Related papers: Structural Stability and Immunogenicity of Peptide…
Vesicles are important surrogate structures made up of multiple phospholipids and cholesterol distributed in the form of a lipid bilayer. Tubular vesicles can undergo pearling i.e., formation of beads on the liquid thread akin to the…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
The issue of the stability of Pickering emulsions is tackled at a mesoscopic level using dissipative particle dynamics simulations within the Adiabatic Biased Molecular Dynamics framework. We consider the early stage of the coalescence…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
In this paper, we model the configurations of a system of hard rods by viewing each rod in a cell formed by its neighbors. By minimizing the free energy in the model and performing molecular dynamics, where, in both cases, the shape of the…
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…
The packing of elastic bodies has emerged as a paradigm for the study of macroscopic disordered systems. However, progress is hampered by the lack of controlled experiments. Here we consider a model experiment for the isotropic…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
We analyze static properties of a strongly confined semiflexible polymer, i.e. either trapped in a closed space or compressed by external forces, in an athermal solvent. Like a flexible polymer case, we can resort to an analogy with the…
Polarized ferrofluids, lipid monolayers and magnetic bubbles form domains with deformable boundaries. Stability analysis of these domains depends on a family of nontrivial integrals. We present a closed form evaluation of these integrals as…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
We investigate the stability of growing vesicles using the formalism of nonequilibrium thermodynamics. The vesicles are growing due to the accretion of lipids to the bilayer which forms the vesicle membrane. The thermodynamic description is…
Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…