相关论文: Visualizing Conformations in Molecular Dynamics

Intermolecular correlations in liquid acetonitrile (CH3CN) have been revisited by calculating orientational correlation functions. In the present approach, hydrogen atoms are included, so that a concept applicable for molecules of (nearly)…

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…

Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…

Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…

Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…

We describe the applications of clustering and visualization tools using the so-called neutral B anomalies as an example. Clustering permits parameter space partitioning into regions that can be separated with some given measurements. It…

Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…

A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…

Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…

Molecular dynamics simulations are performed for a finite non-relativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable…

Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…

Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…

We present a new numerical model to simulate settling trajectories of discretized individual or a mixture of particles of different geometrical shapes in a quiescent fluid and their flow trajectories in a flowing fluid. Simulations unveiled…

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…

We adapt Vertex models to understand the physical origin of the formation of long-range ordered structures in repulsive soft particles. The model incorporates contributions from the volume and surface area of each particle. Sampling using…

Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…

In this work we propose a new approach for the numerical simulation of kinetic equations through Monte Carlo schemes. We introduce a new technique which permits to reduce the variance of particle methods through a matching with a set of…

We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…

A realistic 3D anthropomorphic software model of microcalcifications may serve as a useful tool to assess the performance of breast imaging applications through simulations. We present a method allowing to simulate visually realistic…