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2014 Summer School of Biological Mathematics

Introduction

The 2014 summer school of biological mathematics will be hosted from July 14 - July 27, 2014 by the Institute of Natural Sciences at Shanghai Jiao Tong University, China. Top experts will be invited to deliver lectures on mathematical modeling, theoretical analysis, scientific computing, and applications in biology and life sciences. The summer school aims to introduce important research topics with modern styles and to provide participants new perspectives in the frontiers of biological mathematics and applied mathematics.

Organizers

Application and Registration

Please send your application form (as e-mail attachment) to yingyunie@sjtu.edu.cn by July 12, 2014, with the subject line “2014 Summer School of Biological Mathematics Application — Your name”. Approved applicants will be notified by email. Please print the application form with signature, and submit it on registration day.

[Application Download]

Participants should cover their own lodging and meals.

Instructor

Hao Ge, Peking University

Outline

  1. Introduction1: Mathematical modeling of biochemical systems;
  2. Introduction2: Stochastic models in biology and its applications;
  3. Stochastic processes around central dogma;
  4. Stochastic theory of nonequilibrium steady states in chemistry;
  5. Nonequilibrium landscape theory and related rate formulae;
  6. Fluctuation theorems and related single-molecule observations;
  7. Related topics on diffusion and langevin dynamics;

Schedule of lectures

Every morning (two and half hours’ lecture plus half hour discussion) from July 14th to July 19th.

Mathematical introduction to the chemical kinetic modeling and simulation

Instructor

Tiejun Li, Peking University

Abstract

The chemical reaction kinetics has been widely used in the modeling for systems biology. This lecture series are designed to introduce the basic mathematical modeling and simulations for chemical reaction kinetics (CKS).

Outline

  1. Basic ODE modeling for cellular systems;
  2. Stochastic modeling, SSA and tau-leaping;
  3. Large volume limit and fluctuations;
  4. Multiscale analysis and algorithms for CKS;
  5. Rare events in CKS;
  6. Biological applications;
  7. Outlook.

Schedule of lectures

from July 24th to July 27th.

Computation of Saddle Point and its Applications in Systems Biology

Instructor

Lei Zhang, Peking University

Outline

  1. Rare events and transition state theory
    • Introduction of rare events
    • Transition state theory
    • Large Deviation theory
  2. Numerical methods for computing saddle point and minimum energy path
    • String method
    • Nudged elastic band method
    • Gentlest ascent dynamics
    • Shrinking dimer dynamics
  3. Applications in biology
    • Noise attenuation during the development of spatial pattern
    • Phase field modeling of cell ingression
    • Modeling cell lineage and pattern formation in intestinal crypts

Schedule of lectures

Every afternoon (two and half hours’ lecture plus half hour discussion) from July 14th to July 19th.

Biophysical Modeling of Molecular Motor

Instructor

Yunxin Zhang, Fudan University

Outline

  1. Forces related to molecular motor
    • Mechanical Force
    • Thermal Forces and Diffusion
    • Chemical Force
  2. Models for single molecular motor
    • Brown Ratchet Model
    • Discrete Model (Chemical Master Equation)
    • Continuous model (Fokker-Planck Equation)
    • Energy Efficient and Effective Diffusion Coefficient
    • Synthetic Light Driven Molecular Motor
  3. Cargo Motion in Cells by Multiple Molecular motors
    • Cargo Motion by One Motor Species
    • Tug-of-war Model for Cargo Motion by Two Motor Species
    • Models with Inter-motor Interaction
    • Cargo motion with memory
  4. TASEP for Motor Traffic
    • Existence of Domain Wall and Boundary Layer
    • TASEP of Motor with Internal States
    • TASEP properties with finite length of Microtubule

Schedule of lectures

From July 21th to July 23th. For each day, two and half hours’ lecture plus half hour discussion both in the morning and in the afternoon.

Tentative Schedule

Date Time Speaker Title
14-Jul 9:00-12:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
  14:00-17:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
15-Jul 9:00-12:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
  14:00-17:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
16-Jul 9:00-12:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
  14:00-17:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
17-Jul 9:00-12:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
  14:00-17:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
18-Jul 9:00-12:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
  14:00-17:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
19-Jul 9:00-12:00 Lei Zhang Computation of Saddle Point and its Applications in Systems Biology
  14:00-17:00 Hao Ge Stochastic dynamics in cell biology and related nonequilibrium dynamics
21-Jul 9:00-12:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
  14:00-17:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
22-Jul 9:00-12:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
  14:00-17:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
23-Jul 9:00-12:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
  14:00-17:00 Yunxin Zhang Biophysical Modeling of Molecular Motor
24-Jul 9:00-11:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
  14:00-16:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
25-Jul 9:00-11:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
  14:00-16:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
26-Jul 9:00-11:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
  14:00-16:45 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation
27-Jul 9:00-11:30 Tiejun Li Mathematical introduction to the chemical kinetic modeling and simulation

Venue

Room 601, Pao Yue-Kong Library, Minhang Campus, Shanghai Jiao Tong University

Contact Us

Sandy NIE (yingyunie@sjtu.edu.cn)

Phone/Fax

86-21-54747161 86-15921910571

Directions to INS

http://ins.sjtu.edu.cn/for-vistors/arrive.html