skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Visualizing Structure and Dynamics of Disaccharide Simulations

Abstract

We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

Authors:
; ; ;
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy Biomass Program
OSTI Identifier:
1042511
DOE Contract Number:
AC36-08GO28308
Resource Type:
Conference
Resource Relation:
Conference: American Chemical Society. Abstracts of Papers of the 243rd ACS National Meeting, 25-29 March 2012, San Diego, California; Related Information: Abstract No. CARB-136
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; CELLOBIOSE; DISACCHARIDES; LACTOSE; MOLECULAR DYNAMICS METHOD; SIMULATION; SOLVENTS; TRANSFORMATIONS; Chemical and Biosciences; Bioenergy

Citation Formats

Matthews, J. F., Beckham, G. T., Himmel, M. E., and Crowley, M. F. Visualizing Structure and Dynamics of Disaccharide Simulations. United States: N. p., 2012. Web.
Matthews, J. F., Beckham, G. T., Himmel, M. E., & Crowley, M. F. Visualizing Structure and Dynamics of Disaccharide Simulations. United States.
Matthews, J. F., Beckham, G. T., Himmel, M. E., and Crowley, M. F. Sun . "Visualizing Structure and Dynamics of Disaccharide Simulations". United States. doi:.
@article{osti_1042511,
title = {Visualizing Structure and Dynamics of Disaccharide Simulations},
author = {Matthews, J. F. and Beckham, G. T. and Himmel, M. E. and Crowley, M. F.},
abstractNote = {We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2012},
month = {Sun Jan 01 00:00:00 EST 2012}
}

Conference:
Other availability
Please see Document Availability for additional information on obtaining the full-text document. Library patrons may search WorldCat to identify libraries that hold this conference proceeding.

Save / Share:
  • Classical and quantum molecular dynamics simulation methods for investigations of the energetics, structure and dynamics of small clusters are opening new avenues for detailed microscopic studies of these systems. We review the simulation techniques and demonstrate their versatility, and richness of information which they afford, via studies of isomerization and melting transformations in small clusters, modes of electron localization in clusters and the dynamics of fragmentation and energy pathways following an electronic excitation of rare-gas clusters.
  • Lipid bilayers form the foundation of biological membranes. As such, they have important roles in mediating the transport of small molecules into cells and maintaining the structure of transmembrane proteins. Realistic simulations must comprise many thousands of atoms and explicit water molecules. Pertinent biological timescales range from tens of picoseconds to seconds. We will discuss these timescales as they relate to the transport of small molecules within the bilayer construct. The timescales of movement of trans-membrane protein helics will also be addressed. Due to their size and long timescales, methods that allow for simulation of large systems for long periodsmore » will be important advances. We will discuss simulations of these systems on massively-parallel machines. Further, the highly-charged nature of lipid molecules requires that long-range coulombic interactions be employed. We will discuss the application of long cutoffs, Ewald sum, and the particle-particle-particle mesh method.« less
  • The local structure at individual ion sites in simple and multicomponent glasses is simulated using methods of molecular dynamics. Computer simulations of fluoroberyllate glasses predict a range of ion separations and coordination numbers that increases with increasing complexity of the glass composition. This occurs at both glass forming and glass modifying cation sites. Laser-induced fluorescence line-narrowing techniques provide a unique probe of the local environments of selected subsets of ions and are used to measure site to site variations in the electronic energy levels and transition probabilities of rare earth ions. These and additional results from EXAFS, neutron and x-raymore » diffraction, and NMR experiments are compared with simulated glass structures.« less