Related papers: Modeling intermolecular and intramolecular modes o…
We describe a new approach based on semiclassical molecular dynamics that allows to simulate infrared absorption or emission spectra of molecular systems with inclusion of anharmonic intensities. This is achieved from semiclassical power…
We derive and validate a partition function for low-dimensional systems interacting with a heat bath, addressing the general issue of thermodynamic modeling of nanoscale systems. In contrast to bulk systems in the canonical (NVT) ensemble…
The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better…
Modeling the heat capacity of liquids present fundamental difficulties due to the strong intermolecular particle interactions and large diffusive-like displacements. Based on the experimental evidence that the microscopic dynamics of…
Stellar streams retain a memory of their gravitational interactions with small-scale perturbations. While perturbative models for streams have been formulated in action-angle coordinates, a direct transformation to these coordinates is only…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Electronic decoherence processes in molecules and materials are usually thought and modeled via schemes for the system-bath evolution in which the bath is treated either implicitly or approximately. Here we present computations of the…
A Smolyak algorithm adapted to system-bath separation is proposed for rigorous quantum simulations. This technique combines a sparse grid method with the system-bath concept in a specific configuration without limitations on the form of the…
We apply the physics-learning duality to molecular systems by complementing the physical description of interacting particles with a dual learning description, where each particle is modeled as an agent minimizing a loss function. In the…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H. Fujisaki, Y. Zhang, and J.E. Straub, J. Chem. Phys. {\bf…
The simulation of open quantum systems coupled to a reservoir through multiple channels remains a substantial challenge. This kind of open quantum system arises when considering the radiationless decay of excited states that are coupled to…
Vibrational spectroscopy is a key technique to elucidate microscopic structure and dynamics. Without the aid of theoretical approaches, it is however, often difficult to understand such spectra at a microscopic level. Ab initio molecular…
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be…
An open quantum system refers to a system that is further coupled to a bath system consisting of surrounding radiation fields, atoms, molecules, or proteins. The bath system is typically modeled by an infinite number of harmonic…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
Humans can easily describe, imagine, and, crucially, predict a wide variety of behaviors of liquids--splashing, squirting, gushing, sloshing, soaking, dripping, draining, trickling, pooling, and pouring--despite tremendous variability in…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…