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Course, academic year 2023/2024
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Simulation and Theory of Biological and Soft Matter Systems II - Interfaces, Self-Assembly and Networks - NMMO568
Title: Simulation and Theory of Biological and Soft Matter Systems II - Interfaces, Self-Assembly and Networks
Guaranteed by: Mathematical Institute of Charles University (32-MUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2021
Semester: summer
E-Credits: 3
Hours per week, examination: summer s.:2/0, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: yes / unlimited
Key competences: 4EU+ Flagship 3
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Guarantor: Christoph Allolio, Ph.D.
Class: M Mgr. MOD > Volitelné
Mat. modelování
Classification: Mathematics > Mathematical Modeling in Physics
Annotation -
Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)
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.
Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)

Israelachvili, Jacob N: Intermolecular and Surface Forces.

Stryer L, Berg JM, Tymoczko JL (2007): Biochemistry.

Last update: Christoph Allolio, Ph.D. (28.07.2021)
  • 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.

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