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Physics of Life - From Motors to Nerve Pulses

Vak
2021-2022

Admission Requirements

You should know the basic concepts from statistical physics (such as: the laws of thermodynamics, random walks, equipartition theorem, entropy, free energies, partition function, Boltzmann distribution, Ising model, fluctuation-dissipation theorem) and the main structure of a cell (plasma membrane, cytoskeleton, nucleus). Most of this is covered in the course ”Fysica van Leven” in the first semester, and the "Statistical Physics" course of the study program. If you are missing part of this background, you may want to study chapters 1-7 of the book “Biological physics: energy, information, life” by Philip Nelson. We will have one programming exercise in Python.

The class is taught in English.

Description

In "Physics of Life - From Motors to Nerve Pulses" we explore how the dazzling complexity of life at the nanoscale is understood through key concepts of physics. We will see that entropy plays an essential role. We will discover how molecular machines can carry out diverse tasks in the cell, and understand how brain cells communicate through electrical impulses.

Course objectives

At the end of the course you will be able to:

  1. Analyze biological processes to identify where (statistical) physics comes into play
  2. Conceptualize biological processes such, that they get tracktable by physics concepts and methods
  3. Understand how physics dictates how the cellular machinery functions
  4. Understand that life descibes systems far from equilibrium

Specifically, five cellular/molecular processes will be treated:

  • Self-assembly of lipids and proteins; chemical reactions => chemical potential, grand canonical ensemble

  • DNA elasticity, helix-coil transition => Ising model, freely jointed chain

  • Allostery, cooperative binding => phase transitions

  • Molecular motors => Brownian ratchet, Michaelis-Menten kinetics

  • Action potentials in neurons => electrodiffusion

Mode of instruction

The background knowledge is aquired in self-study by reading the book and following the online video clips on BS. The interactive sessions are meant to reflect on that knowledge, place the knowledge into a biology or physics perspective, and joinedly solve extended problems.

Each topic is discussed in two sessions, hence in total there will be ten sessions. Before the session you are supposed to aquire the respective background knowledge through reading the book and working through the video clips on BS. In class there will be a brief recap on the topic before we will consolidate our knowledge in solving questions that highlight the underlying principles just learned. Exercise problems will be solved in order to deepen our understandig and apply the new knowledge.

Every week there will be a homework problem issued, which the student may use as self-assessment and preparation for the exam. One of those will be a computational problem that fits into the "Python leerlijn" of the study program.

Timetable

Schedule
For detailed information go to Timetable in Brightspace

Assessment method

An exam will be held at the end of the course. The format (written/oral) will be decided on after the first sessions.

Brightspace

Registration for Brightspace occurs via uSis by registration for a class activity using a class number

Reading list

Philip Nelson, "Biological Physics: Energy, Information, Life".
We will cover chapters 8-12.

Contact

Contact details lecturer: Prof.dr. T. Schmidt