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Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
The mitotic spindle partitions chromosomes during cell division by connecting the poles to kinetochores through microtubules (MTs). Their plus-ends, facing the chromosomes, exhibit dynamic instability, which is critical for proper…
Hydrogen bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which…
Path optimization methods have been widely used and highly successful for the analysis of chemical reactions. Yet, they can fail to capture intrinsically multidimensional features of potential energy surfaces (PES). We introduce the nudged…
A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the…
Electrical charging of parallel plates confining a model ionic liquid down to nanoscale distances yields a variety of charge-induced changes in the structural features of the confined film. That includes even-odd switching of the structural…
A numerical model able to simulate solid-state constrained sintering is presented. The model couples an existing kinetic Monte Carlo (kMC) model for free sintering with a finite element model (FEM) for calculating stresses on a…
A nonlinear dynamical system model that approximates a microscopic Gibbs field model for the yielding of a viscoplastic material subjected to varying external stress recently reported in [1] is presented. The predictions of the model are in…
The role of electrostatics on the interfacial properties of polyelectrolyte microgels has been discussed controversially in the literature. It is not yet clear if, or how, Coulomb interactions affect their behavior under interfacial…
The Menshutkin reaction is a methyl transfer reaction relevant in fields ranging from biochemistry to chemical synthesis. In the present work, energetics and solvent distributions for NH$_{3}$+MeCl and Pyr+MeBr reactions were investigated…
Active sites of molybdenum and tungsten enzymes, particularly mononuclear tungsten formate dehydrogenase (FDH) have been theoretically investigated towards their interaction with CO2. Obvious {\pi} interaction has been found between the 2e…
On Titan, methane (CH4) and ethane (C2H6) are the dominant species found in the lakes and seas. In this study, we have combined laboratory work and modeling to refine the methane-ethane binary phase diagram at low temperatures and probe how…
Comparisons of Gibbs ensemble Monte Carlo simulations with experimental data for the cage occupancies in N2 clathrate hydrates are performed to assess the accuracy of such simulations, to refine the effective potentials employed, and to…
When two or more atoms bind to a solid surface, the substrate can mediate an interaction between them. In this paper, we use density-functional theory to quantify the substrate-mediated pair interaction between two adatoms on a…
The electric field of biological membranes has long been treated as a one-dimensional quantity, defined solely by the component normal to the bilayer (E_VERT). Here, we present a bioelectronic platform that enables controlled generation of…
The stabilization of macromolecules is fundamental to developing biological formulations, such as vaccines and protein therapeutics. In this study, we employ coarse grained polymer models to investigate the impact of four sugars:…
Motivated by results from an earlier Brownian Dynamics (BD) simulation for the collapse of a single, stiff polymer in a poor solvent [B. Schnurr, F. C. MacKintosh, and D. R. M. Williams, Europhys. Lett. 51 (3), 279 (2000)] we calculate the…
For certain crystalline systems, most notably the organic compound EtMe3Sb[Pd(dmit)2]2, experimental evidence has accumulated of an insulating state with a high density of gapless neutral excitations that produce Fermi-liquid-like power…
Flowing liquid lithium is a promising fusion technology because it can provide a renewable Plasma-Facing Component (PFC) surface, modify recycling, support power exhaust, and potentially connect plasma-facing components with fuel recovery.…
The step edge barrier of a prototypical organic semiconductor molecule, 3,4,9,10-perylene-tetracaboxylic-dianhydride (PTCDA) has been analysed by means of calculations based on emperical potentials. The minimum energy path (MEP) has been…