Related papers: Simulating dynamic bonding in soft materials
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
Magnetic materials play a key role in the contemporary industry, providing unique features with a wide application potential. To study physical phenomena and design new materials, it is important to possess an appropriate tool, a model…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
Functional soft materials, comprising colloidal and molecular building blocks that self-organize into complex structures as a result of their tunable interactions, enable a wide array of technological applications. Inverse methods provide…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
The focus in this paper is an analysis of existing state of the arts directed toward the development of the next generation of vibration damping systems. The research work concentrates on an investigation related to…
The physics of glasses can be studied from many viewpoints, from material scientists interested in the development of new materials to statistical physicists inventing new theoretical tools to deal with disordered systems. In these lectures…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with…
An increasing variety of crystal structures has been observed in soft condensed matter over the past two decades, surpassing most expectations for the diversity of arrangements accessible through classical driving forces. Here, we survey…
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…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
When atoms come together and bond, we call these new states molecules, and their properties determine many aspects of our daily life. Strangely enough, it is conceivable for light and molecules to bond, creating new hybrid light-matter…
Cooperative binding affects many processes in biology, but it is commonly addressed only in equilibrium. In this work we explore dynamical cooperativity in driven systems, where the cooperation occurs because some of the bonds change the…