相关论文: Folding Lennard-Jones proteins by a contact potent…

It is well-known that any Lennard-Jones type potential energy must have a periodic ground state given by a triangular lattice in dimension 2. In this paper, we describe a computer-assisted method that rigorously shows such global minimality…

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…

In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and…

It is well known that elastic effects can cause surface instability. In this paper, we analyze a one-dimensional discrete system which can reveal pattern formation mechanism resembling the "step-bunching" phenomena for epitaxial growth on…

Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…

Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…

We derive a novel formulation for the interaction potential between deformable fibers due to short-range fields arising from intermolecular forces. The formulation improves the existing section-section interaction potential law for in-plane…

In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and…

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…

The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…

In Molecular Dynamics (MD) simulations, interactions between water molecules and graphitic surfaces are often modeled as a simple Lennard-Jones potential between oxygen and carbon atoms. A possible method for tuning this parameter consists…

The dynamical correlations of a model consisting of particles constrained on the line and interacting with a nearest--neighbour Lennard--Jones potential are computed by molecular--dynamics simulations. A drastic qualitative change of the…

We study the convergence of the empirical measure of moderately interacting particle systems subject to singular forces derived by Lennard-Jones potential. Although the classical Lennard-Jones force is widely used in molecular dynamics,…

An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…

We introduced some contact potentials that can be written as a linear combination of the Dirac delta and its first derivative, the $\delta$-$\delta'$ interaction. After a simple general presentation in one dimension, we briefly discuss a…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…

Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…

The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…

The aim of this work is to provide further insight into the qualitative behavior of mechanical systems that are well described by Lennard-Jones type interactions on an atomistic scale. By means of $\Gamma$-convergence techniques, we study…