Related papers: Local Interactions and Protein Folding: A Model St…
Very recently the Wood-Saxon (WS) type interaction in the single-folding potential approach are constructed to simulate the $ \phi{\text -}\alpha $ potentials. One set of the $ \phi{\text -}\alpha $ potentials are based on the first…
The Hubbard model on a semi-infinite three-dimensional lattice is considered to investigate electron-correlation effects at single-crystal surfaces. The standard second-order perturbation theory in the interaction U is used to calculate the…
Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical…
We construct matrix product steady state for a class of interacting particle systems where particles do not obey hardcore exclusion, meaning each site can occupy any number of particles subjected to the global conservation of total number…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We investigate the time-evolution of elastoplastic materials reinforced by randomly distributed long-range interactions. Starting from a rate-independent system on a discrete spring lattice that combines local linearized elasticity,…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
Microscopic models of quantum antiferromagnets are investigated on the basis of a mapping onto effective low energy hamiltonians. Lattice effects are carefully taken into account and their role is discussed. We show that the presence of an…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are…
Naturally occuring or man-made systems displaying periodic spatial modulations of their properties on a nanoscale constitute superlattices. Such modulated structures are important both as prototypes of simple nanotechnological devices and…
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…
Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices, all of these models assume central-force interactions between…
The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…