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We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…

Vibrational spectroscopy provides a powerful connection between molecular dynamics (MD) simulations and experiment, but its routine use in condensed-phase systems remains limited. We introduce mimyria, a modular and automated framework that…

Solid-water interfaces are crucial to many physical and chemical processes and are extensively studied using surface-specific sum-frequency generation (SFG) spectroscopy. To establish clear correlations between specific spectral signatures…

We present two methods for efficient detection of chiral molecules based on sequences of single pulses and Raman pulse pairs. The chiral molecules are modelled by a closed-loop three-state system with different signs in one of the couplings…

Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…

The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…

Determining the complexity of molecules has important applications from molecular design to understanding the history of the process that led to the formation of the molecule. Currently, it is not possible to experimentally determine,…

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…

With the path integral approach, the thermal average in a multi-electronic-state quantum systems can be approximated by the ring polymer representation on an extended configuration space, where the additional degrees of freedom are…

The Anderson Mixing (AM) method is a popular approach for accelerating fixed-point iterations by leveraging historical information from previous steps. In this paper, we introduce the Riemannian Anderson Mixing (RAM) method, an extension of…

The ion-electron coupling properties for a ion impurity in an electron gas and for a two component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely…

Radiation from stars and AGN plays an important role in galaxy formation and evolution, and profoundly transforms the IGM, CGM & ISM. On-the-fly RT has started being incorporated in cosmological simulations, but the complex, evolving…

Ab initio molecular dynamics (AIMD) is a powerful tool to predict properties of molecular and condensed matter systems. The quality of this procedure is based on accurate electronic structure calculations. The development of quantum…

We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…

Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio…

We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…

Deflection of atoms in \Lambda-type configuration passing through two crossed standing light waves is proposed for probing and visualization of atomic superposition states. For this goal, we use both the large-dispersive and Raman-resonant…

Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…

We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…

We derive the non-adiabatic ring polymer molecular dynamics (RPMD) approach in the phase space of the SU(N) Lie Group. This method, which we refer to as the spin mapping non-adiabatic RPMD (SM-NRPMD), is based on the spin-mapping formalism…