UCSD Workshop on Biological Molecules, Cells, and Fluids. August 4 and 5, 2014.

Brainstorm Workshop on Biological Molecules, Cells, and Beyond

August 4 and 5, 2014
AP&M 6402, UCSD

Organizing Committee

  • Bo Li
  • J. Andrew McCammon
  • Yinglong Miao
  • Christopher Pierse
  • Nuo Wang
  • Yaojun Zhang
  • Shenggao Zhou

Topics

  • Accelerated molecular dynamics simulations
  • Advanced theories of biomolecular solvation
  • Electrostatic interactions
  • Hydrodynamic interactions
  • Diffusion and anomalous diffusion
  • Hybrid Brownian dynamics simulations and diffusion equation modeling
  • Energetics and kinetics of molecular binding with application to drug design
  • Lipid self assembly
  • Modeling E. Coli bacteria division
  • From stem cells to blood repopulation
  • Interfacial dynamics and fluctuations
  • New computational technologies

Schedule

Monday, August 4, 2014

8:30 - 8:55
Coffee and Bagels
8:55 - 9:00
Opening Remarks by Bo Li (Math, UCSD)
Morning Session.       Chair: Christopher Pierse
Time
Speaker
Title and Abstract
9:00 - 9:30
Gary Huber
(HHMI, & Biochem, UCSD)
New Development in Brownian Dynamics Simulations
Abstract
9:30 - 10:00
Zhenli Xu
(Math, Shanghai Jiaotong Univ.)
Self-Consistent Continuum Theory and Monte Carlo Simulations for Coulomb Many-Body Systems in Inhomogeneous Environments
Abstract
10:00 - 10:20
Break
10:20 - 10:50
Yaojun Zhang
(Physics, UCSD)
Anomalous Diffusion of DNA Elements and First-Passage Times of Genomic Interactions
Abstract
10:50 - 11:20
Alvaro Ruiz Martinez
(MAE, UCSD)
Hybrid-Multiscale Modeling of the E. Coli Bacteria Division Process
Abstract
11:20 - 11:40
Break
11:40 - 12:10
Tom Chou
(Biomath, UCLA)
Modeling and Clonal Analysis of Stem Cell-Mediated Blood Repopulation
Abstract
Afternoon Session.       Chair: Yaojun Zhang
Time
Speaker
Title and Abstract
1:30 - 2:00
Christopher Pierse
(Physics, UCSD)
Kinetics and Energetics of Biomolecular Folding and Binding
Abstract
2:00 - 2:30
Yinglong Miao
(HHMI, UCSD)
Accelerated Molecular Dynamics Simulations of Drug Binding to a Muscarinic G-protein Coupled Receptor and Hybrid Finite Element-Brownian Dynamics for Diffusion of Charged Particles
Abstract
2:30 - 3:00
Break
3:00 - 3:30
Lane Votapka
(Biochem, UCSD)
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Markov State Models
Abstract
3:30 - 4:00
Nuo Wang
(Chemistry, UCSD)
SMPB: A More Accurate Mean-Field Electrostatic Method for Biomolecules
Abstract

Tuesday, August 5, 2014

8:30 - 9:00
Coffee and Bagels
Morning Session.       Chair: Nuo Wang
Time
Speaker
Title and Abstract
9:00 - 9:30
Crystal Nguyen
(Pharmac. Sci., UCSD)
Understanding water Structure and Thermodynamics Using GIST (Grid Inhomogeneous Solvation Theory)
Abstract
9:30 - 10:00
Shenggao Zhou
(Math, UCSD)
VISM-LSM: A Software Package for Bimolecular Solvation Analysis
10:00 - 10:30
Break
10:30 - 11:00
Li Xiao
(Biochem, UC Irvine)
A Multi-Scale Method for Biomolecular Simulations
11:00 - 11:30
Hui Sun
(Math, UCSD)
Linear Stability of a Cylindrical Solute-Solvent Interface
Abstract
Afternoon Session.       Chair: Yinglong Miao
Time
Speaker
Title and Abstract
1:00 - 1:30
Ross Walker
(SDSC & Biochem, UCSD)
Lights, Computer, Action: Taking Molecular Simulation to 11, from GPUs to Lipid Self Assembly.
1:30 - 2:00
Li-Tien Cheng
(Math, UCSD)
New Computational Methods for Variational Implicit Solvation
2:00 - 2:30
Break
2:30 - 3:00
Zhiping Li
(Math, Peking Univ.)
Cavitation Computation in Nonlinear Elasticity
Abstract
3:00 - 3:30
Jianwei Che/Bo Li
(GNF/Math, UCSD)
Variational Implicit Solvation with Application to Identifying Protein-Ligand Binding Sites
Abstract
3:30
Adjourn