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Introduction
PROJECT DESCRIPTION
Introduction
Objectives of proposal
Impact of proposed work
Problems and proposed solutions
Multiscale molecular dynamics
Scalable hybrid Monte Carlo statistical sampling
Dissemination of methods and software complexity
Ion channel dynamics and function
Computational study of effectiveness of anti breast-cancer drugs
Specific aims and approach
Preliminary work
Multiscale algorithms for molecular dynamics
Linear instability in multiple time stepping
Nonlinear instabilities in multiple time stepping
The mollified method
Multiscale Semi-Implicit Constrained MD (M
USICO
)
Semi-implicit integrators
Splitting of time scales
Initial results (M
USICO
)
Discussion of method
Scalable biased hybrid Monte Carlo algorithm for statistical sampling
Scaling of plain hybrid Monte Carlo
Improved scaling of hybrid Monte Carlo by using shadow Hamiltonian
Dissemination of methods and software
Collaborative applications
Ion channel simulations
Computational study of effectiveness of anti breast-cancer drugs
Planned research activities
Multiscale integrators for dynamics of biomolecules
Year I: Nonlinear MOLLY filter
Year I: Time scale splitting
Multiscale Semi-Implicit Constrained MD (M
USICO
)
Year II: M
USICO
1
Year III: M
USICO
2
Years IV and V: M
USICO
3
Scalable biased Monte Carlo sampling algorithm for statistical sampling
Year I: Validation of new method
Years II and III: Multiple time stepping and fast electrostatics
Dissemination of Results
P
ROTO
M
OL
Development
Years I and II: Automated Empirical Optimization of Software
Collaborative applications
Permeation and gating in ion channels
Computational study of effectiveness of anti breast-cancer drugs
Educational contributions
Interdisciplinary training
Courses
Research Experiences for Undergraduates
NSF prior support
Bibliography
About this document ...
Jesus Izaguirre 2001-07-27
