相关论文: Differences in Solution Behavior among Four Semico…
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane…
We use molecular dynamics simulations to study the thermodynamics and kinetics of alanine dipeptide isomerization at the air-water interface. Thermodynamically, we find an affinity of the dipeptide to the interface. This affinity arises…
In this work we study and contrast implicit solvation models against explicit atomistic, quantum mechanical models in the description of the band alignment of semiconductors in aqueous environment, using simulations based on density…
Soft supramolecular materials are promising for the design of innovative and highly tunable adhesives. These materials are composed of polymer chains functionalized by strongly interacting moieties, sometimes called "stickers". In order to…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
We studied the electronic and the structural properties of amino acids (alanine, glycine, and histidine) attached to graphene oxide (GO) by peptide bonding, via plane wave pseudopotential total-energy calculations within the local spin…
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
We present a unified model of compound semiconductor growth based on kinetic Monte Carlo simulations in tandem with new experimental results that can describe and predict the mechanisms for the formation of various types of nanostructures…
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD)…
The primary structures of peptides, originating from food proteins, affect their taste. Connecting primary structure to taste, however, is difficult because the size of the peptide sequence space increases exponentially with increasing…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic…
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…
The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved…
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…
Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular…
The behavior of quantum fluids (4He and H2) within nanopores is explored in various regimes, using several different methods. A focus is the evolution of each fluid's behavior as pore radius R is increased. Results are derived with the path…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…