相关论文: Visualizing Conformations in Molecular Dynamics

The structure of nanoclusters is complex to describe due to their noncrystallinity, even though bonding and packing constraints limit the local atomic arrangements to only a few types. A computational scheme is presented to extract…

In this paper, we address the challenge of obtaining a comprehensive and symmetric representation of point particle groups, such as atoms in a molecule, which is crucial in physics and theoretical chemistry. The problem has become even more…

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…

This paper proposes a machine learning (ML) method to predict stable molecular geometries from their chemical composition. The method is useful for generating molecular conformations which may serve as initial geometries for saving time…

We use Monte Carlo simulation to study the phase diagram of three-dimensional dynamical triangulations with a boundary. Three phases are indentified and characterized. One of these phases is a new, boundary dominated phase; a simple…

We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the…

Numerical simulations of clusters of galaxies provide a unique way to follow the dynamics of these systems. The models reveal many characteristics of the merging process of subclusters: shock structure and strength, temperature distribution…

Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship…

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…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

The configurations of the molecules nearest to a single vacancy in solid CO2 were studied by the Metropolis Monte Carlo (MC) simulation at temperatures T = 0, 100, and 200 K. It was found that distorted orientational configurations at T = 0…

We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…

Monte Carlo simulation is an essential component of experimental particle physics in all the phases of its life-cycle: the investigation of the physics reach of detector concepts, the design of facilities and detectors, the development and…

We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…

We present a multilevel Monte Carlo simulation method for analysing multi-scale physical systems via a hierarchy of coarse-grained representations, to obtain numerically-exact results, at the most detailed level. We apply the method to a…

Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…

We outline the steps needed in to calibrate the Monte Carlo code in order to perform large scale simulations of real globular clusters. We calibrate the results against $N$-body simulations for $N = 2500$, 10000 and for the old open cluster…

Colloidal droplets are used in a variety of practical applications. Some of these applications require particles of different sizes. These include medical diagnostic methods, the creation of photonic crystals, the formation of…

Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…

In this manuscript, we describe a new configurational bias Monte Carlo technique for the simulation of peptides. We focus on the biologically relevant cases of linear and cyclic peptides. Our approach leads to an efficient,…