2017 Summer School on Soft Matters and Biophysics

Brief Introduction

This summer school provides a week long introduction to the field of experiments, theories and simulations on soft-matter materials. Soft matters, including biomaterials, colloids and polymers, etc. are essential in our daily life. Understanding the structure, function and dynamics of soft matters as well as their interplay is crucial in the fields of biology, chemistry and material science, etc. Our program brings together internationally recognized experimentalists, modelers and theoreticians to illustrate the diverse approaches in this exciting field. The 2017 SJTU soft-matter summer school is sponsored by the SJTU Institute of Natural Sciences, and the National Natural Science Foundation of China.


July 3-6, 2017


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

Application and Registration

No registration fee. Please register online. Apply Online




July 3, 2017

Time Lecturer
09:00 - 10:30 Xiaolin Cheng
10:40 - 12:10 Jay X. Tang
14:00 - 15:30 Xiaolin Cheng
15:40 - 17:10 Jay X. Tang

July 4, 2017

Time Lecturer
09:00 - 10:30 Jay X. Tang
10:40 - 12:10 Xiaolin Cheng
14:00 - 15:30 Jay X. Tang
15:40 - 17:10 Xiaolin Cheng

July 5, 2017

Time Lecturer
09:00 - 10:30 Alexei Sokolov
10:40 - 12:10 Walter Schirmacher
14:00 - 15:30 Alexei Sokolov
15:40 - 17:10 Walter Schirmacher

July 6, 2017

Time Lecturer
09:00 - 10:30 Walter Schirmacher
10:40 - 12:10 Alexei Sokolov
14:00 - 15:30 Walter Schirmacher
15:40 - 17:10 Alexei Sokolov


Protein dynamics, allostery and function

Xiaolin Cheng, UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory

Protein dynamics is concerned with the transitions between different conformational states. These structural transitions occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and is directly linked to allosteric signaling and enzyme catalysis, thus critical to protein function. This lecture series will cover topics on understanding protein dynamics from both thermodynamic and dynamic perspectives. Specifically, we will discuss 1) molecular forces and conformational states in proteins; 2) conformational dynamics and protein allostery; 3) mapping allosteric pathways in proteins; and 4) Brownian and non-Brownian motions in proteins.

Lecture notes:

Lecture 1
Lecture 2
Lecture 3
Lecture 4

Theory of disordered condensed-matter systems

Walter Schirmacher, University of Mainz

The starting point of the lectures will be a general classification of disorder in condensed-matter systems, namely annealed and quenched disorder. An annealed-disordered system is in thermal equilibrium like a liquid in contrast to a quenched-disordered system, which has been brought out of equilibrium by the quenching process. A prominent example is a glass, which is produced by quenching a liquid while avoiding crystallization. Another example of quenched disorder is an ensemble of impurities in crystals. Following this introduction an overview over the present theoretical approaches to the liquid-glass transition will be given. The only existing analytical theory of the liquid-glass transition is the mode-coupling theory, which will be explained.

The second part will be devoted to diffusion in quenched-disordered systems. Two examples are the hopping motions of electrons in doped and amorphous semiconductors and diffusion of ions in ionic-conducting glasses.

The quenched disorder gives rise to peculiar temperature and frequency dependences. The temperature dependence of the conductivity is traditionally explained by Mott’s optimization argument and the percolation

model. A powerful theory of diffusion in disordered systems is the coherent-potential approximation (CPA) which will be explained in detail. It will be shown that the CPA includes the phenomenological optimization and percolation aspect, but includes the observed anomalous frequency dependence of the diffusivity/conductivity.

The third part will be devoted to vibrational anomalies in glasses. The lecture starts with an introduction of Debye’s theory of sound and thermal properties of solids. The anomalies in glasses are deviations from Debye’s prediction, namely an enhancement of the vibrational density of state. It will be shown that a mathematical corresponence between these anomalies and the anomalous diffusion in quenched-disordered systems can be established. Therefore in principle the theory for the diffusion could be taken over. However, the atomic displacements in a solid are vector quantities. Therefore we have to generalize Debye’s elasticity theory to include disorder. This leads to heterogeneous elasticity theory, which is solved in self-consistent Born approximation (SCBA) and CPA. The results of SCBA and CPA calculations are compared with simulations and experiments.

The fourth part of the lectures is devoted to Anderson localization of classical waves in disordered solids, namely sound waves and electromagnetic waves (light). Introductory remarks about Anderson localization of electrons will be given. Then a theory of Anderson localization based on heterogeneous elasticity theory will be formulated and solved. Via a correspondence of elasticity theory and the Maxwell equations this theory will be applied to localization of light. The experimental evidence for sound and light localization will be demonstrated.

Background literature

Original and Review papers

Lecture notes:

Lecture 1
Lecture 2
Lecture 3
Lecture 4

Polymer Dynamics

Alexei Sokolov, University of Tenessee, Knoxville & Oak Rigde National Laboratory

Molecular motions are the key to many macroscopic materials properties. Understanding fundamentals of molecular motion is crucial for rational design and synthesis of advanced materials for many applications, including energy and bio-tech related technologies. This course presents fundamentals of dynamics in liquid and solid materials. Although the course focuses mostly on polymeric materials, it will also discuss many general aspects of Dynamics in Soft Matter. The course starts from overview of various experimental techniques that probes dynamics on different time and length scales. Then it discusses different types of molecular motions from vibrations and fast picoseconds fluctuations, to structural and secondary relaxation and slower dynamic processes, such as the chain relaxation in polymers. Among various topics, it discusses glass transition and ageing phenomena, viscoelastic properties of materials and dynamics of biological macromolecules. Special focus is on the relationship between chemical structure, dynamics and macroscopic properties of polymers.

The course is designed for graduate or senior undergraduate students from Physics, Chemistry, Materials Science and Engineering. Although prior knowledge of polymers is helpful, it is not required.


Instructor’s notes with supplemental reading from current texts and journal articles.

Books (optional):

M.Doi, S.F.Edwards: “The Theory of Polymer Dynamics”.

Y.Grosberg, A.Khokhlov: “Statistical Physics of Macromolecules”.

J.Higgins, H.Benoit: “Polymers and Neutron Scattering”.

Lecture notes:

Lecture 1
Lecture 2
Lecture 3
Lecture 4

Dynamic patterns and collective motion of self-assembled biomolecular systems and motile bacteria

Jay X. Tang, Brown University

Biological entities from DNA and proteins to species derive their forms and functions from fundamental properties of the molecules they assemble from. They obey all the laws of physics applicable to complex fluid and interface environment, such as solution electrostatics, phase transitions, hydrodynamics, diffusion, transport, surface phenomena, adsorption, adhesion, etc. From the perspective of a biological physicist, most biological phenomena pertinent to dynamic pattern formation and collective motion can be accounted for by the physical properties involved in these systems. Therefore, understanding these physical properties underlining the biological phenomena provides us with huge benefits towards manipulating the biological process of relevance to environmental conditions for life, including human health.

Lecture Plan

I plan to cover a broad range of physics concepts with a focus on the pattern dynamics and collective motion of both self-assembled protein networks and live bacteria. The tentative plan is to cover the following topics in a series of four lectures.

Lecture 1: Bio-macromolecules and intermolecular interactions

Introductory Info: DNA, proteins, hydrogen bonding, ionic interaction, Biophysical properties: crosslinking, protein aggregation [1], phase transitions [2], etc.

Lecture 2: Collective dynamics in patterns formed by protein filaments and their motors

Biological background: actin and myosin [1, 2]; microtubules [3, 4], kinesin and dynein [5]

Physical properties: network rheology [6], self-assembled structures, growth and motion in assembled structures.

Lecture 3: Bacteria swimming motility

Biological background: flagellated bacteria, helical flagellum, flagellar motor [7], swimming speed, torque-speed curve, motor switching [8], swimming trajectories, run-and-tumble [7], forward-backward-flick [9], chemotaxis

Physics concepts: Low Reynold number hydrodynamics [10, 11], pusher and puller swimming modes [12], accumulation near surfaces [13, 14], swimming in non-Newtonian fluids, etc.

Lecture 4: Bacterial swarming motility, pattern evolution and collective motion

Phenomena: Colony growth on agar plate, bacterial swarming, pattern development, collective motion [15-17].

Physics concepts: viscous fingering, Marangoni flow, capillary flow, hyper-elastic buckling, Rayleigh Plateau instability, etc.

List of references for better understanding the lecture contents:

  1. Tang, J.X. and P.A. Janmey, Polyelectrolyte Nature of F-actin and Mechanism of Actin Bundle Formation. Journal of Biological Chemistry, 1996. 271: p. 8556-8563.

  2. Viamontes, J., P.W. Oakes, and J.X. Tang, Isotropic to nematic liquid crystalline phase transition of F-actin varies from continuous to first order. Phys Rev Lett, 2006. 97(11): p. 118103.

  3. Liu, Y., Y. Guo, J.M. Valles, Jr., and J.X. Tang, Microtubule bundling and nested buckling drive stripe formation in polymerizing tubulin solutions. Proc Natl Acad Sci U S A, 2006. 103(28): p. 10654-9.

  4. Sanchez, T., D.T. Chen, S.J. DeCamp, M. Heymann, and Z. Dogic, Spontaneous motion in hierarchically assembled active matter. Nature, 2012. 491(7424): p. 431-434.

  5. Sanchez, T., D. Welch, D. Nicastro, and Z. Dogic, Cilia-like beating of active microtubule bundles. Science, 2011. 333(6041): p. 456-459.

  6. Mizuno, D., C. Tardin, C.F. Schmidt, and F.C. MacKintosh, Nonequilibrium mechanics of active cytoskeletal networks. Science, 2007. 315(5810): p. 370-373.

  7. Berg, H.C., The rotary motor of bacterial flagella. Annu. Rev. Biochem., 2003. 72: p. 19-54.

  8. Morse, M., J. Bell, G. Li, and J.X. Tang, Flagellar Motor Switching in Caulobacter Crescentus Obeys First Passage Time Statistics. Physical review letters, 2015. 115(19): p. 198103.

  9. Son, K., J. Guasto, and R. Stocker, Bacteria can exploit a flagellar buckling instability to change direction. Nat Physics, 2013. 9: p. 494-498.

  10. Lauga, E. and T.P. Powers, The hydrodynamics of swimming microorganisms. Rep. Prog. Phys., 2009. 72: p. 096601.

  11. Purcell, E.M., Life at low Reynolds number. American journal of physics, 1977. 45(1): p. 3-11.

  12. Drescher, K., R.E. Goldstein, N. Michel, M. Polin, and I. Tuval, Direct measurement of the flow field around swimming microorganisms. Physical Review Letters, 2010. 105(16): p. 168101.

  13. Li, G., L.K. Tam, and J.X. Tang, Amplified effect of Brownian motion in bacterial near-surface swimming. Proc Natl Acad Sci U S A, 2008. 105(47): p. 18355-9.

  14. Li, G. and J.X. Tang, Accumulation of microswimmers near a surface mediated by collision and rotational Brownian motion. Phys Rev Lett, 2009. 103(7): p. 078101.

  15. Dunkel, J., S. Heidenreich, K. Drescher, H.H. Wensink, M. Bär, and R.E. Goldstein, Fluid dynamics of bacterial turbulence. Physical review letters, 2013. 110(22): p. 228102.

  16. Wu, Y. and H.C. Berg, Water reservoir maintained by cell growth fuels the spreading of a bacterial swarm. Proceedings of the National Academy of Sciences, 2012. 109(11): p. 4128-4133.

  17. Zhang, H.-P., A. Be’er, E.-L. Florin, and H.L. Swinney, Collective motion and density fluctuations in bacterial colonies. Proceedings of the National Academy of Sciences, 2010. 107(31): p. 13626-13630.

Lecture notes:

Lecture 1
Lecture 2
Lecture 3
Lecture 4

Contact us

June Yu

How to Arrive

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