相关论文: Folding Lennard-Jones proteins by a contact potent…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
We investigate, within a local density functional theory formalism, the interactions between like-charged polyions immersed in a confined electrolyte. We obtain a simple condition for a repulsive effective pair potential, that can be…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
The pion-mass-dependent nucleon-nucleon ($NN$) potentials in term of one-pion exchange and contact terms are obtained from the latest lattice QCD simulations of two-nucleon system, which employ the forms of leading order (LO) $NN$ potential…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
Accurate estimation of surface wettability for various degrees of hydrophobicity becomes increasingly important in the molecular design of membrane. In this paper, we develop simple yet physically realistic model for estimating contact…
We revisit an old tree graph formula, namely the Brydges-Federbush tree identity, and use it to get new bounds for the convergence radius of the Mayer series for gases of continuous particles interacting via non absolutely summable pair…
Accurate interaction potentials between microscopic components such as colloidal particles or cells are crucial to understanding a range of processes, including colloidal crystallization, bacterial colony formation, and cancer metastasis.…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
Microscopic optical potentials for low energy proton reactions have been obtained by folding density dependent M3Y interaction derived from nuclear matter calculation with densities from mean field approach to study astrophysically…
The supercooled dynamics of a Lennard-Jones model liquid is numerically investigated studying relevant points of the potential energy surface, i.e. the minima of the square gradient of total potential energy $V$. The main findings are:…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
For the well-known model of a system of N particles with interaction (N-body problem), we consider the spatial problem of finding the minimum of the function of the kinetic energy of a system on its phase space under conditions on its size…
The Landau-de Gennes free energy is used to study theoretically the interaction of parallel cylindrical colloidal particles trapped at a nematic-isotropic interface. We find that the effective interaction potential is non-monotonic. The…
We take a bottom-up approach to find the interaction potential between the $AdS$ black hole molecules under mean-field approximation. We start with the equation of state of dyonic $AdS$ black holes in fixed charge ensemble and use the…
In Molecular Dynamics (MD), the forces applied to atoms derive from potentials which describe the energy of bonds, valence angles, torsion angles, and Lennard-Jones interactions of which molecules are made. These de finitions are classic;…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
In the paper we consider non-relativistic analog of the Nambu-Jona-Lasinio model and demonstrate, by this most simplified example, the method of dynamical mappings of Heisenberg fields on "physical" fields. We obtain the expressions for one…