相关论文: Effects of constraints in general branched molecul…
If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the Conformational Equilibrium Distribution (CED) of the model…
We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
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…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
Total energy shaping through interconnection and damping assignment passivity-based control (IDA-PBC) provides a powerful and systematic framework for stabilizing underactuated mechanical systems. Despite its theoretical appeal,…
The AdS/QCD models are believed to interpolate between low and high energy sectors of QCD. This belief is usually based on observations that many phenomenologically reasonable predictions follow from bounds imposed at high energies although…
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement…
Highly accurate measurements of quantum level energies in molecular systems provide a test ground for new physics, as such effects could manifest themselves as minute shifts in the quantum level structures of atoms and molecules. For the…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Optimization problems associated with the interaction of linked particles are at the heart of polymer science, protein folding and other important problems in the physical sciences. In this review we explain how to recast these problems as…
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Constrained molecular dynamics(CoMD) model, previously introduced for nuclear dynamics, has been extended to the atomic structure and collision calculations. Quantum effects corresponding to the Pauli and Heisenberg principle are enforced…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…