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United States Department of Agriculture

Agricultural Research Service

Related Topics


Location: Cotton Structure and Quality Research

2012 Annual Report

1a. Objectives (from AD-416):
Overall project objectives include: Collecting the best available information on the structures within the cotton fiber; Constructing fundamental models of these structures at different size scales; Providing additional fundamental models that have partial surfaces of hydrophobic molecules; and Monitoring moisture movement through the model structure during molecular dynamics simulations. Specific aspects of this work to be carried out by the CCRC include development of improvements of atomistic models of cotton cellulose and their interaction with water.

1b. Approach (from AD-416):
The main feature of this effort will be to examine the abilities of an improved version of the water model (TIP5P) and a parameter set that utilizes explicit lone pairs of electrons. The models will be examined for reproduction of known properties such as unit cell dimensions and retention of the geometric features of the cellulose structure. Distinctions in results between molecular dynamics and energy minimization will be explored. Necessary adjustments will be made to the modeling parameters to develop a final set. A model involving several smaller crystals will be devised to mimic a portion of a cotton fiber, and the behavior of interacting water will be observed. An ultimate goal, possibly not practical within the scope of this project, will be to gain insight on the division between “bound water” and “bulk water” and the sensitivity of the results to the exact details of the simulation. Deviations from the above plan are not necessarily expected but can be accommodated. For example, water models other than TIP5P might be more helpful, or other force field modifications other than the addition of explicit lone pairs may be more useful.

3. Progress Report:
This project, new in 2009, has separate efforts at Tulane University and at the University of Georgia (the effort detailed in this report). Both groups have substantial expertise in computerized molecular modeling. ARS scientists at Southern Regional Reseearch Center (SRRC) in New Orleans, LA provide the expertise in cotton cellulose and carry out related research as part of their normally funded project. A foundation for this work is the detailed crystal structure of native cellulose. It provides x, y and z coordinates for each of the atoms. The University of Georgia effort was directed to solving a problem observed in modeling cellulose crystals, namely, a twist occurs when the GLYCAM computerized molecular modeling force field developed by the University of Georgia group (and used by the Tulane University group) acts on model crystals. Normally, crystals are not twisted, so the models at Tulane University are used with otherwise undesirable constraints so that the twisting cannot happen. Many other possible issues with GLYCAM have been addressed during the year but the twisting was retained. Calculated diffraction patterns from the various models have been employed and a means of separating the effects on the pattern from the twist as opposed to other small discrepancies in the model were developed. During the final year of the project, the student at the University of Georgia advanced further with modeling the twisting and understanding the twisting of model cellulose crystals. The student at the University of Georgia is committed to publishing the results after the formal end of the project.

4. Accomplishments

Last Modified: 2/23/2016
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