Dynamics Of Molecular Systems Research Articles

Combining dual domain material point method with molecular dynamics for thermodynamic nonequilibriums

The dual domain material point method (DDMP) combined with molecular dynamics (MD) is used to simulate a material undergoing a large deformation with a high strain rate. In the simulation, the continuum scale equation of motion is solved using DDMP, while the stresses required at the material points are obtained by performing MD simulations in small domains surrounding the material points following the entire history of the material deformation without reinitialization of the MD systems; therefore the history dependence, a common feature for thermodynamically nonequilibrium systems, can be tracked accurately.Two algorithms are introduced to avoid distortion of the MD domains and to ensure consistence in the energy density between the MD and macroscopic calculations. As an example, a hyper-velocity impact problem is simulated. The results of the combined DDMP–MD calculations are compared to a pure MD simulation. The method of the combined simulation is applicable to macroscopic systems, although the size of the simulation domain is only a few hundred nanometers in this example because of the limitation of the pure MD simulation.

Dynamics of molecular systems

Dynamics of molecular systems

Pyridine as a Resonantly Addressable Group to Study Electron-Transfer Dynamics in Self-Assembled Monolayers

Resonant Auger electron spectroscopy (RAES) in combination with the core-hole clock (CHC) approach represents a unique tool to study femtosecond electron transfer (ET) dynamics in molecular systems and self-assembled monolayers (SAMs) in particular. A most promising experimental strategy to apply this approach to SAMs involves the decoration of the target films with a group, which can be resonantly excited by narrow-band X-rays. Using a series of well-defined SAMs with a terminal pyridine moiety, we demonstrate here that pyridine can be used as such a group, as an alternative to the nitrile group, which has been utilized for this purpose in the past. For these SAMs, we evaluate the characteristic time for ET from the terminal nitrogen atom of the pyridine group through the molecular framework to the substrate and discuss the results in terms of conjugation and coupling of the relevant electronic states in the molecules. The obtained ET times correlate well with the literature values obtained for the analo...

Laser pulse induced multi-exciton dynamics in molecular systems

Ultrafast optical excitation of an arrangement of identical molecules is analyzed theoretically. The computations are particularly dedicated to molecules where the excitation energy into the second excited singlet state E(S2) − E(S0) is larger than twice the excitation energy into the first excited singlet state E(S1) − E(S0). Then, exciton–exciton annihilation is diminished and resonant and intensive excitation may simultaneously move different molecules into their first excited singlet state . To describe the temporal evolution of the thus created multi-exciton state a direct computation of the related wave function is circumvented. Instead, we derive equations of motion for expectation values formed by different arrangements of single-molecule transition operators . First simulation results are presented and the approximate treatment suggested recently in 2016 Phys. Rev. B 94 195413 is evaluated.

A Multiscale Perturbation Expansion Approach for Markov State Modeling of Nonstationary Molecular Dynamics

We investigate metastable dynamical systems subject to nonstationary forcing as they appear in molecular dynamics for systems driven by external fields. We show that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation---a Markov state model---can be assembled by constructing two equilibrium Markov state models, one for the unforced system and one for a slightly perturbed one.

Molecular dynamics for ion-tuned wettability in oil/brine/rock systems

The dependence of wettability on brine ionic composition in oil/brine/rock systems, which is denoted as ion-tuned wettability, has important applications in geoscience. Due to the involvement of non-continuum effects, molecular dynamics (MD) simulation is necessary to improve understanding of its mechanism. This work establishes a reliable molecular dynamics (MD) framework to study ion-tuned wettability. We prove that our model system can well represent the wettability of the real oil/brine/rock system, and that the wettability alteration from the MD results is qualitatively consistent with the EDL repulsion theory when ion-binding does not exist. In the process to establish the MD framework, our work suggests that adding counter ions to balance interface charges is good for studying concentration effect on wettability, and the contact angle defined from mass center coordinates is effective to measure the wettability of the nano-scale MD system. This work provides the basis for on-going studies using MD simulation to reveal the mechanism of ion-tuned wettability.

Perspective: THz-driven nuclear dynamics from solids to molecules.

Recent years have seen dramatic developments in the technology of intense pulsed light sources in the THz frequency range. Since many dipole-active excitations in solids and molecules also lie in this range, there is now a tremendous potential to use these light sources to study linear and nonlinear dynamics in such systems. While several experimental investigations of THz-driven dynamics in solid-state systems have demonstrated a variety of interesting linear and nonlinear phenomena, comparatively few efforts have been made to drive analogous dynamics in molecular systems. In the present Perspective article, we discuss the similarities and differences between THz-driven dynamics in solid-state and molecular systems on both conceptual and practical levels. We also discuss the experimental parameters needed for these types of experiments and thereby provide design criteria for a further development of this new research branch. Finally, we present a few recent examples to illustrate the rich physics that may be learned from nonlinear THz excitations of phonons in solids as well as inter-molecular vibrations in liquid and gas-phase systems.

A nonlocal adaptive discrete empirical interpolation method combined with modified hp-refinement for order reduction of molecular dynamics systems

Model order reduction is an emerging technique to tackle the computational complexities of molecular dynamics (MD) simulations. Different strategies are required to adequately obtain the reduced solutions of different classes of molecular dynamics systems. In this work, a proper orthogonal decomposition (POD) is combined with the discrete empirical interpolation method (DEIM) to study atomic systems. Due to the limitations of the DEIM in capturing the nonlocal response of the nonlinear force field of MD systems, a nonlocal adaptive discrete empirical interpolation method (ADEIM) is proposed. Furthermore, a modified hp-refinement algorithm is introduced to extend the application of the POD-DEIM approach to order reduction of multi-dimensional MD systems. In the DEIM, the distance between atoms and hence the reduced internal force vector is estimated based on a local interpolation of the state variables. The internal forces of a multi-dimensional MD system depend on the distance between the atoms, represented in space by more than one coordinate. Therefore, the ADEIM approach seeks to obtain a nonlocal interpolation of the state variables to accurately predict the distance between the interpolated atoms and hence the reduced force vector. Simulation of MD systems with frequently changing neighbour atoms leads to change in the system dynamics, which further leads to change of properties of the snapshots. Therefore, the temporal domain is adaptively subdivided into smaller sub-domains using the adopted hp-refinement procedure. The reduced system parameters are effectively derived over the sub-domains. Considering the computational cost, a modified hp-refinement algorithm is developed in this study, which is further coupled with the POD-ADEIM approach to obtain the reduced-order solution of the MD systems. The results of the proposed approach demonstrate the efficiency and accuracy of the reduced solutions.

STRUCTURAL DYNAMICS OF FREE MOLECULES AND CONDENSED STATE OF MATTER. Part II. TRANSIENT STRUCTURES IN CHEMICAL REACTIONS

Basic knowledge of mankind so far relates to the description of electrons and atoms in the material in a state of equilibrium, where the behavior changes slowly over time. The electron diffraction with a high temporal and space resolution has opened the possibility of direct observation of the processes occurring in the transient state of the substance (molecular movie). Here it is necessary to provide a temporary resolution of the order of 100 fs, which corresponds to the transition of the system through the energy barrier of the potential surface, which describes the chemical reaction - the process of the breaking and the formation of new bonds between the interacting agents. Thus, the possibility of the investigation of the coherent nuclear dynamics of molecular systems and the condensed matter can be opened. In the past two decades, it has been possible to observe the nuclear motion in the temporal interval corresponding to the period of the nuclear oscillation. The observed coherent changes in the nuclear system at such temporal intervals determine the fundamental shift from the standard kinetics of chemical reactions to the dynamics of the phase trajectory of a single molecule, the molecular quantum state tomography.

Simulation of Quantum Dynamics of Excitonic Systems at Finite Temperature: an efficient method based on Thermo Field Dynamics

Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on Thermo Field Dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. The solution of Thermo Field Dynamics equations with a novel technique for the propagation of Tensor Trains (Matrix Product States) is implemented and discussed. The methodology is applied to the study of the exciton dynamics in the Fenna-Mathews-Olsen complex using a realistic structured spectral density to model the electron-phonon interaction. The results of the simulations highlight the effect of specific vibrational modes on the exciton dynamics and energy transfer process, as well as call for careful modeling of electron-phonon couplings.

Accurate computation of above threshold ionization spectra for stretched in strong laser fields

Investigations on the simplest benchmark system can reveal most underlying mechanisms for the intricate dynamics of molecular systems induced by strong laser pulses. However, due to the two-center Coulomb potential and the highly nonlinear nature of the electron dynamics, the accurate computation of the above threshold ionization spectra remains challenging, especially at large internuclear distances and high laser intensities. In the present work, we implement a new Gauss-quadrature approximation (GA) in the framework of finite element discrete variable representation to solve the time-dependent Schrödinger equation of in strong laser fields. By using this GA, one can arrive at a matrix representation of the first derivative operator that keeps its anti-hermiticity. This crucial feature allows a very stable propagation of the wavefunction under the usual Lanczos scheme. Combining with a wavefunction splitting in the asymptotic region, we show that our present numerical method can reliably deal with the electronic dynamics of stretched molecules at large internuclear distances for high laser intensities and long pulse durations. Accurate photoelectron momentum distributions under these conditions are presented and the distinct features due to the two-center potential are discussed.

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods.

We review the tremendous advances in ultrafast X-ray science, over the past 15 years, making the best use of new ultrashort X-ray sources including table-top or large-scale facilities. Different complementary X-ray-based techniques, including spectroscopy, scattering, and diffraction, are presented. The broad and expanding spectrum of these techniques in the ultrafast time domain is delivering new insight into the dynamics of molecular systems, of solutions, of solids, and of biosystems. Probing the time evolution of the electronic and structural degrees of freedom of these systems on the time scales of femtosecond to picoseconds delivers new insight into our understanding of dynamical matter.

Isolating strong-field dynamics in molecular systems

Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed

An open-source framework for analyzing N-electron dynamics. I. Multideterminantal wave functions.

The aim of the present contribution is to provide a framework for analyzing and visualizing the correlated many-electron dynamics of molecular systems, where an explicitly time-dependent electronic wave packet is represented as a linear combination of N-electron wave functions. The central quantity of interest is the electronic flux density, which contains all information about the transient electronic density, the associated phase, and their temporal evolution. It is computed from the associated one-electron operator by reducing the multideterminantal, many-electron wave packet using the Slater-Condon rules. Here, we introduce a general tool for post-processing multideterminant configuration-interaction wave functions obtained at various levels of theory. It is tailored to extract directly the data from the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions. The procedure is implemented in the open-source Python program detCI@ORBKIT, which shares and builds on the modular design of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). The new procedure is applied to ultrafast charge migration processes in different molecular systems, demonstrating its broad applicability. Convergence of the N-electron dynamics with respect to the electronic structure theory level and basis set size is investigated. This provides an assessment of the robustness of qualitative and quantitative statements that can be made concerning dynamical features observed in charge migration simulations. © 2017 Wiley Periodicals, Inc.

An improved dissipative coupling scheme for a system of Molecular Dynamics particles interacting with a Lattice Boltzmann fluid

We consider the dissipative coupling between a stochastic Lattice Boltzmann (LB) fluid and a particle-based Molecular Dynamics (MD) system, as it was first introduced by Ahlrichs and Dünweg (1999). The fluid velocity at the position of a particle is determined by interpolation, such that a Stokes friction force gives rise to an exchange of momentum between the particle and the surrounding fluid nodes. For efficiency reasons, the LB time step is chosen as a multiple of the MD time step, such that the MD system is updated more frequently than the LB fluid. In this situation, there are different ways to implement the coupling: Either the fluid velocity at the surrounding nodes is only updated every LB time step, or it is updated every MD step. It is demonstrated that the latter choice, which enforces momentum conservation on a significantly shorter time scale, is clearly superior in terms of temperature stability and accuracy, and nevertheless only marginally slower in terms of execution speed. The second variant is therefore the recommended implementation.

Generation of Attosecond Light Pulses from Gas and Solid State Media

Real-time observation of ultrafast dynamics in the microcosm is a fundamental approach for understanding the internal evolution of physical, chemical and biological systems. Tools for tracing such dynamics are flashes of light with duration comparable to or shorter than the characteristic evolution times of the system under investigation. While femtosecond (fs) pulses are successfully used to investigate vibrational dynamics in molecular systems, real time observation of electron motion in all states of matter requires temporal resolution in the attosecond (1 attosecond (asec) = 10−18 s) time scale. During the last decades, continuous efforts in ultra-short pulse engineering led to the development of table-top sources which can produce asec pulses. These pulses have been synthesized by using broadband coherent radiation in the extreme ultraviolet (XUV) spectral region generated by the interaction of matter with intense fs pulses. Here, we will review asec pulses generated by the interaction of gas phase media and solid surfaces with intense fs IR laser fields. After a brief overview of the fundamental process underlying the XUV emission form these media, we will review the current technology, specifications and the ongoing developments of such asec sources.

Origin of non-Gaussian site energy disorder in molecular aggregates

Gaussian site energy disorder is an ad hoc concept usually implemented in simulations of excitation dynamics in molecular systems. In this letter we suggest a mechanism which may cause correlated static energy disorder in a broad range of molecular systems. Our approach leads to non-Gaussian site energy distribution, which strongly affects statistical properties of exciton wavefunctions and consequently changes material functional characteristics.

Phase-Resolved Heterodyne-Detected Transient Grating Enhances the Capabilities of 2D IR Echo Spectroscopy.

2D IR echo spectroscopy, with high sensitivity and femtosecond time resolution, enables us to understand structure and ultrafast dynamics of molecular systems. Application of this experimental technique on weakly absorbing samples, however, had been limited by the precise and unambiguous phase determination of the echo signals. In this study, we propose a new experimental scheme that significantly increases the phase stability of the involved IR pulses. We have demonstrated that the incorporation of phase-resolved heterodyne-detected transient grating (PR-HDTG) spectroscopy greatly enhances the capabilities of 2D IR spectroscopy. The new experimental scheme has been used to obtain 2D IR spectra on weakly absorbing azide ions (N3-) in H2O (absorbance ∼0.025), free of phase ambiguity even at large waiting times. We report the estimated spectral diffusion time scale (1.056 ps) of azide ions in aqueous solution from the 2D IR spectra and the vibrational lifetime (750 ± 3 fs) and the reorientation time (1108 ± 24 fs) from the PR-HDTG spectra.

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts.

Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.

Photoinduced dynamics in cycloparaphenylenes: planarization, electron-phonon coupling, localization and intra-ring migration of the electronic excitation.

Cycloparaphenylenes represent the smallest possible fragments of armchair carbon nanotubes. Due to their cyclic and curved conjugation, these nanohoops own unique photophysical properties. Herein, the internal conversion processes of cycloparaphenylenes of sizes 9 through 16 are simulated using Non-Adiabatic Excited States Molecular Dynamics. In order to analyze effects of increased conformational disorder, simulations are done at both low temperature (10 K) and room temperature (300 K). We found the photoexcitation and subsequent electronic energy relaxation and redistribution lead to different structural and electronic signatures such as planarization of the chain, electron-phonon couplings, wavefunction localization, and intra-ring migration of excitons. During excited state dynamics on a picosecond time-scale, an electronic excitation becomes partially localized on a portion of the ring (about 3-5 phenyl rings), which is not a mere static contraction of the wavefunction. In a process of non-radiative relaxation involving non-adiabatic transitions, the latter exhibits significant dynamical mobility by sampling uniformly the entire molecular structure. Such randomized migration involving all phenyl rings, occurs in a wave-like fashion coupled to vibrational degrees of freedom. These results can be connected to unpolarized emission observed in single-molecule fluorescence experiments. Observed intra-ring energy transfer is subdued for lower temperatures and adiabatic dynamics involving low-energy photoexcitation to the first excited state. Overall our analysis provides a detailed description of photo excited dynamics in molecular systems with circular geometry, outlines size-dependent trends and connotes specific spectroscopic signatures appearing in time-resolved experimental probes.