Related papers: Optimized Baxter Model of Protein Solutions: Elect…
In Part I of this two part series, we presented a multi-neighbor dependent contact model for adhesive elastic-plastic particles built upon the method of dimensionality reduction that is valid for the elastic and fully-plastic contact…
A theoretical approach has been undertaken in order to model the thermodynamic equilibrium of a vesicle adhering to a flat substrate. The vesicle is treated in a canonical description with a fixed number of sites. A finite number of these…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
In equilibrium, the collective behaviour of particles interacting via steep, short-ranged potentials is well captured by the virial expansion of the free energy at low density. Here, we extend this approach beyond equilibrium to the case of…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
We propose an improved effective-medium theory to obtain the concentration dependence of the viscosity of particle suspensions at arbitrary volume fractions. Our methodology can be applied, in principle, to any particle shape as long as the…
A general model covering a large variety of the so-called adhesive or cohesive, possibly also frictional, contact interfaces between visco-elastic bodies with inertia considered in a thermodynamical context is presented. A semi-implicit…
We propose and analyze a class of vectorial crystallization problems, with applications to crystallization of anisotropic molecules and collective behavior such as birds flocking and fish schooling. We focus on two-dimensional systems of…
A variational approach is employed to find stationary solutions to a free boundary problem modeling an idealized electrostatically actuated MEMS device made of an elastic plate coated with a thin dielectric film and suspended above a rigid…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The compressibility equation of state for a multicomponent fluid of particles interacting via an infinitely narrow and deep potential, is considered within the mean spherical approximation (MSA). It is shown that for a class of models…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We develop an analytical theory of adhesive interaction of viscoelastic spheres in quasistatic approximation. Deformations and deformation rates are assumed to be small, which allows for the application of the Hertz contact theory, modified…
We discuss structural and thermodynamical properties of Baxter's adhesive hard sphere model within a class of closures which includes the Percus-Yevick (PY) one. The common feature of all these closures is to have a direct correlation…
This papers shows the convergence of optimal control problems where the constraint function is discretised by a particle method. In particular, we investigate the viscous Burgers equation in the whole space $\mathbb R$ by using…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
The scaling property of the thermodynamic free energy ($\Phi$) of a system at global equilibrium has been examined using a real-time method known as the virial theorem. We demonstrate these scaling properties through a derived relation…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…