Modelling free energy of a rigid protein in solid water: Comparison between rigid-body motions and harmonic oscillators

Shuzo Yoshioki

Physica A: Statistical Mechanics and its Applications, 2004, vol. 331, issue 3, 552-570

Abstract: We test two methods to estimate a partition function of a system consisting of multi-atom molecules with intermolecular interaction. Our test case is a protein in water. The first method is based on rigid-body motions. The space in which the protein (bovine pancreatic trypsin inhibitor) would be moving is limited, so by making a correction to a partition function of a rigid body, we can obtain the function. The function depends on temperature and space. The second method is based on harmonic oscillators. Under the potential field produced by surrounding water molecules, a protein behaves like a set of harmonic oscillators. We obtain the partition function for the oscillators within a harmonic approximation. The function also depends on temperature and the strength of potential energy between the protein and waters. Comparison of the two methods indicates that the second method is better for estimating a partition function for a protein in water.

Keywords: Partition function; Rigid-body motion; Harmonic oscillator; A protein in water; Free energy; Bovine pancreatic trypsin inhibitor (BPTI) (search for similar items in EconPapers)
Date: 2004
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0378437103009099
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:331:y:2004:i:3:p:552-570

DOI: 10.1016/j.physa.2003.09.039

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().