Related papers: Structural Stability and Immunogenicity of Peptide…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
We consider the problem of embedding a dynamic network, to obtain time-evolving vector representations of each node, which can then be used to describe changes in behaviour of individual nodes, communities, or the entire graph. Given this…
The goal of this paper is to investigate some rigidity properties of stable solutions of elliptic equations set on manifolds with boundary. We provide several types of results, according to the dimension of the manifold and the sign of its…
Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
We study the mechanism of the `pearling' instability seen recently in experiments on lipid tubules under a local applied laser intensity. We argue that the correct boundary conditions are fixed chemical potentials, or surface tensions…
Membrane deformation inside living cells is crucial for the proper shaping of various intracellular organelles and is necessary during the fission/fusion processes that allow membrane recycling and transport (e.g. endocytosis). Proteins…
We incorporate the role of free volume in the density function of the amorphous structure and study its effects on the stability of such structures. The Density Functional Theory is used to explore this ``Free Volume Model'' of the…
We analyse the asymptotic behaviour of a nonlinear mathematical model of cellular proliferation which describes the production of blood cells in the bone marrow. This model takes the form of a system of two maturity structured partial…
A recent paper by Huang et al. [Computer Physics Communications 207, 123 (2016)] thoroughly analyzed the Finite Grid Instability(FGI) and spectral fidelity of standard Particle-In-Cell (PIC) methods. Numerical experiments were carried out…
Many charged polymers, including nucleic acids, are locally stiff. Their bending rigidity -- quantified by the persistence length --, depends crucially on Coulombic features, such as the ionic strength of the solution which offers a…
The aim of this paper is to prove that under some conditions the modified entropy equation is stable on its one-dimensional domain.
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…
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…
Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales…
Filopodia are long, finger-like membrane tubes supported by cytoskeletal filaments. Their shape is determined by the stiffness of the actin filament bundles found inside them and by the interplay between the surface tension and bending…
Particles confined in droplets are called compound particles. They are encountered in various biological and soft matter systems. Hydrodynamics can play a decisive role in determining the configuration and stability of these multiphase…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to…