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We present a theoretical analysis of a simple model of the depinning of an anchored semiflexible polymer from a fixed planar substrate in (1+1) dimensions. We consider a polymer with a discrete sequence of pinning sites along its contour.…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…
The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We explore the impact of hydrodynamic interactions on the conformational and dynamical properties of wet tangentially-driven active polymers using multiparticle collision dynamics simulations. By analyzing active filaments with varying…
The (isothermic) compressibility of lattice knots can be examined as a model of the effects of topology and geometry on the compressibility of ring polymers. In this paper, the compressibility of minimal length lattice knots in the simple…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
A binary mixture of oppositely charged components confined to a plane such as cationic and anionic lipid bilayers may exhibit local segregation. The relative strength of the net short range interactions, which favors macroscopic…
A new approach to chemical bonding is introduced in order to provide an improved understanding of the connection between basic quantum mechanics and the covalent pair bond. It's focus is on the fact that the energy of the bond is largely…
Solutions of interacting linear polymers are mapped onto a system of ``soft'' spherical particles interacting via an effective pair potential. This coarse-graining reduces the individual monomer-level description to a problem involving only…
The Langevin Equation for cooperative dynamics represents the dynamics of polymer melts with chains of increasing degree of polymerization, covering the full range of behavior from the unentangled to the entangled regime. This equation…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…
We consider a kinetic relaxation model and an associated macroscopic scalar nonlinear hyperbolic equation on a network. Coupling conditions for the macroscopic equations are derived from the kinetic coupling conditions via an asymptotic…
We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear…
We present a numerical study of the slip link model introduced by Likhtman for describing the dy- namics of dense polymer melts. After reviewing the technical aspects associated with the implemen- tation of the model, we extend previous…
When injected through a contraction, high molecular weight polymer solutions exhibit a sharp increase of apparent viscosity which originates from stretching polymer chains above a critical extension rate. This chain stretching can also…
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…
We examine how the shape of cells and the geometry of experiment affect the reaction-diffusion kinetics at the binding between target and probe molecules on molecular biochips. In particular, we compare the binding kinetics for the probes…
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…