Simulation and Theory of Biological and Soft Matter Systems II - Interfaces, Self-Assembly and Networks

Syllabus

- Introduction to the cell (an Overview)

- Contents of the cell

- Structure and function of important organelles

- Selected biochemical mechanisms and pathways

- Gene transcription and translation

- Vesicle trafficking

- Biointerfaces

- Interfaces in solution

- Lifshitz theory

- Charge: Poisson-Boltzmann equation

- Success and limits of DLVO theory

- Hydration forces

- Surface tension and the Gibbs isotherm

- Depletion forces

- Self-Assembly

- Surfactants and their phase diagrams

- Lipid membranes

- Helfrich theory

- Phases in lipid membranes

- Membrane proteins

-Simulation of interfaces

- Coarse-grained molecular simulations

- Continuum models and their parameters

- Lattice models

- The protein expression point of view

- Expression analysis

- Gene regulatory networks, metabolic networks

- Modeling via ODEs

- Modeling via stochastic processes

- Examples in current research

- The top-down point of view

- Phenomenological cell models

- Epidemiological models

- Swarm behavior

- Social interactions and Ising models

Means of Instruction:

The entire class, its materials as the final exercise will be provided online for those students that wish to take the course online. The course will be weekly from the start of the summer semester. To acquire the credits, students will need to successfully complete an exercise project at home.

Annotation

This lecture takes a mesoscopic to macroscopic view. It introduces the theory of interfaces, membranes and self-assembly and some phenomenological models of biological systems.  Suitable for master students MFF UK and PřF UK, given in English, first part not a precondition.