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Interpreting high-dimensional data from molecular dynamics simulations is a persistent challenge. In this paper, we show that for a small peptide, deca-alanine, metastable states can be identified through a neural net based on structural information alone. While processing molecular dynamics data, dimensionality reduction is a necessary step that projects high-dimensional data onto a low-dimensional representation that, ideally, captures the conformational changes in the underlying data. Conventional methods make use of the temporal information contained in trajectories generated through integrating the equations of motion, which forgoes more efficient sampling schemes. We demonstrate that EncoderMap, an autoencoder architecture with an additional distance metric, can find a suitable low-dimensional representation to identify long-lived molecular conformations using exclusively structural information. For deca-alanine, which exhibits several helix-forming pathways, we show that this approach allows us to combine simulations with different biasing forces and yields representations comparable in quality to other established methods. Our results contribute to computational strategies for the rapid automatic exploration of the configuration space of peptides and proteins. [ABSTRACT FROM AUTHOR]

In this paper, we present an extended dissipaton equation of motion for studying the dynamics of electronic impurity systems. Compared with the original theoretical formalism, the quadratic couplings are introduced into the Hamiltonian accounting for the interaction between the impurity and its surrounding environment. By exploiting the quadratic fermionic dissipaton algebra, the proposed extended dissipaton equation of motion offers a powerful tool for studying the dynamical behaviors of electronic impurity systems, particularly in situations where nonequilibrium and strongly correlated effects play significant roles. Numerical demonstrations are carried out to investigate the temperature dependence of the Kondo resonance in the Kondo impurity model. [ABSTRACT FROM AUTHOR]

In the previous paper [C. W. Kim and I. Franco, J. Chem. Phys. 160, 214111-1–214111-13 (2024)], we developed a theory called MQME-D, which allows us to decompose the overall energy dissipation process in open quantum system dynamics into contributions by individual components of the bath when the subsystem dynamics is governed by a Markovian quantum master equation (MQME). Here, we contrast the predictions of MQME-D against the numerically exact results obtained by combining hierarchical equations of motion (HEOM) with a recently reported protocol for monitoring the statistics of the bath. Overall, MQME-D accurately captures the contributions of specific bath components to the overall dissipation while greatly reducing the computational cost compared to exact computations using HEOM. The computations show that MQME-D exhibits errors originating from its inherent Markov approximation. We demonstrate that its accuracy can be significantly increased by incorporating non-Markovianity by exploiting time scale separations (TSS) in different components of the bath. Our work demonstrates that MQME-D combined with TSS can be reliably used to understand how energy is dissipated in realistic open quantum system dynamics. [ABSTRACT FROM AUTHOR]

In this paper, we present a comprehensive account of quantum dissipation theories with the quadratic environment couplings. The theoretical development includes the Brownian solvation mode embedded hierarchical quantum master equations, a core-system hierarchy construction that verifies the extended dissipaton equation of motion (DEOM) formalism [R. X. Xu et al., J. Chem. Phys. 148, 114103 (2018)]. Developed are also the quadratic imaginary-time DEOM for equilibrium and the λ(t)-DEOM for nonequilibrium thermodynamics problems. Both the celebrated Jarzynski equality and Crooks relation are accurately reproduced, which, in turn, confirms the rigorousness of the extended DEOM theories. While the extended DEOM is more numerically efficient, the core-system hierarchy quantum master equation is favorable for "visualizing" the correlated solvation dynamics. [ABSTRACT FROM AUTHOR]

Quantum mechanics has a deterministic Schrödinger equation for the wave function. The Göttingen–Copenhagen statistical interpretation is based on the Born Rule that interprets the wave function as a "probability amplitude." A precept of this interpretation is the lack of determinism in quantum mechanics. The Bohm interpretation is that the wave function is a source of a field experienced by the electrons, thereby attributing determinism to quantum theory. In this paper, we present a new perspective on such determinism. The ideas are based on the equations of motion or "Quantal Newtonian" Laws obeyed by each electron. These Laws, derived from the temporal and stationary-state Schrödinger equation, are interpreted in terms of "classical" fields whose sources are quantal expectations of Hermitian operators taken with respect to the wave function. According to the Second Law, each electron experiences an external field—the quantal Coulomb-Lorentz law. It also experiences an internal field representative of properties of the system: correlations due to Coulomb repulsion and Pauli principle; the density; kinetic effects; and an internal magnetic field component. There is a response field. The First Law states that the sum of the external and internal fields experienced by each electron vanishes. These fields are akin to those of classical physics: They pervade all space; their structure is descriptive of the quantum system; the energy of the system is stored in these fields. It is in the classical behavior of these fields, which arise from quantal sources that one may then speak of determinism in quantum mechanics. [ABSTRACT FROM AUTHOR]

The formalism of the generalized quantum master equation (GQME) is an effective tool to simultaneously increase the accuracy and the efficiency of quasiclassical trajectory methods in the simulation of nonadiabatic quantum dynamics. The GQME expresses correlation functions in terms of a non-Markovian equation of motion, involving memory kernels that are typically fast-decaying and can therefore be computed by short-time quasiclassical trajectories. In this paper, we study the approximate solution of the GQME, obtained by calculating the kernels with two methods: Ehrenfest mean-field theory and spin-mapping. We test the approaches on a range of spin–boson models with increasing energy bias between the two electronic levels and place a particular focus on the long-time limits of the populations. We find that the accuracy of the predictions of the GQME depends strongly on the specific technique used to calculate the kernels. In particular, spin-mapping outperforms Ehrenfest for all the systems studied. The problem of unphysical negative electronic populations affecting spin-mapping is resolved by coupling the method with the master equation. Conversely, Ehrenfest in conjunction with the GQME can predict negative populations, despite the fact that the populations calculated from direct dynamics are positive definite. [ABSTRACT FROM AUTHOR]

In this paper, we present a quantum stochastic model for spectroscopic lineshapes in the presence of a co-evolving and non-stationary background population of excitations. Starting from a field theory description for interacting bosonic excitons, we derive a reduced model whereby optical excitons are coupled to an incoherent background via scattering as mediated by their screened Coulomb coupling. The Heisenberg equations of motion for the optical excitons are then driven by an auxiliary stochastic population variable, which we take to be the solution of an Ornstein–Uhlenbeck process. Itô's lemma then allows us to easily construct and evaluate correlation functions and response functions. Focusing on the linear response, we compare our model to the classic Anderson–Kubo model. While similar in motivation, there are differences in the predicted lineshapes, notably in terms of asymmetry, and variation with the increasing background population. [ABSTRACT FROM AUTHOR]

Quantum master equations (QMEs) provide a general framework for describing electronic dynamics within a complex molecular system. Off-diagonal QMEs (OD-QMEs) correspond to a family of QMEs that describe the electronic dynamics in the interaction picture based on treating the off-diagonal coupling terms between electronic states as a small perturbation within the framework of second-order perturbation theory. The fact that OD-QMEs are given in terms of the interaction picture makes it non-trivial to obtain Schrödinger picture electronic coherences from them. A key experimental quantity that relies on the ability to obtain accurate Schrödinger picture electronic coherences is the absorption spectrum. In this paper, we propose using a recently introduced procedure for extracting Schrödinger picture electronic coherences from interaction picture inputs to calculate electronic absorption spectra from the electronic dynamics generated by OD-QMEs. The accuracy of the absorption spectra obtained this way is studied in the context of a biexciton benchmark model, by comparing spectra calculated based on time-local and time-nonlocal OD-QMEs to spectra calculated based on a Redfield-type QME and the non-perturbative and quantum-mechanically exact hierarchical equations of motion method. [ABSTRACT FROM AUTHOR]

Within the well-established optical response function formalism, a new strategy with the central idea of employing the forward-backward stochastic Schrödinger equations in a segmented way to accurately obtain the two-dimensional (2D) electronic spectrum is presented in this paper. Based on the simple excitonically coupled dimer model system, the validity and efficiency of the proposed schemes are demonstrated in detail, along with the comparison against the deterministic hierarchy equations of motion and perturbative second-order time-convolutionless quantum master equations. In addition, an important insight is provided in this paper that the characteristic frequency of the overdamped environment is an extremely crucial factor to regulate the lifetimes of the oscillating signals in 2D electronic spectra and of quantum coherence features of system dynamics. It is worth noting that the proposed scheme benefiting from its stochastic nature and wavefunction framework and many other advantages of substantially reducing the numerical cost has a great potential to systematically investigate various quantum effects observed in realistic large-scale natural and artificial photosynthetic systems. [ABSTRACT FROM AUTHOR]

Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to study complex organization and transport phenomena beyond the molecular scale. Even though these models are designed based on results from physics at the meso- and macroscale, such as fluid mechanics and statistical field theory, the underlying microscopic foundation of these models is not as well defined. This paper aims to build such a systematic connection using bottom-up coarse-graining methods. From the recently developed dynamic coarse-graining scheme, we introduce a statistical inference framework of explicit many-body conservative interaction that quantitatively recapitulates the mesoscopic structure of the underlying fluid. To further consider the dissipative and fluctuation forces, we design a novel algorithm that parameterizes these forces. By utilizing this algorithm, we derive pairwise decomposable friction kernels under both non-Markovian and Markovian limits where both short- and long-time features of the coarse-grained dynamics are reproduced. Finally, through these new developments, the many-body dissipative particle dynamics type of equations of motion are successfully derived. The methodologies developed in this work thus open a new avenue for the construction of direct bottom-up mesoscopic models that naturally bridge the meso- and macroscopic physics. [ABSTRACT FROM AUTHOR]

X-ray photon absorption leads to the creation of highly excited species, which often decay through the Auger process. The theoretical treatment of Auger decay is challenging because of the resonance nature of the initial core-excited or core-ionized states and the continuous nature of the ejected electron. In Paper I [W. Skomorowski and A. I. Krylov, J. Chem. Phys. 154, 084124 (2021)], we have introduced a theoretical framework for computing Auger rates based on the Feshbach–Fano approach and the equation-of-motion coupled-cluster ansätze augmented with core–valence separation. The outgoing Auger electron is described with a continuum orbital. We considered two approximate descriptions—a plane wave and a Coulomb wave with an effective charge. Here, we use the developed methodology to calculate Auger transition rates in core-ionized and core-excited benchmark systems (Ne, H2O, CH4, and CO2). Comparison with the available experimental spectra shows that the proposed computational scheme provides reliable ab initio predictions of the Auger spectra. The reliability, cost efficiency, and robust computational setup of this methodology offer advantages in applications to a large variety of systems. [ABSTRACT FROM AUTHOR]

The hierarchical equations of motion (HEOMs) have developed into an important tool in simulating quantum dynamics in condensed phases. Yet, it has recently been found that the HEOM may become numerically unstable in simulations using discrete harmonic oscillator modes [I. S. Dunn, et al., J. Chem. Phys. 150, 184109 (2019)]. In this paper, a new set of equations of motion are obtained based on the equivalence between the HEOM for discrete harmonic oscillator modes and the mixed quantum-classical Liouville equation. The new set of equations can thus be regarded as the expansion of the same phase space partial differential equation using different basis sets. It is shown that they have similar structures as the original HEOM but are free from the problem of numerical instability. The new set of equations are also incorporated into the matrix product state method, where it is found that the trace of the reduced density operator is not well conserved during the propagation. A modified time-dependent variational principle is then proposed to achieve better trace conservation. [ABSTRACT FROM AUTHOR]

We present a new partially linearized mapping-based approach for approximating real-time quantum correlation functions in condensed-phase nonadiabatic systems, called the spin partially linearized density matrix (spin-PLDM) approach. Within a classical trajectory picture, partially linearized methods treat the electronic dynamics along forward and backward paths separately by explicitly evolving two sets of mapping variables. Unlike previously derived partially linearized methods based on the Meyer–Miller–Stock–Thoss mapping, spin-PLDM uses the Stratonovich–Weyl transform to describe the electronic dynamics for each path within the spin-mapping space; this automatically restricts the Cartesian mapping variables to lie on a hypersphere and means that the classical equations of motion can no longer propagate the mapping variables out of the physical subspace. The presence of a rigorously derived zero-point energy parameter also distinguishes spin-PLDM from other partially linearized approaches. These new features appear to give the method superior accuracy for computing dynamical observables of interest when compared with other methods within the same class. The superior accuracy of spin-PLDM is demonstrated in this paper through application of the method to a wide range of spin-boson models as well as to the Fenna–Matthews–Olsen complex. [ABSTRACT FROM AUTHOR]

We show two more approaches for generating trajectory-based dynamics in the phase space formulation of quantum mechanics: 'equilibrium continuity dynamics' (ECD) in the spirit of the phase space continuity equation in classical mechanics, and 'equilibrium Hamiltonian dynamics' (EHD) in the spirit of the Hamilton equations of motion in classical mechanics. Both ECD and EHD can recover exact thermal correlation functions (of even nonlinear operators, i.e., nonlinear functions of position or momentum operators) in the classical, high temperature, and harmonic limits. Both ECD and EHD conserve the quasi-probability within the infinitesimal volume dxtdpt around the phase point (xt, pt) along the trajectory. Numerical tests of both approaches in the Wigner phase space have been made for two strongly anharmonic model problems and a double well system, for each potential auto-correlation functions of both linear and nonlinear operators have been calculated. The results suggest EHD and ECD are two additional potential useful approaches for describing quantum effects for complex systems in condense phase. [ABSTRACT FROM AUTHOR]

The main quantity that controls excitation relaxation and transport in molecular systems is the environment-induced fluctuation correlation function. Commonly used models assume the exponentially decaying correlation function, characterized by a given characteristic time, which allows us to define the Markovian conditions and, hence, allows us to use rate equations for excitation dynamics. A long memory fractional correlation function is studied in this paper as an alternative model. Such a function has an infinite characteristic decay time, and thus, system decay to equilibrium becomes poorly defined. Consequently, it becomes impossible to define the Markovian regime. By assuming the weak system–bath coupling regime, we apply the non-Markovian equations of motion to describe the equilibration process in an excitonic molecular aggregate. The long memory model causes a weaker decay of coherent components in excitonic system relaxation dynamics. Nevertheless, the short time dynamics, which is important in optical spectroscopy, depends on the short time interval of the fluctuation correlation function. Excitation relaxation in this window appears to be well described by non-Markovian approaches. [ABSTRACT FROM AUTHOR]

This paper provides a detailed account of the numerical implementation of the stochastic equation of motion (SEOM) method for the dissipative dynamics of fermionic open quantum systems. To enable direct stochastic calculations, a minimal auxiliary space (MAS) mapping scheme is adopted, with which the time-dependent Grassmann fields are represented by c-number noises and a set of pseudo-operators. We elaborate on the construction of the system operators and pseudo-operators involved in the MAS-SEOM, along with the analytic expression for the particle current. The MAS-SEOM is applied to study the relaxation and voltage-driven dynamics of quantum impurity systems described by the single-level Anderson impurity model, and the numerical results are benchmarked against those of the highly accurate hierarchical equations of motion method. The advantages and limitations of the present MAS-SEOM approach are discussed extensively. [ABSTRACT FROM AUTHOR]

This paper presents core excitation spectra from coupled-cluster (CC) theory obtained from both a time-independent and a new time-dependent formalism. The conventional time-independent CC formulation for excited states is the equation-of-motion (EOM-CC) method whose eigenvalues and eigenvectors describe the core excited states. An alternative computational procedure is offered by a time-dependent CC description. In that case, the dipole transition operator is expressed in the CC effective Hamiltonian form and propagated with respect to time. The absorption spectrum is obtained from the CC dipole autocorrelation function via a Fourier transformation. Comparisons are made among the time-dependent results obtained from second-order perturbation theory, to coupled cluster doubles and their linearized forms (CCD and LCCD), to CC singles and doubles (CCSD) and the linearized form (LCCSD). In the time-independent case, considerations of triples (EOM-CCSDT) and quadruples (EOM-CCSDTQ) are used to approach sub-electron volt accuracy. A particular target is the allyl radical, as an example of an open-shell molecule. As the results have to ultimately be the same, the two procedures offer a complementary approach toward analyzing experimental results. [ABSTRACT FROM AUTHOR]

Emerging photovoltaic technologies continue to march forward with power conversion efficiencies of lead halide perovskite solar cells (PSCs) nearing 26%, perovskite-Si tandems now exceeding the single junction detailed balance limit of 33%, and organic solar cells (OSCs) showing efficiencies nearing 20%. Yang and Yang[16] use transient absorption spectroscopy to investigate the recombination dynamics of photocarriers in a multilayer indium selenide nanofilm, showing that exciton-exciton annihilation is inefficient in multilayers due to weaker Coulomb interactions. [Extracted from the article]

In the present paper, the chain of spheres exchange (COSX) approximation is applied to the highest scaling terms in the equation of motion (EOM) coupled cluster equations with single and double excitations, in particular, the terms involving integrals with four virtual labels. It is found that even the acceleration of this single term yields significant computational gains without compromising the desired accuracy of the method. For an excitation energy calculation on a cluster of five water molecules using 585 basis functions, the four virtual term is 9.4 times faster using COSX with a loose grid than using the canonical implementation, which yields a 2.6 fold acceleration for the whole of the EOM calculation. For electron attachment calculations, the four virtual term is 15 times and the total EOM calculation is 10 times faster than the canonical calculation for the same system. The accuracy of the new method was tested using Thiel's test set for excited states using the same settings and the maximum absolute deviation over the whole test set was found to be 12.945 cm−1 (59 μHartree) for excitation energies and 6.799 cm−1 (31 μHartree) for electron attachments. Using MP2 amplitudes for the ground state in combination with the parallel evaluation of the full EOM equations in the manner discussed in this paper enabled us to perform calculations for large systems. Electron affinity values for the two lowest states of a Zn protoporphyrine model compound (224 correlated electrons and 1120 basis functions) were obtained in 3 days 19 h using 4 cores of a Xeon E5-2670 processor allocating 10 GB memory per core. Calculating the lowest two excitation energies for trans-retinal (114 correlated electrons and 539 basis functions) took 1 day 21 h using eight cores of the same processor and identical memory allocation per core. [ABSTRACT FROM AUTHOR]

Previously, we introduced two versions of the Multiconfigurational Ehrenfest (MCE) approach to high dimensional quantum dynamics. It has been shown that the first version, MCEv1, converges well to the existing benchmarks for high dimensional model systems. At the same time, it was found that the second version, MCEv2, had more difficulty converging in some regimes. As MCEv2 is particularly suited for direct dynamics, it is important to facilitate its convergence. This paper investigates an efficient method of basis set sampling, called Quantum Superposition Sampling (QSS), which dramatically improves the performance of the MCEv2 approach. QSS is tested on the spin-boson model, often used for modeling of open quantum systems. It is also shown that the quantum subsystem in the spin-boson model can be conveniently treated with the help of two level system coherent states. Generalized coherent states, which combine two level system coherent states for the description of the system and Gaussian coherent states for description of the bath, are introduced. Various forms of quantum equations of motion in the basis of generalized coherent states can be developed by analogy with known quantum dynamics equations in the basis of Gaussian coherent states; in particular, the multiconfigurational Ehrenfest method becomes a version of coupled generalized coherent states, and QSS can then be viewed as a generalization of a sampling method known for the existing coupled coherent states method which uses Gaussian coherent states. [ABSTRACT FROM AUTHOR]

Auger decay is an efficient ultrafast relaxation process of core-shell or inner-shell excited atom or molecule. Generally, it occurs in femto-second or even atto-second time domain. Direct measurement of lifetimes of Auger process of single ionized and double ionized inner-shell state of an atom or molecule is an extremely difficult task. In this paper, we have applied the highly correlated complex absorbing potential-equation-of-motion coupled cluster (CAP-EOMCC) approach which is a combination of CAP and EOMCC approach to calculate the lifetime of the states arising from 2p inner-shell ionization of an Ar atom and 3d inner-shell ionization of Kr atom. We have also calculated the lifetime of Ar2+(2p-13p-1)¹D, Ar2+(2p-13p-1)¹S, and Ar2+(2p-13s-1) 1P double ionized states. The predicted results are compared with the other theoretical results as well as experimental results available in the literature. [ABSTRACT FROM AUTHOR]

We report in this paper an implementation of a 4-component relativistic Hamiltonian based Equation-of-Motion Coupled-Cluster with singles and doubles (EOM-CCSD) theory for the calculation of ionization potential, electron affinity, and excitation energy. In this work, we utilize the previously developed double group symmetry-based generalized tensor contraction scheme and also extend it in order to carry out tensor contractions involving non-totally symmetric and odd-ranked tensors. Several approximated spin-free and two-component Hamiltonians can also be accessed in this implementation. We have applied this method to the halogen monoxide (XO, X = Cl, Br, I, At, Ts) species, in order to assess the quality of a few other recent EOM-CCSD implementations, where spin-orbit coupling contribution has been approximated in different degrees. Besides, we have also studied various excited states of CH2IBr, CH2I2, and I 3 − (as well as single electron attachment and detachment electronic states of the same species) where comparison has been made with a closely related multi-reference coupled-cluster method, namely, Intermediate Hamiltonian Fock Space Coupled-Cluster singles and doubles theory. [ABSTRACT FROM AUTHOR]

In the present paper, a generalized hybrid Monte Carlo method to generate the multicanonical ensemble has been developed, which is a generalization of the multicanonical hybrid Monte Carlo (HMC) method by Hansmann and co-workers [Chem. Phys. Lett. 259, 321 (1996)]. The generalized hybrid Monte Carlo (GHMC) method is an equations-of-motion guided Monte Carlo combined with partial momentum refreshment. We successfully applied our multicanonical GHMC to dense Lennard-Jones fluids and a coarse grained protein model. It is found that good computational efficiency can be gained in the case of the acceptance ratio around 60% for the models examined. While a large number of molecular dynamics (MD) steps in a single GHMC cycle is needed to yield good computational efficiency at a large mixing ratio of momenta with thermal noise vectors, corresponding to the original multicanonical HMC method, a small number of MD steps are enough to achieve good efficiency at a small mixing ratio. This property is useful to develop a composite algorithm combining the present GHMC method with other Monte Carlo moves. [ABSTRACT FROM AUTHOR]

We use the "generalized hierarchical equation of motion" proposed in Paper I [C.-Y. Hsieh and J. Cao, J. Chem. Phys. 148, 014103 (2018)] to study decoherence in a system coupled to a spin bath. The present methodology allows a systematic incorporation of higher-order anharmonic effects of the bath in dynamical calculations. We investigate the leading order corrections to the linear response approximations for spin bath models. Two kinds of spin-based environments are considered: (1) a bath of spins discretized from a continuous spectral density and (2) a bath of localized nuclear or electron spins. The main difference resides with how the bath frequency and the system-bath coupling parameters are distributed in an environment. When discretized from a continuous spectral density, the system-bath coupling typically scales as ~1/ √NB where NB is the number of bath spins. This scaling suppresses the non-Gaussian characteristics of the spin bath and justifies the linear response approximations in the thermodynamic limit. For the nuclear/electron spin bath models, system-bath couplings are directly deduced from spin-spin interactions and do not necessarily obey the 1/ √NB scaling. It is not always possible to justify the linear response approximations in this case. Furthermore, if the spin-spin Hamiltonian is highly symmetrical, there exist additional constraints that generate highly non-Markovian and persistent dynamics that is beyond the linear response treatments. [ABSTRACT FROM AUTHOR]

We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion which simultaneously describe the molecular and quantum transport dynamics, and obey the fluctuation/dissipation relationship. We also introduce an algorithm which yields the most probable molecular and quantum transport pathways in rare, thermally activated reactions. In the second part of the paper, we apply this formalism to simulate the propagation of a quantum charge during the collapse of a polymer from an initial stretched conformation to a final globular state. We find that the charge dynamics is quenched when the chain reaches a molten globule state. Using random matrix theory we show that this transition is due to an increase of quantum localization driven by dynamical disorder. We argue that collapsing conducting polymers may represent a physical realization of quantum small-world networks with dynamical rewiring probability. [ABSTRACT FROM AUTHOR]

This paper presents a new approach to propagating the density matrix based on a time stepping procedure arising from a Trotter factorization and combining the forward and backward incremental propagators. The sums over intermediate states of the discrete quantum subsystem are implemented by a Monte Carlo surface hopping-like procedure, while the integrals over the continuous variables are performed using a linearization in the difference between the forward and backward paths of these variables leading to classical-like equations of motion with forces determined by the quantum subsystem states. The approach is tested on several models and numerical convergence is explored. [ABSTRACT FROM AUTHOR]

In this paper (Paper II), the isokinetic dynamics scheme described in Paper I is combined with the plane-wave based Car-Parrinello (CP) ab initio molecular dynamics (MD) method [R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)] to enable the efficient study of chemical reactions and metallic systems. The Car-Parrinello approach employs "on the fly" electronic structure calculations as a means of generating accurate internuclear forces for use in a molecular dynamics simulation. This is accomplished by the introduction of an extended Lagrangian that contains the electronic orbitals as fictitious dynamical variables (often expressed directly in terms of the expansion coefficients of the orbitals in a particular basis set). Thus, rather than quench the expansion coefficients to obtain the ground state energy and nuclear forces at every time step, the orbitals are "propagated" under conditions that allow them to fluctuate rapidly around their global minimum and, hence, generate an accurate approximation to the nuclear forces as the simulation proceeds. Indeed, the CP technique requires the dynamics of the orbitals to be both fast compared to the nuclear degrees of freedom while keeping the fictitious kinetic energy that allows them to be propagated dynamically as small as possible. While these conditions can be easy to achieve in many types of systems, in metals and highly exothermic chemical reactions difficulties arise. (Note, the CP dynamics of metals is incorrect because the nuclear motion does not occur on the ground state electronic surface but it can, nonetheless, provide useful information.) In order to alleviate these difficulties the isokinetic methods of Paper I are applied to derive isokinetic CP equations of motion. The efficacy of the new isokinetic CPMD method is demonstrated on model and realistic systems. The latter include, metallic systems, liquid aluminum, a small silicon sample, the 2 × 1 reconstruction of the silicon 100... [ABSTRACT FROM AUTHOR]

The Meyer-Miller (MM) classical vibronic (electronic + nuclear) Hamiltonian for electronically nonadiabatic dynamics--as used, for example, with the recently developed symmetrical quasiclassical (SQC) windowing model--can be written in either a diabatic or an adiabatic representation of the electronic degrees of freedom, the two being a canonical transformation of each other, thus giving the same dynamics. Although most recent applications of this SQC/MM approach have been carried out in the diabatic representation--because most of the benchmark model problems that have exact quantum results available for comparison are typically defined in a diabatic representation--it will typically be much more convenient to work in the adiabatic representation, e.g., when using Born-Oppenheimer potential energy surfaces (PESs) and derivative couplings that come from electronic structure calculations. The canonical equations of motion (EOMs) (i.e., Hamilton's equations) that come from the adiabatic MM Hamiltonian, however, in addition to the common first-derivative couplings, also involve second-derivative non-adiabatic coupling terms (as does the quantum Schrödinger equation), and the latter are considerably more difficult to calculate. This paper thus revisits the adiabatic version of the MM Hamiltonian and describes a modification of the classical adiabatic EOMs that are entirely equivalent to Hamilton's equations but that do not involve the second-derivative couplings. The second-derivative coupling terms have not been neglected; they simply do not appear in these modified adiabatic EOMs. This means that SQC/MM calculations can be carried out in the adiabatic representation, without approximation, needing only the PESs and the first-derivative coupling elements. The results of example SQC/MM calculations are presented, which illustrate this point, and also the fact that simply neglecting the second-derivative couplings in Hamilton's equations (and presumably also in the Schrödinger equation) can cause very significant errors. [ABSTRACT FROM AUTHOR]

Simplifications or modifications of coupled cluster methods such as the CCSD (coupled cluster singles and doubles) model often perform better than the original method in providing the total energy, equilibrium geometries, and harmonic vibration frequencies for the ground state. Three such methods that have been recently proposed include 2CC, parameterized CCSD generalizations, and distinguishable cluster singles and doubles (DCSD) approach. In this paper, we lay the theoretical foundation needed to treat excited states via the equation of motion (EOM) approach using these ground state CC methods. As these ground state approximations to CCSD share its property of being exact for two-electron systems, so will their excited state extensions. These methods are tested for two complementary benchmark sets of excited states for a wide range of organic molecules with focus on singlet and triplet excited states of both valence and Rydberg nature. We also test these methods for doubly excited states, taking CH+ as an example to test their performance at equilibrium and stretched bond geometries. Finally, we assess if any of these methods perform consistently better than EOM CCSD. [ABSTRACT FROM AUTHOR]

We present a coarse-grained particle-based simulation technique for modeling flow of complex soft matter fluids such as polymer solutions in the presence of solid interfaces. In our coarse-grained description of the system, we track the motion of polymer molecules using their centers-of-mass as our coarse-grain co-ordinates and also keep track of another set of variables that describe the background flow field. The coarse-grain motion is thus influenced not only by the interactions based on appropriate potentials used to model the particular polymer system of interest and the random kicks associated with thermal fluctuations, but also by the motion of the background fluid. In order to couple the motion of the coarse-grain co-ordinates with the background fluid motion, we use a Galilean invariant, first order Brownian dynamics algorithm developed by Padding and Briels [J. Chem. Phys. 141, 244108 (2014)], which on the one hand draws inspiration from smoothed particle hydrodynamics in a way that the motion of the background fluid is efficiently calculated based on a discretization of the Navier-Stokes equation at the positions of the coarse-grain coordinates where it is actually needed, but also differs from it because of the inclusion of thermal fluctuations by having momentumconserving pairwise stochastic updates. In this paper, we make a few modifications to this algorithm and introduce a new parameter, viz., a friction coefficient associated with the background fluid, and analyze the relationship of the model parameters with the dynamic properties of the system. We also test this algorithm for flow in the presence of solid interfaces to show that appropriate boundary conditions can be imposed at solid-fluid interfaces by using artificial particles embedded in the solid walls which offer friction to the real fluid particles in the vicinity of the wall. We have tested our method using a model system of a star polymer solution at the overlap concentration. [ABSTRACT FROM AUTHOR]

Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown that the structures along the RelaxPath trajectories remain protein-like. Open source versions of the two programs MinActionPath and RelaxPath are available by request. [ABSTRACT FROM AUTHOR]

Accurate methods for excited, ionized, and electron-attached states are critical to the study of many chemical species such as reactive intermediates, radicals, and ionized systems. The equation-of-motion coupled cluster singles, doubles, and triples (EOM-CCSDT) family of methods is very accurate (roughly similar in accuracy as for CCSDT calculations of the ground state), but the computational cost scales iteratively as the eighth power of the system size. Many approximations already exist, although most either correct only the excited state or require an iterative O(n7) procedure which can also be prohibitively expensive. In this paper, new methods, termed EOM-CCSD(T)(a) and EOM-CCSD(T)(a)*, are proposed which correct both the ground and excited states based on a shared effective Hamiltonian, and the latter of which includes only non-iterative corrections to both the CCSD and EOM-CCSD energies. These methods are found to significantly improve the description of excited and ionized potential energy surfaces, equilibrium geometries, and harmonic frequencies; the accuracy is very close to that of full EOM-CCSDT. [ABSTRACT FROM AUTHOR]

The issue of efficient hierarchy truncation is related to many approximate theories. In this paper, we revisit this issue from both the numerical efficiency and quantum mechanics prescription invariance aspects. The latter requires that the truncation approximation made in Schrödinger picture, such as the quantum master equations and their self-consistent-Born-approximation improvements, should be transferable to their Heisenberg-picture correspondences, without further approximations. We address this issue with the dissipaton equation of motion (DEOM), which is a unique theory for the dynamics of not only reduced systems but also hybrid bath environments. We also highlight the DEOM theory is not only about how its dynamical variables evolve in time, but also the underlying dissipaton algebra. We demonstrate this unique feature of DEOM with model systems and report some intriguing nonlinear Fano interferences characteristics that are experimentally measurable. [ABSTRACT FROM AUTHOR]

The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature. [ABSTRACT FROM AUTHOR]

This paper presents the first application of the multireference equation of motion coupled-cluster (MR-EOMCC) approach to the calculation and characterization of excitation energies of transition metal complexes. The calculated MR-EOM excitation energies are compared with experimental UV/Vis. band maxima, Brueckner based similarity transformed equation of motion (STEOM) calculations and Brueckner based equation of motion coupled cluster (EOM-CCSD(T)) calculations, as well as results calculated with other methods from the literature. The agreement of the excitation energies with experiment is found to be reasonable, and suitable rationalization is given for the discrepancies. An orbital selection scheme is introduced, which can be employed to extend the applicability of the MR-EOMCC methodology to considerably larger systems. [ABSTRACT FROM AUTHOR]

Electronically excited atom or molecule in an environment can relax via transferring its excess energy to the neighboring atoms or molecules. The process is called Interatomic or Intermolecular coulombic decay (ICD). The ICD is a fast decay process in environment. Generally, the ICD mechanism predominates in weakly bound clusters. In this paper, we have applied the complex absorbing potential approach/equation-of-motion coupled cluster (CAP/EOMCCSD) method which is a combination of CAP and EOMCC approach to study the lifetime of ICD at various geometries of the molecules. We have applied this method to calculate the lifetime of ICD in Ne-X; X = Ne, Mg, Ar, systems. We compare our results with other theoretical and experimental results available in literature. [ABSTRACT FROM AUTHOR]

The objective of the present paper is to show the existence of motion coordination among a bundle of trajectories crossing a saddle point region in the forward direction. For zero total angular momentum, no matter how complicated the anharmonic part of the potential energy function, classical dynamics in the vicinity of a transition state is constrained by symmetry properties. Trajectories that all cross the plane R = R* at time t = 0 (where R* denotes the position of the saddle point) with the same positive translational momentum PR* can be partitioned into two sets, denoted "gerade" and "ungerade," which coordinate their motions. Both sets have very close average equations of motion. This coordination improves tremendously rapidly as the number of degrees of freedom increases. This property can be traced back to the existence of time-dependent constants of the motion. [ABSTRACT FROM AUTHOR]

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. [ABSTRACT FROM AUTHOR]

The hierarchical equations of motion (HEOM) method has recently been widely applied to many problems of quantum dynamics in condensed phase. It is now well known that the auxiliary density operators (ADOs) in the HEOM formalism contain system-bath correlations that are important in calculating various dynamical properties, yet quantitative relations to explicitly calculate such correlations from the ADOs are still scarce. This paper extends a previous study [Q. Shi et al., J. Chem. Phys. 130, 164518 (2009)] in investigating the physical meaning of ADOs to general spectral densities and lower temperature cases. Using the path-integral technique, we derive exact relations between the expectation values of the collective bath coordinate and the ADOs, which could be very useful in investigating the correlated system-bath dynamics directly with the HEOM formalism. Numerical examples concerning the evolution of the expectation values of the collective bath coordinate are also presented. [ABSTRACT FROM AUTHOR]

The damped quantum rotation (DQR) theory describes temperature effects in NMR spectra of hindered molecular rotators composed of identical atoms arranged in regular N-gons. In the standard approach, the relevant coherent dynamics are described quantum mechanically and the stochastic, thermally activated motions classically. The DQR theory is consistent. In place of random jumps over one, two, etc., maxima of the hindering potential, here one has damping processes of certain long-lived coherences between spin-space correlated eigenstates of the rotator. The damping-rate constants outnumber the classical jump-rate constants. The jump picture is recovered when the former cluster appropriately around only as many values as the number of the latter. The DQR theory was confirmed experimentally for hindered methyl groups in solids and even in liquids above 170 K. In this paper it is shown that for three-, four-, and sixfold rotators, the Liouville space equations of NMR line shapes, derived previously with the use of the quantum mechanical reduced density matrix approach, can be be given a heuristic justification. It is based on an equation of motion for the effective spin density matrix, where the relevant spin Hamiltonian contains randomly fluctuating terms. The occurrence of the latter can be rationalized in terms of fluctuations of the tunneling splittings between the torsional sublevels of the rotator, including momentary liftings of the Kramers degeneracies. The question whether such degeneracy liftings are physical or virtual is discussed. The random terms in the effective Hamiltonian can be Monte Carlo modeled as piecewise constant in time, which affords the stochastic equation of motion to be solved numerically in the Hilbert spin space. For sixfold rotators, this way of calculating the spectra can be useful in the instances where the Liouville space formalism of the original DQR theory is numerically unstable. [ABSTRACT FROM AUTHOR]

We present a new algorithm for mixed quantum-classical dynamics that helps bridge the gap between mean-field (Ehrenfest) and surface-hopping dynamics by defining a natural rate of decoherence. In order to derive this decoherence result, we have expanded the number of independent variables in the usual Ehrenfest routine so that mixed quantum-classical derivatives are now propagated in time alongside the usual Ehrenfest variables. Having done so, we compute a unique rate of decoherence using two independent approaches: (i) by comparing the equations of motion for the joint nuclear-electronic probability density in phase space according to Ehrenfest dynamics versus partial Wigner transform dynamics and (ii) by introducing a frozen Gaussian interpretation of Ehrenfest dynamics which allows nuclear wave packets to separate. The first consequence of this work is a means to rigorously check the accuracy of standard Ehrenfest dynamics. Second, this paper suggests a nonadiabatic dynamics algorithm, whereby the nuclei are propagated on the mean-field (Ehrenfest) potential energy surface and undergo stochastic decoherence events. Our work resembles the surface-hopping algorithm of Schwartz and co-workers [J. Chem. Phys. 123, 234106 (2005)]—only now without any adjustable parameters. For the case of two electronic states, we present numerical results on the so-called “Tully problems” and emphasize that future numerical benchmarking is still needed. Future work will also treat the problem of three or more electronic states. [ABSTRACT FROM AUTHOR]

The Zusman equation has been widely used to study the effect of solvent dynamics on electron transfer reactions. However, application of this equation is limited by the classical treatment of the nuclear degrees of freedom. In this paper, we revisit the Zusman equation in the framework of the exact hierarchical equations of motion formalism, and show that a high temperature approximation of the hierarchical theory is equivalent to the Zusman equation in describing electron transfer dynamics. Thus the exact hierarchical formalism naturally extends the Zusman equation to include quantum nuclear dynamics at low temperatures. This new finding has also inspired us to rescale the original hierarchical equations and incorporate a filtering algorithm to efficiently propagate the hierarchical equations. Numerical exact results are also presented for the electron transfer reaction dynamics and rate constant calculations. [ABSTRACT FROM AUTHOR]

In this paper, we construct a phase-space surface hopping algorithm for use in systems that exhibit strong nonadiabatic coupling. The algorithm is derived from a representation of the electronic basis which is a function of the nuclear phase-space coordinates rather than the nuclear position coordinates. This phase-space adiabatic basis can be understood in the context of Berry’s superadiabatic basis formalism as the first-order superadiabatic correction to the conventional position-space adiabatic basis. This superadiabatic representation leads to nuclear dynamics described not by Newton’s equations of motion but by generalized Hamilton’s equations of motion. The phase-space surface hopping algorithm captures physical effects that cannot be described by traditional algorithms. For a simple model problem, we show that phase-space surface hopping is more accurate than position-space surface hopping, especially when the nonadiabatic coupling is strong. [ABSTRACT FROM AUTHOR]

We present a significant improvement to a complex time-dependent WKB (CWKB) formulation developed by Boiron and Lombardi [J. Chem. Phys. 108, 3431 (1998)] in which the time-dependent WKB equations are solved along classical trajectories that propagate in complex space. Boiron and Lombardi showed that the method gives very good agreement with the exact quantum mechanical result as long as the wavefunction does not exhibit interference effects such as oscillations and nodes. In this paper, we show that this limitation can be overcome by superposing the contributions of crossing trajectories. Secondly, we demonstrate that the approximation improves when incorporating higher order terms in the expansion. Thirdly, equations of motion for caustics and Stokes lines are implemented to help overcome Stokes discontinuities. These improvements could make the CWKB formulation a competitive alternative to current time-dependent semiclassical methods. [ABSTRACT FROM AUTHOR]

One-dimensional time-independent scattering problems are investigated in the framework of the quantum Hamilton–Jacobi formalism. The equation for the local approximate quantum trajectories near the stagnation point of the quantum momentum function is derived, and the first derivative of the quantum momentum function is related to the local structure of quantum trajectories. Exact complex quantum trajectories are determined for two examples by numerically integrating the equations of motion. For the soft potential step, some particles penetrate into the nonclassical region, and then turn back to the reflection region. For the barrier scattering problem, quantum trajectories may spiral into the attractors or from the repellers in the barrier region. Although the classical potentials extended to complex space show different pole structures for each problem, the quantum potentials present the same second-order pole structure in the reflection region. This paper not only analyzes complex quantum trajectories and the total potentials for these examples but also demonstrates general properties and similar structures of the complex quantum trajectories and the quantum potentials for one-dimensional time-independent scattering problems. [ABSTRACT FROM AUTHOR]

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating “bath” modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum. [ABSTRACT FROM AUTHOR]

The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a “shell” particle is used to define uniquely the volume of the system [M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. In addition, we also verify that the Hoover NpT MD algorithm [W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986)] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods. [ABSTRACT FROM AUTHOR]

Current constant pressure molecular-dynamics (MD) algorithms are not consistent with the recent reformulation of the isothermal-isobaric (NpT) ensemble. The NpT ensemble partition function requires the use of a “shell” molecule to identify uniquely the volume of the system, thereby avoiding the redundant counting of configurations [e.g., G. J. M. Koper and H. Reiss, J. Phys. Chem. 100, 422 (1996); D. S. Corti, Phys. Rev. E, 64, 016128 (2001)]. So far, only the NpT Monte Carlo method has been updated to allow the system volume to be defined by a shell particle [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. A shell particle has yet to be incorporated into MD simulations. The proper modification of the NpT MD algorithm is therefore the subject of this paper. Unlike Andersen’s method [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] where a piston of unknown mass serves to control the response time of volume fluctuations, the newly proposed equations of motion impose a constant external pressure via the introduction of a shell particle of known mass. Hence, the system itself sets the time scales for pressure and volume fluctuations. The new algorithm is subject to a number of fundamentally rigorous tests to ensure that the equations of motion sample phase space correctly. We also show that the Hoover NpT algorithm [W. G. Hoover, Phys. Rev. A. 31, 1695 (1985); 34, 2499 (1986)] does sample phase correctly, but only when periodic boundary conditions are employed. [ABSTRACT FROM AUTHOR]

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures “on the fly” localization of the electronic orbitals within a periodic supercell in the Γ-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn–Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We investigate the dissipative dynamics of a Morse oscillator coupled nonlinearly to a heat bath. To this end, we compare several reduced equations of motion with the dynamics of a full-dimensional wave packet with up to 61 spatial degrees of freedom. The discretized bath is converged for the relevant times considered in this paper. The propagations are done with a general purpose implementation of the multiconfiguration time-dependent Hartree method. [ABSTRACT FROM AUTHOR]