Monte Carlo

2

Folding of Small Proteins by Monte Carlo Simulations with Chemical Shift Restraints

http://pubs.acs.org
Year of publication: 
2009
Journal name: 
Journal of Physical Chemistry.
t has recently been shown that protein structures can be determined from nuclear magnetic resonance (NMR) chemical shifts using a molecular fragment replacement strategy. In these approaches, structural motifs are selected from existing protein structures on the basis of chemical shift and sequence homology and assembled to generate new structures. Read more »
dammerung's picture
Created by dammerung 2 years 42 weeks ago – Made popular 2 years 42 weeks ago
Category: Other   Tags:
2

Reconstruction and stability of secondary structure elements in the context of protein structure prediction.

http://www.ncbi.nlm.nih.gov
Year of publication: 
2009
Journal name: 
Biophys J.
Efficient and accurate reconstruction of secondary structure elements in the context of protein structure prediction is the major focus of this work. We present a novel approach capable of reconstructing alpha-helices and beta-sheets in atomic detail. The method is based on Metropolis Monte Carlo simulations in a force field of empirical potentials that are designed to stabilize secondary structure elements in room-temperature simulations. Read more »
5

Shape and motility of a model cell: A computational study

http://scitation.aip.org
Year of publication: 
2004
Journal name: 
J. Chem. Phys.
We have investigated the shape, size, and motility of a minimal model of an adherent biological cell using the Monte Carlo method. The cell is modeled as a two dimensional ring polymer on the square lattice enclosing continuously polymerizing and depolymerizing actin networks. Our lattice model is an approximate representation of a real cell at a resolution of one actin molecule, 5 nm. The polymerization kinetics for the actin network are controlled by appropriate reaction probabilities which correspond to the correct experimental reaction rates. Read more »
jamali's picture
Created by jamali 2 years 42 weeks ago – Made popular 2 years 42 weeks ago
Category: Cytoskeletal Dynamics   Tags:
3

An Artificial Intelligence Approach for Modeling Molecular Self-assembly: Agent-based Simulations of Rigid Molecules

http://pubs.acs.org Agent-based simulations are rule-based models traditionally used for the simulations of complex systems. In this paper, an algorithm based on the concept of agent-based simulations is developed to predict the lowest energy packing of a set of identical rigid molecules. The agents are identified with rigid portions of the system under investigation, and they evolve following a set of rules designed to drive the system toward the lowest energy minimum. Read more »
jamali's picture
Created by jamali 2 years 43 weeks ago – Made popular 2 years 43 weeks ago
Category: Molecular Mechanotransduction   Tags:

Search

User login