Related papers: Discrete molecular dynamics simulations of peptide…
Molecular dynamics (MD) simulations were performed to study the cumulative bombardments of low-energy (60-200 eV) helium (He) atoms on tungsten (W) surfaces. The behaviour of He and the response of the W surface were investigated. The He…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
Finite-temperature properties of graphene monolayers under tensile stress have been studied by path-integral molecular dynamics (PIMD) simulations. This method allows one to consider the quantization of vibrational modes in these…
Short peptides with antimicrobial activity have therapeutic potential for treating bacterial infections. Mechanisms of actions for antimicrobial peptides require binding the biological membrane of their target, which often represents a key…
The study of vesicles in suspension is important to understand the complicated dynamics exhibited by cells in vivo and in vitro. We developed a computer simulation based on the boundary-integral method to model the three dimensional…
This paper considers the issue of modeling fractional data observed in the interval [0,1), (0,1] or [0,1]. Mixed continuous-discrete distributions are proposed. The beta distribution is used to describe the continuous component of the model…
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area…
Dynamical heterogeneities in a colloidal fluid close to gelation are studied by means of computer simulations. A clear distinction between some fast particles and the rest, slow ones, is observed, yielding a picture of the gel composed by…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model…
Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a…
Amphipathic peptides are considered promising antibiotics because of their ability to form pores in bacterial membranes. In two companion papers, we analyzed both experimentally and theoretically the mechanisms and consequences of the…
We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase…
Pancreatic $\beta-$cells regulate insulin secretion through complex oscillations, which are vital for glucose control and diabetes research. In this paper, an existing mathematical model of $\beta-$cell dynamics is analyzed using a…
Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules.…
We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
The adhesion bonds connecting a lipid bilayer to an underlying surface may undergo a condensation transition resulting from an interplay between a short range attractive potential between them, and a long range fluctuation-induced potential…
We present further evidence that gelation is an arrested phase separation in attractive colloid-polymer mixtures, based on a method combining confocal microscopy experiments with numerical simulations recently established in {\bf Nature…