Related papers: Structural Stability and Immunogenicity of Peptide…
Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Genetic robustness, the preservation of evolved phenotypes against genotypic mutations, is one of the central concepts in evolution. In recent years a large body of work has focused on the origins, mechanisms, and consequences of robustness…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The tensile force along a cylindrical lipid bilayer tube is proportional to the membrane's bending modulus and inversely proportional to the tube radius. We show that this relation, which is experimentally exploited to measure bending…
This research paper comprehensively explores the effects of molecular weight and chain architecture on the interfacial and thermodynamic properties of cyclic and linear polymer blends. Utilizing the Kremer-Grest bead-spring model, the study…
This paper focuses on the study of the Filament Based Lamellipodium Model (FBLM) and the corresponding Finite Element Method (FEM) from a numerical point of view. We study fundamental numerical properties of the FEM and justify the further…
The formation of amyloid fibrils comprising amyloid $\beta$ (A$\beta$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$\beta$ structure at the fibril end using the density…
We investigate the dynamics of cellular solidification patterns using three-dimensional phase-field simulations. The cells can organize into stable hexagonal patterns or exhibit unsteady evolutions. We identify the relevant secondary…
The main purpose of this work is to provide a non-local approach to study aspects of structural stability of 3D Filippov systems. We introduce a notion of semi-local structural stability which detects when a piecewise smooth vector field is…
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…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
Given a power grid and a transmission (coupling) strength, basin stability is a measure of synchronization stability for individual nodes. Earlier studies have focused on the basin stability's dependence of the position of the nodes in the…
We investigate the steady states and dynamical instabilities resulting from ``particles'' depositing on (fusion) and pinching off (fission) a fluid membrane. These particles could be either small lipid vesicles or isolated proteins. In the…
Peptide compounds demonstrate considerable potential as therapeutic agents due to their high target affinity and low toxicity, yet their drug development is constrained by their low membrane permeability. Molecular weight and peptide length…