Global minimization algorithm is indispensable to solving the protein folding problem based upon thermodynamic hypothesis. Here we propose a pseudo potential function, contact difference(CD), for simulating empirical contact potential functions and testing global minimization algorithm. The present paper covers conformational sampling and global minimization algorithm called BML03, based upon Monte Carlo and simulated annealing, which is able to locate CD‘s global minimum and refold extended protein structures into one swith root mean square distance(RMSD) as small as 0.03 nm from the native structures. For empirieal contact potential functions, these results demonstrate that their global minimization problems may be solvable. 相似文献
We performed Monte Carlo simulations to study the destabilization processes of large neutral and flexible polymer chains
due to irreversibly adsorbed colloidal particles attached to the chains like beads on a necklace. The particles are modeled
as charged spherical units which interact with each other via repulsive electrostatic and attractive van der Waals (vdW) potentials.
The usual Monte Carlo search procedure is extended and carefully checked to completely sample the chain conformational space
and achieve dense conformations in the limit of both strong attractive and repulsive interaction potentials. Configurational
properties, such as the radius of gyration, the end-to-end length, and the Kuhn length, are calculated as a function of the
intensity of the vdW interactions and ionic strength values. It is observed that chains exhibit a new range of possible conformations
compared to the classical random walk and self avoiding walk chains or polyelectrolytes. In the limit of low salt concentration,
by gradually increasing vdW interactions, chains undergo a cascade of transitions from extended structures to dumbbells, from
dumbbells to pearl necklaces, and from pearl necklaces to collapsed coils. Because of strong competition between the vdW and
electrostatic forces, the distance along the chain between the interacting particles, and the sampling limitations, these
transitions are found to sample metastable domains and to depend on the initial conformations. To gain insight into the spatial
organization of the collapsed conformations, the pair correlation functions of both monomers and particles are calculated.
It is shown that collapsed conformations which are the result of strong particle–particle interactions exhibit two distinct
parts: a hard core mainly composed of particles and a surrounding polymeric shell composed of loops and tails. Possible effects
of such a collapsed transition on the kinetics of flocculation of a mixture containing large flexible chains and small adsorbing
colloidal particles are discussed.
Received: 26 July 1999 Accepted in revised form: 9 November 1999 相似文献
The kinetics of structural relaxation was simulated using the bond fluctuation model. Annealing of the system in the glassy state produces a clearly nonexponential decrease in the energy in a certain temperature interval. At lower temperatures, the decrease in energy takes place by successive small steps, due to the change of the energy of individual polymer chains that modify their conformation into small neighbourhoods. This cooperativity is behind the nonexponential behaviour shown by structural relaxation at higher temperatures. A second order Markov chain is able to reproduce the nonexponentiality with quite good agreement with the bond fluctuation simulated curves. Cooperativity comes from the fact that the transition probability of a polymer chain between two energy levels depends on the history of previous transitions that took place in its neighbourhood.
Coil-to-globule transitions are fundamental problems existing in polymer science for several decades; however, some features are still unclear, such as the effect of chain monomer interaction. Herein, we use Monte Carlo simulation to study the coil-to-globule transition of simple compact polymer chains. We first consider the finite-size effects for a given monomer interaction, where the short chain exhibits a one-step collapse while long chains demonstrate a two-step collapse, indicated by the specific heat. More interestingly, with the decrease of chain monomer interaction, the critical temperatures marked by the peaks of heat capacity shift to low values. A closer examination from the energy, mean-squared radius of gyration and shape factor also suggests the lower temperature of coil-to-globule transition. 相似文献
Abstract Reverse Monte Carlo (RMC) modelling has been used to create three dimensional particle configurations of condensed 4He that are consistent with diffraction data at ten different temperatures across the superfluid transition. Here it is shown that all observable changes in the data are within the experimental uncertainties, so no conclusions can be drawn concerning possible structural differences between normal fluid and superfluid. The local structure is found to be dominantly icosahedral. 相似文献
Summary: Crystallization, melting and annealing of nanoparticles of tetracontane were simulated via a Monte Carlo method on the second nearest neighbor diamond (2nnd) lattice by including short‐ and long‐range interactions. Nanoparticles can be obtained from an equilibrated tetracontane melt by increasing three periodic lengths to values that are effectively infinite. Nanoparticles, which contain 155 chains of C40H82, have been produced. After a deep quench from 473 K to 298 K, the crystallization process was investigated by the evolution of the density profile, fraction of bonds in the trans state, and the orientational order parameter. The vicinity of the center is less dense and less well ordered than portions of the nanoparticle located further from the center. The crystals form first in the region close to the surface. Each nanoparticle usually contains multiple crystalline domains. A melting phenomenon was observed at a temperature about 365 K when the nanoparticle crystal was heated. Annealing of the multiple domain crystal at 360 K can transform the structure to a more regular one without a grain boundary.
Snapshot of the final structure containing a single domain crystal after 20 million MCS. 相似文献
