2015 SJTU Summer School on Modeling and Analysis of Biological Network Dynamics

Brief Introduction

This short course provides a two-week long introduction to the field of Biological Network Dynamics. The summer school aims at introducing fundamentals as well as advanced topics in the dynamics of biological networks, including physiological regulation networks, chemical reaction network, blood vessel networks, and rare event dynamics on and of biological networks. The summer school will be followed by a two-day workshop on Biological Network Dynamics.

The 2015 SJTU short course is sponsored by the SJTU Department of mathematics, the SJTU Institute of Natural Sciences, the SJTU Zhiyuan College.


July 27 ~ August 7, 2015

Program Committee




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

Application and Registration

Please register online. [Apply Online]

Preference is given to, but not limited to, applicants with a basic understanding of ordinary differential equations and probability and a working knowledge of Matlab.

No registration fee. SJTU covers the lodging. Participants should cover their own meals.


Chemical Reaction Kinetics

By Tiejun Li,Peking University

Course Time:

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, analysis and simulations for chemical reaction kinetics (CKS).


  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.

By Hao Ge, Peking University

Course Time:


  1. Introduction1: Mathematical modeling of biochemical systems (1 lecture);
  2. Law of mass action and phase planes and (1 lecture);
  3. Stochastic modeling and chemical master equation (1 lecture);
  4. Stochastic processes around central dogma (1-2 lectures);
  5. Stochastic theory of nonequilibrium steady states in chemistry (2 lecture);
  6. Nonequilibrium landscape theory and related rate formulae (3-4 lecture).

Mathematical Modeling of Kidney Function: Autoregulation and Solute Transport

By Anita Layton, Duke University

Course Time:

The kidney is a major component of the excretory system. Its functions include the removal of waste products from the bloodstream, the regulation of body water balance and electrolytes balance, and the control of blood volume and blood pressure. Impairment of kidney functions is often associated with serious health conditions such as diabetes, hypertension, and congestive heart failure. Despite intense research, aspects of kidney functions remain incompletely understood. I will discuss how mathematical modeling techniques can be used to address a host of previously unanswered questions in renal physiology and pathophysiology: When deprived of water, how does a mammal produce a highly concentrated urine? Why is the mammalian kidney so susceptible to hypoxia, despite receiving ~25% of the cardiac output? What are the mechanisms underlying the development of acute kidney injury in a patient who has undergone cardiac surgery performed on cardiopulmonary bypass? What is the effect of inhibiting sodium-glucose transport, a novel treatment for reducing blood glucose levels in diabetes, on renal salt transport and oxygen consumption?”


Modelling Blood Flow in Vessel Networks of the Cardiovascular System

By Jordi Alastruey, Imperial College London

Course Time:

These lectures will show how to apply concepts of fluid dynamics to model blood flow in vessel networks of the cardiovascular system. We will start with a brief introduction to cardiovascular anatomy and physiology, focusing on concepts that are relevant to blood flow modelling. We will then introduce mathematical models of different degree of complexity: from zero-dimensional (0-D) lumped parameter models of the whole circulation, to one-dimensional (1-D) models of pulse wave propagation in vessel networks, to three-dimensional (3-D) fluid-structure interaction formulations. We will focus on modelling pulse wave propagation in arterial networks using the 1-D formulation. By analysing the nonlinear 1-D governing equations using the method of characteristics, we will describe theoretically the wave nature of blood flow and the pulse. Lastly, we will study several pulse wave analysis tools (based on the 1-D formulation), which enable us to analyse the effect of physical properties of the cardiovascular system on blood pressure and flow pulse waves, under normal conditions and with disease.

Contact Us

Qing Chen (qingchen2013@sjtu.edu.cn)

Tel: 86-21-54742994
Fax: 86-21-54747161

Directions to INS