Related papers: Deriving molecular bonding from macromolecular sel…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We study the adhesive contact between elastic solids with randomly rough, self affine fractal surfaces. We present molecular dynamics (MD) simulation results for the interfacial stress distribution and the wall-wall separation. We compare…
We developed a new physical model to predict macroscopic properties of inorganic molten systems using a realistic description of inter-atomic interactions. Unlike the conventional approach, which tends to overestimate viscosity by several…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Scanning tunneling microscopy (STM) has been a fundamental tool to characterize many-body effects in condensed matter systems, from extended solids to quantum dots. STM of molecules decoupled from the supporting conductive substrate has the…
We extend the live-cell motility Filament Based Lamellipodium Model to incorporate the forces exerted on the lamellipodium of the cells due to cell-cell collision and cadherin induced cell-cell adhesion. We take into account the nature of…
We have carried out extensive Monte Carlo simulations of the fusion of tense apposed bilayers formed by amphiphilic molecules within the framework of a coarse grained lattice model. The fusion pathway differs from the usual stalk mechanism.…
We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte…
Low-temperature scanning tunneling microscopy is used here to study dynamic bonding of gold atoms on surfaces under low coordination conditions. In the experiments, using an atomically-sharp gold tip, a gold adatom is deposited onto a gold…
X-ray photoemission and x-ray absorption spectroscopy are important techniques to characterize chemical bonding at surfaces and are often used to identify the strength and nature of adsorbate-substrate interactions. In this study, we judge…
We generate representative structural models of amorphous carbon (a-C) from constant-volume quenching from the liquid with subsequent relaxation of internal stresses in molecular dynamics simulations using empirical and machine-learning…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We theoretically consider specific adhesion of a fluctuating membrane to a hard substrate via the formation of bonds between receptors attached to the substrate and ligands in the membrane. By integrating out the degrees of freedom of the…
Although chemical bonding is the fundamental mechanistic bridge connecting atomic structure to macroscopic material properties, current data-driven materials science largely treats it as an implicit "black box". Existing machine learning…
We present linear ensembles of dangling bond chains on a hydrogen terminated Si(100) surface, patterned in the closest spaced arrangement allowed by the surface lattice. Local density of states maps over a range of voltages extending…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We investigate the effective properties (conductivity, diffusivity and elastic moduli) of model random composite media derived from Gaussian random fields and overlapping hollow spheres. The morphologies generated in the models exhibit low…
Layered materials span a very broad range of solids ranging from van der Waals materials to highly complex crystal structures such as clays. They are commonly believed to have highly anisotropic properties, which is essentially attributed…