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

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small:…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

We have performed a case study investigating a recently proposed scheme to obtain an effective pair potential for active Brownian particles [Farage et al., Phys. Rev. E 91, 042310 (2015)]. Applying this scheme to the Lennard-Jones…

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…

We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size $N$ onto stochastic networks, computing transition probabilities…

A first principle prediction of the binary nanoparticle phase diagram assembled by solvent evaporation has eluded theoretical approaches. In this paper, we show that a binary system interacting through Lennard-Jones (LJ) potential contains…

Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…

Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…

We investigate the minimization of the energy per point $E\_f$ among $d$-dimensional Bravais lattices, depending on the choice of pairwise potential equal to a radially symmetric function $f(|x|^2)$. We formulate criteria for minimality and…

The analysis of coevolution of residues in homologous proteins is a powerful tool to predict their native conformation. The standard framework in which coevolutionary analysis is usually worked out is that of equilibrium Potts models,…

A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…

The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this…

Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…

The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields vary appreciably across the molecular length scale. Rather than incrementally adding higher…

It is shown, that fitting parameters of a $\bar{K}N$ interaction model to different sets of experimental data can lead to physical conclusions which might provide a deeper insight into the physics of this multichannel system. The available…

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…

State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born-Oppenheimer approximation. The interaction potential was obtained…

We consider van der Waals interactions between in-plane fibers, where the computational model employs the Lennard-Jones potential and the coarse-grained approach. The involved 6D integral over two interacting fibers is split into a 4D…