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arXiv2014

A first-principles-based correlation functional for harmonious connection of short-range correlation and long-range dispersion

We present a physically motivated correlation functional belonging to the meta-generalized gradient approximation (meta-GGA) rung, which can be supplemented with long-range dispersion corrections without introducing double-counting of correlation contributions. The functional is derived by the method of constraint satisfaction, starting from an analytical expression for a real-space spin-resolved correlation hole. The model contains a position-dependent function that controls the range of the interelectronic correlations described by the semilocal functional. With minimal empiricism, this function may be adjusted so that the correlation model blends with a specific dispersion correction describing long-range contributions. For a preliminary assessment, our functional has been combined with the DFT-D3 dispersion correction and full Hartree-Fock (HF)-like exchange. Despite the HF-exchange approximation, its predictions compare favorably with reference interaction energies in an extensive set of non-covalently bound dimers.

physics.chem-ph↗

arXiv2012

Extended dynamical density functional theory for colloidal mixtures with temperature gradients

In the past decade, classical dynamical density functional theory (DDFT) has been developed and widely applied to the Brownian dynamics of interacting colloidal particles. One of the possible derivation routes of DDFT from the microscopic dynamics is via the Mori-Zwanzig-Forster projection operator technique with slowly varying variables such as the one-particle density. Here, we use the projection operator approach to extend DDFT into various directions: first, we generalize DDFT toward mixtures of $n$ different species of spherical colloidal particles. We show that there are in general nontrivial cross-coupling terms between the concentration fields and specify them explicitly for colloidal mixtures with pairwise hydrodynamic interactions. Secondly, we treat the energy density as an additional slow variable and derive formal expressions for an extended DDFT containing also the energy density. The latter approach can in principle be applied to colloidal dynamics in a nonzero temperature gradient. For the case without hydrodynamic interactions the diffusion tensor is diagonal, while thermodiffusion -- the dissipative cross-coupling term between energy density and concentration -- is nonzero in this limit. With finite hydrodynamic interactions also cross-diffusion coefficients assume a finite value. We demonstrate that our results for the extended DDFT contain the transport coefficients in the hydrodynamic limit (long wavelengths, low frequencies) as a special case.

cond-mat.soft↗

arXiv2014

The flexible nature of exchange, correlation and Hartree physics: resolving "delocalization" errors in a 'correlation free' density functional

By exploiting freedoms in the definitions of 'correlation', 'exchange' and 'Hartree' physics in ensemble systems we better generalise the notion of 'exact exchange' (EXX) to systems with fractional occupations functions of the frontier orbitals, arising in the dissociation limit of some molecules. We introduce the Linear EXX ("LEXX") theory whose pair distribution and energy are explicitly \emph{piecewise linear} in the occupations $f^σ_{i}$. {\hi}We provide explicit expressions for these functions for frontier $s$ and $p$ shells. Used in an optimised effective potential (OEP) approach it yields energies bounded by the piecewise linear 'ensemble EXX' (EEXX) energy and standard fractional optimised EXX energy: $E^{EEXX}\leq E^{LEXX} \leq E^{EXX}$. Analysis of the LEXX explains the success of standard OEP methods for diatoms at large spacing, and why they can fail when both spins are allowed to be non-integer so that "ghost" Hartree interactions appear between \emph{opposite} spin electrons in the usual formula. The energy $E^{LEXX}$ contains a cancellation term for the spin ghost case. It is evaluated for H, Li and Na fractional ions with clear derivative discontinuities for all cases. The $p$-shell form reproduces accurate correlation-free energies of B-F and Al-Cl. We further test LEXX plus correlation energy calculations on fractional ions of C and F and again shows both derivative discontinuities and good agreement with exact results.

physics.atom-ph↗

arXiv2013

Four-component united-atom model of bitumen

We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are being carried out using Graphic-Processor-Units based software in time spans in order of microseconds, and this enables the study of slow relaxation processes characterizing bitumen. This paper focuses on the high-temperature dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales as a result of the different constituents in the system. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear modulus are evaluated at the highest temperature, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is different from the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity.

physics.chem-ph↗

arXiv2012

Adsorption of lactic acid on chiral Pt surfaces - A Density Functional Theory study

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 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 sampling 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 reveal rather small chiral selectivities on 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.

cond-mat.mtrl-sci↗

arXiv2013

Excitation energy transfer efficiency: equivalence of transient and stationary setting and the absence of non-Markovian effects

We analyze efficiency of excitation energy transfer in photosynthetic complexes in transient and stationary setting. In the transient setting the absorption process is modeled as an individual event resulting in a subsequent relaxation dynamics. In the stationary setting the absorption is a continuous stationary process, leading to the nonequilibrium steady state. We show that, as far as the efficiency is concerned, both settings can be considered to be the same, as they result in almost identical efficiency. We also show that non-Markovianity has no effect on the resulting efficiency, i.e., corresponding Markovian dynamics results in identical efficiency. Even more, if one maps dynamics to appropriate classical rate equations, the same efficiency as in quantum case is obtained.

physics.chem-ph↗

arXiv2013

Nonlocal van der Waals functionals: The case of rare-gas dimers and solids

Recently, the nonlocal van der Waals (vdW) density functionals [M. Dion, H. Rydberg, E. Schroeder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)] have attracted considerable attention due to their good performance for systems where weak interactions are important. Since the physics of dispersion is included in these functionals, they are usually more accurate and show less erratic behavior than the semilocal and hybrid methods. In this work, several variants of the vdW functionals have been tested on rare-gas dimers (from He2 to Kr2) and solids (Ne, Ar, and Kr) and their accuracy compared to standard semilocal approximations supplemented or not by an atom-pairwise dispersion correction [S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010)]. An analysis of the results in terms of energy decomposition is also provided.

physics.chem-ph↗

arXiv2013

Assessment of various natural orbitals as the basis of large active space density matrix renormalization group calculations

It is well-known that not only the orbital ordering but also the choice of the orbitals themselves as the basis may significantly influence the computational efficiency of density-matrix renormalization group (DMRG) calculations. In this study, for assessing the efficiency of using various natural orbitals (NOs) as the DMRG basis, we performed benchmark DMRG calculations with different bases, which included the NOs obtained by various traditional electron correlation methods, as well as NOs acquired from preliminary moderate DMRG calculations (e.g., preserved states less than 500). The tested systems included N$_2$, transition metal Cr$_2$ systems, as well as 1-D hydrogen polyradical chain systems under equilibrium and dissociation conditions and 2-D hydrogen aggregates. The results indicate that a good compromise between the requirement for low computational costs of acquiring NOs and the demand for high efficiency of NOs as the basis of DMRG calculations may be very dependent on the studied systems' diverse electron correlation characteristics and the size of the active space. It is also shown that a DMRG-complete active space configuration interaction (DMRG-CASCI) calculation in a basis of carefully chosen NOs can provide a less expensive alternative to the standard DMRG-CASSCF calculation and avoid the convergence difficulties of orbital optimization for large active spaces. The effect of different NO ordering schemes on DMRG-CASCI calculations is also discussed.

cond-mat.str-el↗

arXiv2013

Predicting the thermodynamics by using state-dependent interactions

We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard expressions for pressure and chemical potential applied to this family of coarse-grained models with density-dependent interactions and show that they only provide approximations to the pressure and chemical potential of the underlying original system. These approximations are then carefully compared in two cases: we consider a generic microscopic system in the low-density regime and polymer solutions under good-solvent conditions. Moreover, we show that the state-dependent potentials depend on the ensemble in which they have been derived. Therefore, care must be used in applying canonical state-dependent potentials to predict phase lines, which is typically performed in other ensembles.

cond-mat.stat-mech↗

arXiv2012

Classical nucleation theory from a dynamical approach to nucleation

It is shown that diffusion-limited classical nucleation theory (CNT) can be recovered as a simple limit of the recently proposed dynamical theory of nucleation based on fluctuating hydrodynamics (Lutsko, JCP 136, 034509 (2012)). The same framework is also used to construct a more realistic theory in which clusters have finite interfacial width. When applied to the dilute solution/dense solution transition in globular proteins, it is found that the extension gives corrections to the the nucleation rate even for the case of small supersaturations due to changes in the monomer distribution function and to the excess free energy. It is also found that the monomer attachement/detachment picture breaks down at high supersaturations corresponding to clusters smaller than about 100 molecules. The results also confirm the usual assumption that most important corrections to CNT can be acheived by means of improved estimates of the free energy barrier. The theory also illustrates two topics that have received considerable attention in the recent literature on nucleation: the importance sub-dominant corrections to the capillary model for the free energy and of the correct choice of the reaction coordinate.

physics.chem-ph↗

arXiv2013

Excited-state potential-energy surfaces of metal-adsorbed organic molecules from Linear Expansion Δ-Self-Consistent Field Density-Functional Theory (ΔSCF-DFT)

Accurate and efficient simulation of excited state properties is an important and much aspired cornerstone in the study of adsorbate dynamics on metal surfaces. To this end, the recently proposed linear expansion ΔSelf-Consistent Field (leΔSCF) method by Gavnholt et al. [Phys. Rev. B 78, 075441 (2008)] presents an efficient alternative to time consuming quasi-particle calculations. In this method the standard Kohn-Sham equations of Density-Functional Theory are solved with the constraint of a non-equilibrium occupation in a region of Hilbert-space resembling gas-phase orbitals of the adsorbate. In this work we discuss the applicability of this method for the excited-state dynamics of metal-surface mounted organic adsorbates, specifically in the context of molecular switching. We present necessary advancements to allow for a consistent quality description of excited-state potential-energy surfaces (PESs), and illustrate the concept with the application to Azobenzene adsorbed on Ag(111) and Au(111) surfaces. We find that the explicit inclusion of substrate electronic states modifies the topologies of intra-molecular excited-state PESs of the molecule due to image charge and hybridization effects. While the molecule in gas phase shows a clear energetic separation of resonances that induce isomerization and backreaction, the surface-adsorbed molecule does not. The concomitant possibly simultaneous induction of both processes would lead to a significantly reduced switching efficiency of such a mechanism.

cond-mat.mtrl-sci↗

arXiv2013

Controlling the efficiency of trapping in treelike fractals

Efficiently controlling the trapping process, especially the trapping efficiency, is central in the study of trap problem in complex systems, since it is a fundamental mechanism for diverse other dynamic processes. Thus, it is of theoretical and practical significance to study the control technique for trapping problem. In this paper, we study the trapping problem in a family of proposed directed fractals with a deep trap at a central node. The directed fractals are a generalization of previous undirected fractals by introducing the directed edge weights dominated by a parameter. We characterize all the eigenvalues and their degeneracies for an associated matrix governing the trapping process. The eigenvalues are provided through an exact recursive relation deduced from the self-similar structure of the fractals. We also obtain the expressions for the smallest eigenvalue and the mean first-passage time (MFPT) as a measure of trapping efficiency, which is the expected time for the walker to first visit the trap. The MFPT is evaluated according to the proved fact that it is approximately equal to reciprocal of the smallest eigenvalue. We show that the MFPT is controlled by the weight parameter, by modifying which, the MFPT can scale superlinealy, linearly, or sublinearly with the system size. Thus, this work paves a way to delicately controlling the trapping process in the fractals.

cond-mat.stat-mech↗

arXiv2013

The distinguishable cluster approximation

A new method that accurately describes strongly correlated states and captures dynamical correlation is presented. It is derived as a modification of coupled-cluster theory with single and double excitations (CCSD) through consideration of particle distinguishability between dissociated fragments, whilst retaining the key desirable properties of particle-hole symmetry, size extensivity, invariance to rotations within the occupied and virtual spaces, and exactness for two-electron subsystems. The resulting method called the distinguishable cluster approximation, smoothly dissociates difficult cases such as the nitrogen molecule, with the modest N^6 computational cost of CCSD. Even for molecules near their equilibrium geometries, the new model outperforms CCSD. It also accurately describes the massively correlated states encountered when dissociating hydrogen lattices, a proxy for the metal-insulator transition, and the fully dissociated system is treated exactly.

physics.chem-ph↗

arXiv2013

Entanglement dynamics of a two-qubit system coupled individually to Ohmic baths

Developed originally for the Holstein polaron, the Davydov D1 ansatz is an efficient, yet extremely accurate trial state for time-dependent variation of the spin-boson model [J. Chem. Phys. 138, 084111 (2013)]. In this work, the Dirac-Frenkel time-dependent variational procedure utilizing the Davydov D1 ansatz is implemented to study entanglement dynamics of two qubits under the influence of two independent baths. The Ohmic spectral density is used without the Born-Markov approximation or the rotating-wave approximation. In the strong coupling regime finite-time disentanglement is always found to exist, while at the intermediate coupling regime, the entanglement dynamics calculated by Davydov D1 ansatz displays oscillatory behavior in addition to entanglement disappearance and revival.

quant-ph↗

arXiv2013

EUV induced defects on few-layer graphene

We use Raman spectroscopy to show that exposing few-layer graphene to extreme ultraviolet (EUV, 13.5 nm) radiation, i.e. relatively low photon energy, results in an increasing density of defects. Furthermore, exposure to EUV radiation in a H2 background increases the graphene dosage sensitivity, due to reactions caused by the EUV induced hydrogen plasma. X-ray photoelectron spectroscopy (XPS) results show that the sp2 bonded carbon fraction decreases while the sp3 bonded carbon and oxide fraction increases with exposure dose. Our experimental results confirm that even in reducing environment oxidation is still one of the main source of inducing defects.

cond-mat.mtrl-sci↗

arXiv2013

Dynamics of a two-level system under the simultaneous influence of a spin bath and a boson bath

We study dynamics of a two-level system coupled simultaneously to a pair of dissimilar reservoirs, namely, a spin bath and a boson bath, which are connected via finite interbath coupling. It is found that the steady-state energy transfer in the two-level system increases with its coupling to the spin bath while optimal transfer occurs at intermediate coupling in the transient process. If the two-level system is strongly coupled to the spin bath, the population transfer is unidirectional barring minor population oscillations of minute amplitudes. If the spin bath is viewed as an atomic ensemble, robust generation of macroscopic superposition states exists against parameter variations of the two-level system and the boson bath.

quant-ph↗

arXiv2013

Redox reactions with empirical potentials: Atomistic battery discharge simulations

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

cond-mat.mtrl-sci↗

arXiv2013

Large Scale Molecular Dynamics Simulations of Homogeneous Nucleation

We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 μs (56 million time-steps). They cover a wide range of supersaturation ratios, S=1.55 to 10^4, and temperatures from kT = 0.3 to 1.0 ε (where ε is the depth of the LJ potential, and k the Boltzmann constant). We have resolved nucleation rates as low as 10^{17} cm^{-3} s^{-1} (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem. Phys. 93, 1273 (1990)] underestimates the nucleation rates by up to 9 orders of magnitudes at low temperatures, and at kT = 1.0 ε it overestimates them by up to 10^5. The predictions from a semi-phenomenological model by Laaksonen et al. [Phys. Rev. E 49, 5517 (1994)] are much closer to our MD results, but still differ by factors of up to 104 in some cases. At low temperatures, the classical theory predicts critical clusters sizes, which match the simulation results (using the first nucleation theorem) quite well, while the semi-phenomenological model slightly underestimates them. At kT = 1.0 ε the critical sizes from both models are clearly too small. (abridged)

physics.chem-ph↗