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We study the interplay between collective and incoherent single-particle motion in a model of two chains of particles whose interaction comprises a non-integrable part. In the perturbative regime, but for a general form of the interaction,…
Starting from a Huxley-type model for an agitated vibrational mode, we propose an embedding of standard active particle models in terms of two-temperature processes. One temperature refers to an ambient thermal bath, and the other…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Machine learning methods are being explored in many areas of science, with the aim of finding solution to problems that evade traditional scientific approaches due to their complexity. In general, an order parameter capable of identifying…
Understanding the dynamics of dissipative quantum systems, particularly beyond the weak coupling approximation, is central to various quantum applications. While numerically exact methods provide accurate solutions, they often lack the…
The work is devoted to the investigation of the influence of a heat bath on the physical processes in a quantum system. We use the density matrix theory as one of the most powerfool tool for investigation of quantum relaxation. In the…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
The energy landscape approach has been useful to help understand the dynamic properties of supercooled liquids and the connection between these properties and thermodynamics. The analysis in numerical models of the inherent structure (IS)…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
A numerical simulation of vibrational excitation of molecules was devised, and used to excite computational models of common molecules into a prescribed, pure, normal vibration mode in the ground electronic state, with varying, controlable…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
The hypersphere model is a simple one-parameter model of the potential energy landscape of viscous liquids, which is defined as a percolating system of same-radius hyperspheres randomly distributed in $\mathbb{R}^{3N}$ in which $N$ is the…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
In this work, we explore various relevant aspects of the Smoothed Particle Hydrodynamics regarding Burger's equation. The stability, precision, and efficiency of the algorithm are investigated in terms of different implementations. In…
Molecular dynamics simulations and instantaneous normal mode (INM) analysis of a fluid with core-softened pair interactions and water-like liquid-state anomalies are performed to obtain an understanding of the relationship between…
This paper presents a comprehensive exposition of a spontaneous laser model for a resonant semi-classical system of radiation and ion cluster-solvated rotating water molecules, which have subtly variable moments of inertia. In this system,…
The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for…
The dynamics of a wide range of technologically important quantum systems are dominated by their interaction with just a few environmental modes. Such highly structured environments give rise to long-lived bath correlations that induce…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…