Calculation of the entropy and free energy from Monte Carlo simulations of a peptide stretched by an external force
Article Abstract:
A study to calculate the absolute entropy, S, and free energy, F, from a trajectory generated by a simulation technique using hypothetical scanning Monte Carlo was conducted. The results for F and S are accurate and significantly better than those obtained by the quasi-harmonic approximation and the local states but the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
User Contributions:
Comment about this article or add new information about this topic:
Effects of quenched and annealed macromolecular crowding elements on a simple model for signaling in T lymphocytes
Article Abstract:
The effects of different extents of crowding on biochemical reactions that involve both membrane proteins and cytosolic molecules is studied by investigating simplified version of signaling in T lymphocytes using a Monte Carlo algorithm. Results show that the effects of macromolecular crowding on signal transduction can be different depending on whether it is fast or slow signal transduction.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
Comment about this article or add new information about this topic:
Long range corrections in inhomogeneous simulations
Article Abstract:
An improved method for the treatment of long-range corrections in molecular simulations of inhomogeneous systems with planar interfaces is presented. To evaluate the quality of the approach, Monte Carlo simulations of the Lennard-Jones fluid are performed in the temperature range T* belongs to (0.7, 1.25).
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
Comment about this article or add new information about this topic:
- Abstracts: Intermolecular potential to represent collisions of protonated peptide ions with fluorinated alkane surfaces. Ab initio study of long-distance electron tunneling in a model peptide system
- Abstracts: Selectivity of 18-crown-6 between Cs(super +) and Rb(super +) ion: solvent effect by a Monte Carlo simulation study
- Abstracts: Evolution of the interface and metal film morphology in the vapor deposition of Ti on hexadecanethiolate hydrocarbon monolayers on Au
- Abstracts: Investigation of the influence of spacer arm on the structural evolution of affinity ligands supported on agarose
- Abstracts: Comparative study on solvation free energy expression in reference interaction site model integral equation theory