Related papers: Modeling intermolecular and intramolecular modes o…
We study the emergence of collective dynamics in the integrable Hamiltonian system of two finite ensembles of coupled harmonic oscillators. After identification of a collective degree of freedom, the Hamiltonian is mapped onto a model of…
In this article, we explore the dissipation dynamics of a strongly coupled multidimensional system in contact with a Markovian bath following a system-bath approach. We use in this endeavour the recently developed stochastic…
Computational studies of liquid water and its phase transition into vapor have traditionally been performed using classical water models. Here we utilize the Deep Potential methodology -- a machine learning approach -- to study this…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
A recent description of the motion of atoms in a classical monatomic system in liquid and supercooled liquid states divides the motion into two parts: oscillations within a given many-particle potential valley, and transit motion which…
A millimetric bouncing droplet sustained on a vibrating bath becomes a moving wave source (particle) through periodically interacting with the local wave field it generates during the droplet-bath impact. By virtue of such particle-wave…
We have adapted a set of classification algorithms, also known as Machine Learning, to the identification of fluid and gel domains close to the main transition of dipalmitoyl-phosphatidylcholine (DPPC) bilayers. Using atomistic molecular…
We address the degree to which machine learning can be used to accurately and transferably predict post-Hartree-Fock correlation energies. Refined strategies for feature design and selection are presented, and the molecular-orbital-based…
Heat conduction in one-dimensional (1D) systems is studied based on an analytical S-matrix method, which is developed in the mesoscopic electronic transport theory and molecular dynamic (MD) simulations. It is found that heat conduction in…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
As the most important solvent, water has been at the center of interest since the advent of computer simulations. While early molecular dynamics and Monte Carlo simulations had to make use of simple model potentials to describe the atomic…
Finding efficient descriptions of how an environment affects a collection of discrete quantum systems would lead to new insights into many areas of modern physics. Markovian, or time-local, methods work well for individual systems, but for…
Molecular dynamics in pure water and aqueous salt solutions remain incompletely understood, partly due to the apparent contradictions between results from different spectroscopic techniques. In this work, we demonstrate, by detailed…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We use the "generalized hierarchical equation of motion" proposed in Paper I to study decoherence in a system coupled to a spin bath. The present methodology allows a systematic incorporation of higher order anharmonic effects of the bath…
In order to study the heating process of water by the microwaves of 2.5-20GHz frequencies, we have performed molecular dynamics simulations by adopting a non-polarized water model that have fixed point charges on rigid-body molecules. All…
The lack of a well-defined equilibrium reference configuration has long hindered a comprehensive atomic-level understanding of liquid dynamics and properties. The Instantaneous Normal Mode (INM) approach, which involves diagonalizing the…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…