Related papers: Simulating dynamic bonding in soft materials
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…
The crystallization of a metastable melt is one of the most important non equilibrium phenomena in condensed matter physics, and hard sphere colloidal model systems have been used for several decades to investigate this process by…
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…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
Design of robots at the small scale is a trial-and-error based process, which is costly and time-consuming. There are few dynamic simulation tools available to accurately predict the motion or performance of untethered microrobots as they…
Understanding the binding dynamics of liquid molecules is of fundamental importance in physical and life sciences. However, nanoscale fast dynamics pose great challenges for experimental characterization. Conventionally, the binding…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Differentiable physics simulation provides an avenue to tackle previously intractable challenges through gradient-based optimization, thereby greatly improving the efficiency of solving robotics-related problems. To apply differentiable…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
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…