Related papers: Modeling intermolecular and intramolecular modes o…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME) mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the…
The molecular Hubbard Hamiltonian (MHH) naturally arises for ultracold ground state polar alkali dimer molecules in optical lattices. We show that, unlike ultracold atoms, different molecules display different many-body phases due to…
Cavity dressing of molecular vibrational dynamics expands the role of characteristic vibrations as spectroscopic markers of underlying ultrafast dynamics. Interacting vibrational modes exhibit a pronounced excited state delocalization due…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
We study the quantum dissipative dynamics of a particle coupled linearly to a set of two-level systems (the heat bath) via the master equation method which we extract from the path integral formalism independently from the form of the bath…
The quantum dynamics of a low-dimensional system in contact with a large but finite harmonic bath is theoretically investigated by coarse-graining the bath into a reduced set of effective energy states. In this model, the couplings between…
In this study some properties of the methanol-water mixture such as diffusivity, density, viscosity, and hydrogen bonding were calculated at different temperatures and atmospheric pressure using molecular dynamics simulations (MDS). The…
In order to investigate the rheological properties of viscoelastic fluids by mesoscopic hydrodynamics methods, we develop a multi-particle collision dynamics (MPC) model for a fluid of harmonic dumbbells. The algorithm consists of…
Computer simulations have been employed in recent years to evaluate the configurational entropy changes in model glass-forming liquids. We consider two methods, both of which involve the calculation of the `intra-basin' entropy as a means…
Strongly interacting, dynamically disordered and with no small parameter, liquids took a theoretical status between gases and solids. We review different approaches to liquids and propose that liquids do not need classifying in terms of…
A vibrational model of transport properties of dense fluids assumes that solid-like oscillations of atoms around their temporary equilibrium positions dominate the dynamical picture. The temporary equilibrium positions of atoms do not form…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
A damped oscillator heat bath model is a modification of the standard heat bath model, wherein each bath oscillator itself has a Markovian coupling to its own heat bath [1]. We modify such a model to one where the resulting damping of the…
The supra-molecular structure of a liquid is strongly connected to its dynamics which in turn controls macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential…
A vibrational model of heat transfer in simple liquids with soft pairwise interatomic interactions is discussed. A general expression is derived, which involves an averaging over the liquid collective mode excitation spectrum. The model is…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
A well-known approach to describe the dynamics of an open quantum system is to compute the master equation evolving the reduced density matrix of the system. This approach plays an important role in describing excitation transfer through…