Statistical Physics of Soft and Living Matter

6 EC

Semester 2, period 4

5354SPSL6Y

Owner Master Physics and Astronomy (joint degree)
Coordinator Edan Lerner
Part of Master Physics and Astronomy, track Advanced Matter and Energy Physics, year 1Master Physics and Astronomy, track Physics of Life and Health, year 1Master Physics and Astronomy, track Theoretical Physics, year 1Master Physics and Astronomy (joint degree), track Biophysics and Biophotonics, year 1

Course manual 2019/2020

Course content

This course focuses on advanced topics in statistical physics, that have particular importance and relevance to Soft Matter and Biophysics research. We will review (and, where necessary, introduce) the following subjects:

  1.  random walks, first passage processes, Levy flights 
  2.  Brownian motion and Langevin dynamics
  3.  Fokker-Planck equation: derivation and application
  4.  linear response near equilibrium, fluctuation-dissipation relations
  5.  regular attractors: fixed points, limit cycles and bifurcations
  6.  chaos
  7.  linear stability analysis
  8. probabilities at higher order: entropy and information theory

Contemporary research directions will be explored through group projects (that include a computational component) and motivated with particular analysis techniques. Group projects will culminate in short presentations towards the end of the course. While our focus is theoretical we will also emphasize important connections to modern experimental research. Students should expect exercises that involve numerical simulations and analysis.

 

 

 

Study materials

Literature

  • Pavel L. Krapivsky, Sidney Redner, and Eli Ben–Naim, 'A Kinetic View of Statistical Physics'.

  • Chaikin and Lubensky, 'Principles of condensed matter physics'.

  • M. E. Tuckerman, 'Statistical Mechanics - Theory and Molecular Simulation'.

  • Steven H. Strogatz, 'Nonlinear Dynamics and Chaos'.

  • James Sethna, 'Statistical Mechanics: Entropy, Order Parameters and Complexity'.

Syllabus

Software

  • Python

Objectives

At the end of the course, the student is able to:

  • Understand and apply a wide variety of statistical analysis tools to soft matter and biophysics problems.
  • Describe the interplay between theoretical and experimental soft matter and biophysics. 
  • Understand the relation between the intricacy and complexity of biophysical and soft matter systems and the scientific methodology employed in their investigation.

Teaching methods

  • Lecture
  • Presentation/symposium
  • Self-study
  • Working independently on e.g. a project or thesis

Learning activities

Activity

Number of hours

Hoorcollege

28

research project

15

Werkcollege

28

homework assignments

40

Attendance

Requirements concerning attendance (OER-B).

  • In addition to, or instead of, classes in the form of lectures, the elements of the master’s examination programme often include a practical component as defined in article 1.2 of part A. The course catalogue contains information on the types of classes in each part of the programme. Attendance during practical components is mandatory.

    • Assessment

    Item and weight Details

    Final grade

    0.5 (100%)

    research project presentations

    The assessment will be comprised of:

    • 2 in-class quizzes (2 x 12.5% = 25%)
    • 2 graded problem sets (2 x 12.5% = 25%)
    • presentation on research project (in pairs, 50%)

    Assignments

    During the course students will be given two assignments that involve both analytical and numerical work. Assignments are to be carried out entirely individually, although relevant group discussions are encouraged. The assignments should be submitted by the specified deadlines, and will be graded to amount to 2 x 12% = 25% of the final grade. Late submissions will be penalized. 

    Fraud and plagiarism

    The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

    Course structure

    Week class (i) class (ii)
    1 Introduction and non-chaotic dynamical systems I Non-chaotic dynamical systems II 
    2 Chaos I Chaos II
      Entropy and variability I, from thermodynamics and statistical physics to information theory Entropy and variability II, from thermodynamics and statistical physics to information theory
    4 Random walks - introduction and central limit theorem Levi stable laws, extremely value statistics, continuous-time random walks and subdiffision, first passage times
    5 Brownian motion The Fokker-Planck equation -- derivation
    6 The Fokker-Planck equation applications Linear response close to equilibrium
    7 project presentations project presentations
    8 project presentations  

    Additional information

    1. Participation in the quizzes is mandatory. No-shows will be given a zero grade. 
    2. Attendance to all presentation (i.e. not just your own) sessions is mandatory. Students who do not show up will be penalized. 
    3. Some working knowledge in programming (preferably in Python) is highly recommended. 

    Contact information

    Coordinator

    • Edan Lerner

    Staff

    • Greg Stephens