Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Abstract: S1.00002 : Scaffolding of peptides using a coarse-grained representation of residues with side chain and backbone nodes
Author:
Monte Carlo simulations are performed to study scaffolding of
peptides (KSL) on a cubic lattice. A residue is represented by
three backbone nodes (C-terminal, C-alpha, N-terminal) and a side
node connected to the central C-alpha node each connected by
fluctuating bond. A peptide is a chain of residues. A solvent
constituent is represented by a particle of the same size as that
of a node. Peptides and solvent are distributed randomly in the
cubic box with concentration $C_{p}$ and $C_{w}$ respectively.
Each residue interacts with other residues and solvent particles
via its side chain with the Lennard-Jones (LJ) potential where a
knowledge-based interaction matrix is used for the
residue-residue interaction. We examine local and global physical
quantities such as mobility and energy of each residue, radial
distribution function, and structure factor. We find that the
scaffolding of
peptides depends on the interaction strength and concentration of
the solvent. The structure factor shows multi-scale structure of
the aggregates.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2011.MAR.S1.2
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2021 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
1 Research Road, Ridge, NY 11961-2701
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700