Semiclassical Molecular Dynamics Simulations Research Articles

Non-Hermitian molecular dynamics simulations of exciton-polaritons in lossy cavities.

The observation that materials can change their properties when placed inside or near an optical resonator has sparked a fervid interest in understanding the effects of strong light-matter coupling on molecular dynamics, and several approaches have been proposed to extend the methods of computational chemistry into this regime. Whereas the majority of these approaches have focused on modeling a single molecule coupled to a single cavity mode, changes to chemistry have so far only been observed experimentally when very many molecules are coupled collectively to multiple modes with short lifetimes. While atomistic simulations of many molecules coupled to multiple cavity modes have been performed with semi-classical molecular dynamics, an explicit description of cavity losses has so far been restricted to simulations in which only a very few molecular degrees of freedom were considered. Here, we have implemented an effective non-Hermitian Hamiltonian to explicitly treat cavity losses in large-scale semi-classical molecular dynamics simulations of organic polaritons and used it to perform both mean-field and surface hopping simulations of polariton relaxation, propagation, and energy transfer.

Modeling pH-Dependent Biomolecular Photochemistry.

The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.

Modeling of second sound in carbon nanostructures

The study of thermal transport in low-dimensional materials has attracted a lot of attention recently after discovery of high thermal conductivity of graphene. Here we study numerically phonon transport in low-dimensional carbon structures being interested in the hydrodynamic regime revealed through the observation of second sound. We demonstrate that correct numerical modeling of such two-dimensional systems requires semi-classical molecular dynamics simulations of temperature waves that take into account quantum statistics of thermalized phonons. We reveal that second sound can be attributed to the maximum group velocity of bending optical oscillations of carbon structures, and the hydrodynamic effects disappear for $T>200$K, being replaced by diffusive dynamics of thermal waves. Our numerical results suggest that the velocity of second sound in such low-dimensional structures is about 6 km/s, and the hydrodynamic effects are manifested stronger in carbon nanotubes rather than in carbon nanoribbons.

Theoretical-computational modelling of the vibrational relaxation of small inorganic species in condensed phase

In this paper we apply a recently developed theoretical-computational procedure for modelling the Vibrational Energy Relaxation (VER) of solvated chromophores represented by small inorganic species. In particular we focus our attention on four different systems, all experimentally well characterized: aqueous cyanide ion and aqueous azide ion, nitrogen dioxide and water both in chloroform. Our method essentially reconstructs the whole vibrational relaxation kinetics (with the chromophore in the ground electronic state) by: (i) determining, through semiclassical Molecular Dynamics (MD) simulation, the electric field (perturbation) produced onto the chromophore by the solvent atom motions; (ii) using the electrostatic perturbation for directly determining the chromophore quantum vibrational dynamics; (iii) calculating the rate constant for the vibrational relaxation as occurring without quantum–classical energy exchange; (iv) introducing the latter effect, a posteriori, hence obtaining the actual relaxation kinetics. Our results, in satisfactory agreement with the available experimental data, show that the VER mechanism is almost entirely determined by the fluctuating perturbation field as produced by the time-dependent motions of the environment atoms (in these cases the solvent) similarly to the well-known effects of the electromagnetic wave causing absorption/emission processes.

Relaxation of bosons in one dimension and the onset of dimensional crossover

We study ultra-cold bosons out of equilibrium in a one-dimensional (1D) setting and probe the breaking of integrability and the resulting relaxation at the onset of the crossover from one to three dimensions. In a quantum Newton's cradle type experiment, we excite the atoms to oscillate and collide in an array of 1D tubes and observe the evolution for up to 4.8 seconds (400 oscillations) with minimal heating and loss. By investigating the dynamics of the longitudinal momentum distribution function and the transverse excitation, we observe and quantify a two-stage relaxation process. In the initial stage single-body dephasing reduces the 1D densities, thus rapidly drives the 1D gas out of the quantum degenerate regime. The momentum distribution function asymptotically approaches the distribution of quasimomenta (rapidities), which are conserved in an integrable system. In the subsequent long time evolution, the 1D gas slowly relaxes towards thermal equilibrium through the collisions with transversely excited atoms. Moreover, we tune the dynamics in the dimensional crossover by initializing the evolution with different imprinted longitudinal momenta (energies). The dynamical evolution towards the relaxed state is quantitatively described by a semiclassical molecular dynamics simulation.

Domains and defects in nuclear pasta

Nuclear pasta topology is an essential ingredient to determine transport properties in the inner crust of neutron stars. We perform semi-classical molecular dynamics simulations of nuclear pasta for proton fractions $Y_p=0.30$ and $Y_p=0.40$ near one third of nuclear saturation density, $n=0.05\,\mathrm{fm}^{-3}$, at a temperature $T=1.0\,\mathrm{MeV}$. Our simulations are, to our knowledge, the largest nuclear pasta simulations to date and contain up to $3\,276\,800$ nucleons in the $Y_p=0.30$ and $819\,200$ nucleons in the $Y_p=0.40$ case. An algorithm to determine which nucleons are part of a given sub-domain in the system is presented. By comparing runs of different sizes we study finite size effects, equilibration time, the formation of multiple domains and defects in the pasta structures, as well as the structure factor dependence on simulation size. Although we find qualitative agreement between the topological structure and the structure factors of runs with $51\,200$ nucleons and those with $819\,200$ nucleons or more, we show that simulations with hundreds of thousands of nucleons may be necessary to accurately predict pasta transport properties.

Extending first principle plasma-surface simulations to experimentally relevant scales

The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the interface. In the majority of plasma simulations these surface processes are either neglected or treated via phenomenological parameters such as sticking coefficients, sputter rates or secondary electron emission coefficients. However, those parameters are known only in some cases, so such an approach is very inaccurate and does not have predictive capability. Therefore, improvements are highly needed. In this paper we briefly summarize relevant theoretical methods from solid state and surface physics that are able to contribute to an improved simulation of plasma-surface interaction in the near future. Even though the (quantum–mechanical) equations of motion for the participating charged and neutral particles are known, in principle, full ab initio quantum simulations are feasible only for extremely short times and/or small system sizes. A substantial simplification is achieved when electronic quantum effects are not treated explicitly. Then one arrives at much simpler semi-classical molecular dynamics (MD) simulations for the heavy particles that have become the main workhorse in surface science simulations. Using microscopically (i.e., density functional theory) founded potentials and force fields as an input, these MD simulations approach the quality of ab initio simulations, in many cases. However, despite their simplified nature, these simulations require a time step that is of the order or below one femtosecond making it prohibitive to reach experimentally relevant scales of seconds or minutes and system sizes of micrometers. To bridge this gap in length and time scales without compromising the first principles character and predictive power of the simulations, many physical and computational strategies have been put forward in surface science. This paper presents a brief overview on different methods and their underlying physical ideas, and we compare their strengths and weaknesses. Finally, we discuss their potential relevance for future plasma-surface simulations. The first class are ‘acceleration’ techniques that include metadynamics, hyperdynamics, temperature accelerated dynamics, collective variable driven hyperdynamics and others. Recently we have presented a novel approach: selective process acceleration (Abraham et al 2016 J. Appl. Phys. 119 185301) which we discuss in some more detail. The second promising route to longer accurate simulations is dynamical freeze out of dominant modes which we have introduced recently for the simulation of neutral atom sticking on a metal surface (Filinov et al 2018 Plasma Sources Sci. Technol. 27 064003). In this article we give a more general view on this method that allows to accurately combine first principles MD simulations with semi-analytical models and discuss possible applications that are of potential relevance for plasma physics.

Colloquium: Astromaterial science and nuclear pasta

We define `astromaterial science' as the study of materials in astronomical objects that are qualitatively denser than materials on earth. Astromaterials can have unique properties related to their large density, though they may be organized in ways similar to more conventional materials. By analogy to terrestrial materials, we divide our study of astromaterials into hard and soft and discuss one example of each. The hard astromaterial discussed here is a crystalline lattice, such as the Coulomb crystals in the interior of cold white dwarfs and in the crust of neutron stars, while the soft astromaterial is nuclear pasta found in the inner crusts of neutron stars. In particular, we discuss how molecular dynamics simulations have been used to calculate the properties of astromaterials to interpret observations of white dwarfs and neutron stars. Coulomb crystals are studied to understand how compact stars freeze. Their incredible strength may make crust "mountains" on rotating neutron stars a source for gravitational waves that the Laser Interferometer Gravitational-Wave Observatory (LIGO) may detect. Nuclear pasta is expected near the base of the neutron star crust at densities of $10^{14}$ g/cm$^3$. Competition between nuclear attraction and Coulomb repulsion rearranges neutrons and protons into complex non-spherical shapes such as sheets (lasagna) or tubes (spaghetti). Semi-classical molecular dynamics simulations of nuclear pasta have been used to study these phases and calculate their transport properties such as neutrino opacity, thermal conductivity, and electrical conductivity. Observations of neutron stars may be sensitive to these properties, and can be be used to interpret observations of supernova neutrinos, magnetic field decay, and crust cooling of accreting neutron stars. We end by comparing nuclear pasta shapes with some similar shapes seen in biological systems.

Recombination-Enhanced Surface Expansion of Clusters in Intense Soft X-Ray Laser Pulses.

We studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster. The measured mean ion energies exceed the value expected without recombination by more than an order of magnitude, indicating that the energy release resulting from electron-ion recombination constitutes a previously unnoticed nanoplasma heating process. This conclusion is supported by results from semiclassical molecular dynamics simulations.

Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.

Development of semiclassical molecular dynamics simulation method.

Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed.

Essential dynamics for the study of microstructures in liquids.

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic-molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen-bonded clusters.

TORSIONAL POTENTIALS AND FULL-DIMENSIONAL SIMULATION OF ELECTRONIC ABSORPTION SPECTRA OF para-PHENYLENEVINYLENE OLIGOMERS USING SEMIEMPIRICAL HAMILTONIANS

A systematic study of torsional potential curves in electronic ground state based on second-order Møller–Plesset energy (MP2), density functional theory (DFT), and Austin mode 1 (AM1) methods is presented for para-phenylenevinylene oligomers constructed from two to four aromatic rings. The semiempirical AM1 approach gives the correct location of potential energy minima in comparison with the reference MP2 calculations and literature data. However, the semiempirical AM1 energy barriers at perpendicular orientation are ca. 30% smaller than the MP2 ones. The DFT calculations indicate optimal planar structures and the barriers are three times higher than MP2 values. Excited-state potential energy curves evaluated from vertical excitations at the time-dependent density functional theory (TD-DFT) and ab initio CI levels exhibit much steeper increase of values in the vicinity of perpendicular orientation than in the semiempirical Zerner's intermediate neglect of differential overlap (ZINDO) and ab initio RI-CC2 cases. The effects of vibrational motion of phenylene rings on the torsional broadening of absorption spectra were estimated from semi-classical molecular dynamics simulations and harmonic oscillator sampling. The simulated spectra agree well with the experiment and allow estimating the conformer distribution of the molecules.

Shear viscosity and thermal conductivity of nuclear “pasta”

We calculate the shear viscosity \ensuremath{\eta} and thermal conductivity \ensuremath{\kappa} of a nuclear pasta phase in neutron star crusts. This involves complex nonspherical shapes. We use semiclassical molecular dynamics simulations involving 40, 000 to 100, 000 nucleons. The viscosity \ensuremath{\eta} can be simply expressed in terms of the height ${Z}^{*}$ and width $\ensuremath{\Delta}q$ of the peak in the static structure factor ${S}_{p}(q)$. We find that \ensuremath{\eta} increases somewhat, compared to a lower density phase involving spherical nuclei, because ${Z}^{*}$ decreases from form factor and ion screening effects. However, we do not find a dramatic increase in \ensuremath{\eta} from nonspherical shapes, as may occur in conventional complex fluids.

Light-harvesting function through one-by-one electron and hole transfer in a methane-lithium system

Carrying out a semiclassical molecular dynamics simulation of a CH4-Li2 system by using the time-dependent local density approximation of the time-dependent density functional theory, we find that one-by-one electron and hole transfer takes place from CH4 to Li2 when an electron is excited in CH4. Probability of the transfer is low when the molecules are fixed, but it increases when the molecules are freely relaxed or Li2 has 1 eV of initial velocity.

Ballistic resistivity in aluminum nanocontacts

We perform a representative series of semiclassical molecular dynamics simulations of aluminum nanocontact breakages, coupled to full quantum conductance calculations. This approach allows to obtain realistic conductance histograms of polyvalent species and understand the origin of their peaked structures. The results show that the conductance depends linearly on the contact minimum cross section for the geometrically favored nanocontact configurations. Valid in a broad range of conductance values, such relation suggests the definition of a transport parameter for the nanoscale, that represents the novel concept of ballistic resistivity.

Semiclassical molecular dynamics simulation of surface processes: Application to the hydrogen atom recombination on graphite

AbstractThe semiclassical collisional method has been applied to get an insight into the most basic behaviors of the H2 formation after atom recombination on a graphite surface at TS = 100 K. The scattering equations are integrated over an adiabatic potential energy surface used in a previous study. Compared with the previously obtained results at TS = 10 K, important surface temperature effects on the recombination dynamics have been found. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Influence of the electronic chaotic motion on the fusion dynamics at astrophysical energies

We perform semi-classical molecular dynamics simulations of screening by bound electrons in low energy nuclear reactions. In our simulations quantum effects corresponding to the Pauli and Heisenberg principle are enforced by constraints. In addition to the well-known adiabatic and sudden limits, we propose a new “dissipative limit” which is expected to be important not only at high energies but in the extremely low energy region. The dissipative limit is associated with the chaotic behavior of the electronic motion. It affects also the magnitude of the enhancement factor. We discuss also numerical experiments using polarized targets. The derived enhancement factors in our simulation are in agreement with those extracted within the R-matrix approach.

Small rare gas clusters in XUV laser pulses

Semi-classical molecular dynamics simulations of small rare gas clusters in short laser pulses of 100 nm wavelength were performed. For comparison, the cluster response to 800 nm laser pulses was investigated as well. The inner ionization dynamics of multi-electron atoms inside the cluster was treated explicitly. The simulation results underpin the belief that at XUV (extreme ultraviolet) wavelengths collisions play an important role in the energy absorption. The generation of the surprisingly high charge states of Xe atoms inside clusters, as they were observed in a free-electron laser experiment at DESY, Hamburg, Germany by Wabnitz et al. is due to the reduced ionization potential of atoms inside charged clusters, the ionization ignition mechanism, and collisions.

Influence of electronic and geometric properties on melting of sodium clusters

Systematics of the melting transition for sodium clusters with 40-355 atoms has been studied with both ab initio and semiclassical molecular dynamics simulations. The melting temperatures obtained with an ab initio method for Na55 + and Na93 + correlate well with the experimental results. The semiclassically determined melting temperatures show similarities with the experimentally determined ones in the size region from 55 to 93 and near size 142, and the latent heat in the size region from 55 to 139, but not elsewhere in the size region studied. This indicates that the nonmonotonical melting behavior observed experimentally cannot be fully explained by geometrical effects. The semiclassically determined melting temperature and the latent heat correlate quite well, indicating that they respond similarly to changes in cluster geometry and size. Similarly, the binding energy per atom seems to correlate with the melting temperature and the latent heat of fusion.