the one-electron density, rho(r1), is a linear combination (LC) of Gaussian functions of position vector variable r1. It is capable to describe the electron clouds in molecules, solids or any media/ensemble of materials, weight W is the distance operator indicated in the title. R stands for nucleus-electron and r for electron-electron distances. The n=m=0 case is trivial, the (n,m)=(1,0) and (0,1) cases, for which analytical expressions are well known, are widely used in the practice of computation chemistry (CC) or physics, and analytical expressions are also known for the cases n,m=0,1,2. The rest of the cases - mainly with any real (integer, non-integer, positive or negative) n and m - needs evaluation. We base this on the Gaussian expansion of |r|^-u, of which only the u=1 is the physical Coulomb potential, but the u.ne.1 cases are useful for (certain series based) correction for (the different) approximate solutions of Schrodinger equation, for example, in its wave-function corrections or correlation calculations. Solving the related linear equation system (LES), the expansion |r|^-u about equal to SUM(k=0toL)SUM(i=1toM) Cik r^2k exp(-Aik r^2) is analyzed for |r| = r12 or RC1 with least square fit (LSF) and modified Taylor expansion. These evaluated analytic expressions for Coulomb integrals (up to Gaussian function integrand and the Gaussian expansion of |r|^-u) are useful for the manipulation with higher moments of inter-electronic distances via W, even for approximating Hamiltonian.

preprint2019arXiv

Generalization of the Kelvin Equation for Arbitrarily Curved Surfaces

Capillary condensation, which takes place in confined geometries, is the first-order vapor-to-liquid phase transition and is explained by the Kelvin equation, but the equations applicability for arbitrarily curved surface has been long debated and is a sever problem. Recently, we have proposed generic dynamic equations for moving surfaces. Application of the equations to static shapes and modelling the pressure at the interface nearly trivially solves the generalization problem for the Kelvin equation. The equations are universally true for any surfaces: atomic, molecular, micro or macro scale, real or virtual, Riemannian or pseudo-Riemannian, active or passive.

preprint2019arXiv

Probing molecular chirality via laser-induced electronic fluxes

Chirality is ubiquitous in nature and of fundamental importance in science. The present work focuses on understanding the conditions required to modify the chirality during ultrafast electronic motion by bringing enantiomers out-of-equilibrium. Different kinds of ultrashort linearly-polarised laser pulses are used to drive an ultrafast charge migration process by the excitation of a small number of low-lying excited states from the ground electronic state of S- and R-epoxypropane. Control over chiral electron dynamics is achieved by choosing the different orientations of the linearly polarised pulse. We find that chirality breaking electric fields are only possible in oriented molecules, and that charge migration remains chiral when the polarisation of the field lies in the mirror plane defining the enantiomer pair, or when it is strictly perpendicular to it. Ultimately, the presence or the absence of a mirror symmetry for the enantiomer pair in the external field determines the chiral properties of the charge migration process.

preprint2020arXiv

Accurate real-time evolution of electron densities and ground-state properties from generalized Kohn-Sham theory

The exact static and time-dependent Kohn-Sham (KS) exchange-correlation (xc) potential is extremely challenging to approximate as it is a local multiplicative potential that depends on the electron density everywhere in the system. The KS approach can be generalised by allowing part of the potential to be spatially nonlocal. We take this nonlocal part to be that of unrestricted Hartree-Fock theory. The additional local correlation potential in principle ensures that the single-particle density exactly equals the many-body density. In our case, the local correlation potential is predominantly nearsighted in its dependence on the density and hence an (adiabatic) local density approximation to this potential yields accurate ground-state properties and real-time densities for one-dimensional test systems.

preprint2020arXiv

Time delay of slow electrons by a diatomic molecule described by non-overlapping atomic potentials model

We study the elastic scattering of slow electrons by two-atomic molecule in the frame of non-overlapping atomic potentials model. The molecular continuum wave function is represented as a combination of a plane wave and two spherical s-waves, generated by the centers of atomic spheres. The asymptotic of this function determines in closed form the amplitude of elastic electron scattering. We show that this amplitude cannot be represented as a series of spherical functions. Therefore, it is impossible to use straightly the usual S-matrix methods to determine the scattering phases for non-spherical targets. We show that far from molecule the continuum wave function can be presented as an expansion in other than spherical orthonormal functions. The coefficients of this expansion determine the molecular scattering phases for non-spherical molecular systems. In such an approach, we calculate the Wigner times delay for slow electron scattered by two-atomic target.

preprint2020arXiv

A Positive and Energy Stable Numerical Scheme for the Poisson-Nernst-Planck-Cahn-Hilliard Equations with Steric Interactions

We consider numerical methods for the Poisson-Nernst-Planck-Cahn-Hilliard (PNPCH) equations with steric interactions. We propose a novel energy stable numerical scheme that respects mass conservation and positivity at the discrete level. Existence and uniqueness of the solution to the proposed nonlinear scheme are established by showing that the solution is a unique minimizer of a convex functional over a closed, convex domain. The positivity of numerical solutions is further theoretically justified by the singularity of the entropy terms, which prevents the minimizer from approaching zero concentrations. A further numerical analysis proves discrete free-energy dissipation. Extensive numerical tests are performed to validate that the numerical scheme is first-order accurate in time and second-order accurate in space, and is capable of preserving the desired properties, such as mass conservation, positivity, and free energy dissipation, at the discrete level. Moreover, the PNPCH equations and the proposed scheme are applied to study charge dynamics and self-assembled nanopatterns in highly concentrated electrolytes that are widely used in electrochemical energy devices. Numerical results demonstrate that the PNPCH equations and our numerical scheme are able to capture nanostructures, such as lamellar patterns and labyrinthine patterns in electric double layers and the bulk, and multiple time relaxation with multiple time scales. In addition, we numerically characterize the interplay between cross steric interactions of short range and the concentration gradient regularization, and their impact on the development of nanostructures in the equilibrium state.

preprint2020arXiv

On the possibility to observe relations between quantum measurements and the entropy of phase transitions in Zn$_2$(BDC)$_2$(DABCO)

The work interprets experimental data for the heat capacity of Zn2(BDC)2(DABCO) in the region of second-order phase transitions. The proposed understanding of the processes occurring during phase transitions may be helpful to reveal quantum Zeno effects in metal-organic frameworks (MOFs) with evolving (unstable) structural subsystems and to establish relations between quantum measurements and the entropy of phase transitions.

preprint2020arXiv

Fission rate of excited nuclei at variable friction in the energy diffusion regime

Presently, it is well established that fission of excited nuclei is a dynamical process being a subject of fluctuations and dissipation. In the literature, there are indications that, at the compact nucleus shapes, the strength of nuclear friction is significantly reduced in comparison with the prediction of the one-body approach. Thus, one can expect that at small deformations the nuclear fission process occurs in the so-called &#34;energy diffusion regime&#34;. The purpose of our present work is to compare an approximate analytical formula for the fission rate in this regime with the quasistationary numerical rate which is exact within the statistical errors. Our calculations demonstrate relatively good agreement between these two rates provided the friction parameter is deformation independent. If one accounts for its deformation dependence, the agreement becomes significantly poorer.

preprint2020arXiv

Attosecond spectroscopy reveals alignment dependent core-hole dynamics in the ICl molecule

The removal of electrons located in the core shells of molecules creates transient states that live between a few femtoseconds to attoseconds. Owing to these short lifetimes, time-resolved studies of these states are challenging and complex molecular dynamics driven solely by electronic correlation are difficult to observe. Here, few-femtosecond core-excited state lifetimes of iodine monochloride are obtained by attosecond transient absorption on iodine 4d-16p transitions around 55 eV. Core-level ligand field splitting allows direct access of excited states aligned along and perpendicular to the ICl molecular axis. Lifetimes of 3.5 fs and 4.3 fs are obtained for core-hole states parallel to the bond and 6.5 fs and 6.9 fs for perpendicular states, while nuclear motion is essentially frozen on this timescale. Theory shows that the dramatic decrease of lifetime for core-vacancies parallel to the covalent bond is a manifestation of non-local interactions with the neighboring Cl atom of ICl.

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