Related papers: Optimized Baxter Model of Protein Solutions: Elect…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
The passive rotation of rigid helical filaments is the propulsion strategy used by flagellated bacteria and some artificial microswimmers to navigate at low Reynolds numbers. In a classical 1976 paper, Lighthill calculated the `optimal'…
Constitutive equations are derived for the viscoelastic behavior of filled elastomers at isothermal loading with finite strains. A particle-reinforced rubber is thought of as a composite where regions with low concentrations of junctions…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory. This provides effective methods to…
The hydrodynamic conservation equations and constitutive relations for a binary granular mixture composed of smooth, nearly elastic, hard spheres with non-equipartition energies and different mean velocities are derived. This research is…
We construct the closed form solution of an elastic beam with axial load using Lie symmetry method. A beam with spatially varying physical properties such as mass and second moment of inertia is considered. The governing fourth order…
To obtain further insight on possible power law generalizations of Boltzmann equilibrium concepts, a stochastic collision model is investigated. We consider the dynamics of a tracer particle of mass $M$, undergoing elastic collisions with…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
We propose an elasticity theory for one and two dimensional arrays of globular proteins for which the free energy is affected by relative position and relative rotation between neighboring molecules. The kinematics of such assemblies is…
The so-called extended law of corresponding states, as proposed by Noro and Frenkel [J. Chem. Phys. 113, 2941 (2000)], involves a mapping of the phase behaviors of systems with short-range attractive interactions. While it has already…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
A variational model for describing the morphology of two-phase continua by allowing for the interplay between coherent and incoherent interfaces is introduced. Coherent interfaces are characterized by the microscopical arrangement of atoms…
The contact between a rigid Hertzian indenter and an adhesive broad-band viscoelastic substrate is considered. The material behaviour is described by a modified power law model, which is characterized by only four parameters, the glassy and…
The fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy. If all chemical problems can be…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…