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

Nonlocal coordinate space optical potentials for the scattering of 65 MeV protons from nuclei ranging in mass from 6Li to 238U have been defined by folding a complex, medium dependent effective interaction with the density matrix elements…

The real part of the optical potential for the nucleon-nucleus scattering at lower energies (E_i<100MeV) has been calculated including nucleonic and mesonic form factors by a double folding approach. Realistic density- and energy-dependent…

The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…

Results of electron-induced one- and two-nucleon hard knockout reactions, $A(e,e'p)$ and $A(e,e'pN)$, in kinematics sensitive to nuclear short-range correlations, are studied using the nuclear contact formalism. A relation between the…

A 3D Cellular Automaton model developed by the authors to deal with the dynamics of N-body interactions has been adapted to investigate the head-on collision of two identical bound clusters of particles, and the ensuing process of…

We study a non-relativistic particle subject to a three-dimensional spherical potential consisting of a finite well and a radial $\delta$-$\delta'$ contact interaction at the well edge. This contact potential is defined by appropriate…

Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…

We solve the Lippman-Schwinger equation (LSE) with a kernel that includes a regular finite-range potential and additional contact terms with derivatives. We employ distorted wave theory and dimensional regularization, as proposed in Physics…

We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…

We consider a discrete-continuum model of a biomembrane with embedded particles. While the membrane is represented by a continuous surface, embedded particles are described by rigid discrete objects which are free to move and rotate in…

Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…

A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…

Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…

By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…

Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors…

We describe a procedure to systematically improve direct diagonalization results for few-particle systems trapped in one-dimensional harmonic potentials interacting by contact interactions. We start from the two-body problem to define a…