Water modeling
From SuperMe
Project Description: Water Modeling in Confined Systems
Water is absolutely necessary for life on earth, and water molecules possess some amazing properties that require a great deal of research. This project researches one of these properties-the behavior of water molecules in confined systems versus the behavior of water molecules in the bulk phase. Water molecules can exist within hydrophobic ("water-repelling") protein cavities, and they play an important role in the functionality of these proteins. It is important to understand the behavior of water molecules in these situations, so the goal of this project is to model the behavior of water molecules in confined systems by utilizing the computing power of the University of Maine's supercomputer clusters.
Objective: To calculate and verify the chemical potential of water in the bulk phase, so that it can be compared to the chemical potential of water in confined systems
- Gain some background knowledge in the chemistry involved in the project
- Learn about prior research done on this topic
- Learn to use Amber, a software package that can do molecular dynamics simulations on biomolecules
- Use Amber on the supercomputers to create a model of water molecules in the bulk phase
- Run the simulation of the model
- Analyze the results of the simulation to calculate the chemical potential of water in the bulk phase
Research Progress
Project Abstract
Due Wednesday, June 2, 2008
Modeling Water to Calculate It’s Chemical Potential in the Bulk Phase
Daniel Dorman
The Department of Chemistry and the Department of Electrical and Computer Engineering at the University of Maine in Orono
Abstract:
Water is necessary for life on earth, and it possesses some amazing properties that require a great deal of research. The ultimate goal of this project is to contribute to the research one of these properties-the behavior of water molecules in the confined systems of hydrophobic protein cavities and the role the water molecules play in the functionality of these proteins. However, in order to understand the behavior of water molecules in confined systems, it is first necessary to research the behavior of water in the bulk phase. Then the behavior of water in confined systems can be researched and then contrasted with the behavior of water in the bulk phase. This phase of the research will calculate and verify the chemical potential of water in the bulk phase. This will involve using the supercomputer clusters at the University of Maine to build a model and to simulate the experiments. The software package Amber will be utilized on the supercomputer for building an experimental model and completing the molecular dynamics simulations using the TIP3P water molecule model. The simulation will be done using the particle insertion/removal method to calculate the chemical potential of water in the bulk phase. The results of the simulation will then be analyzed to determine the chemical potential of water in the bulk phase.
Weekly Progress Reports
- Wednesday, June 11, 2008: Weekly Progress Report for 6-11-08
- Wednesday, June 18, 2008: Weekly Progress Report for 6-18-08
- Wednesday, June 25, 2008: Weekly Progress Report for 6-25-08
- Wednesday, July 2, 2008: Weekly Progress Report for 7-2-08
- Wednesday, July 9, 2008: Weekly Progress Report for 7-9-08
- Wednesday, July 16, 2008: Weekly Progress Report for 7-16-08
Project Poster
Final Project Report
Presentation
Related Research
Links
- NSF Grant for "Computer Simulations of Confined Systems"
- "Metastable water clusters in the the nonpolar cavities of the thermostable protein tetrabrachion"
- "Water Clusters in Nonpolar Cavities"
Research Participant
My name is Daniel Dorman (see my short bio on this page); I am working on this research under the direction of my research adviser, Professor Jay Rasaiah, and his post doctoral fellow, Dr. Guogang Feng.
Tentative Schedule
Week 1 (May 26 - May 30)-Introduction to the program, learn how to use supercomputers
Week 2 (June 2 - June 6)-Meet with research adviser, create project web page and project abstract, begin preliminary research
Week 3 (June 9 - June 13)-Create experimental model using Amber software package
Week 4 (June 16 - June 20)-Begin running simulations on the experimental model
Week 5 (June 23 - June 27)-Continue simulations, conduct background research
Week 6 (June 30 - July 4)-Continue simulations, conduct background research
Week 7 (July 7 - Junly 11)-Continue simulations, begin putting the final report together
Week 8 (July 14 - July 18)-Analyze data from the simulations
Week 9 (July 21- July 25)-Finish the final report
Week 10 (July 28 - August 1)-Finish the poster and prepare the final presentation