Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
Hybrid (organic-inorganic) materials have emerged as a promising class of thermoelectric materials, achieving power factors exceeding those of either constituent. The mechanism of this enhancement is still under debate, and pinpointing the…
We introduce an extension of the lattice model of melting of semiflexible polymers originally proposed by Flory. Along with a bending penalty, present in the original model and involving three sites of the lattice, we introduce an…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…
We present an analytic study of the Potts model partition function on two different types of self-similar lattices of triangular shape with non integer Hausdorff dimension. Both types of lattices analyzed here are interesting examples of…
The boundaries of cooperative helix--coil transitions directly affect protein allostery and conformational dynamics, yet the physical origin of the persistent one-to-two-residue assignment ambiguity at these structural interfaces remains…
An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…
Much work has been devoted to analysing thermodynamic models for solid dispersions with a view to identifying regions in the phase diagram where amorphous phase separation or drug recrystallization can occur. However, detailed partial…
The phase behavior of colloidal particles embedded in a binary fluid is influenced by wetting layers surrounding each particle. The free energy of the fluid film depends on its morphology, i.e., on size, shape and connectivity. Under rather…
We report results from multicanonical simulations of poly-alanine. Homopolymers of up to 30 amino acids were considered and various thermodynamic quantities as a function of temperature calculated. We study the nature of the observed…
A new formulation for the modular construction of flexible multibody systems is presented. By rearranging the equations for a flexible floating body and introducing the appropriate canonical momenta, the model is recast into a coupled…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
In our previous paper [H. K., J.Stat.Mech.(2015) P08020], we investigated an interacting-particle model with infinite-range cosine potentials, and derived the partition function which shows solid-fluid phase transition by exact calculation.…
We introduce the geometric structure underlying the port-Hamiltonian models for distributed parameter systems exhibiting moving material domains.
Metallic open cell foams have multiple applications in industry, e. g. as catalyst supports in chemical processes. Their regular or heterogeneous microscopic structure determines the macroscopic thermodynamic and chemical properties. We…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…