Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)
An introduction to simulation techniques and theoretical concepts relevant for biological systems. The lecture
takes a molecular view and connects this approach to statistical physics. The course is given in English and is
suitable for master students at MFF UK and PřF UK.
Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)
Úvod do simulačních technik a teoretických konceptů relevantních pro studium biologických systémů. Přednáška propojuje molekulární pohled na tyto systémy se statistickou fyzikou. Kurz je vhodný pro magisterské studenty
matematicko-fyzikální a přírodovědecké fakulty a bude probíhat v angličtině.
Literature
Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)
Tuckerman, Mark: Statistical Mechanics: Theory and Molecular Simulation.
Ben-Naim, Aryeh: Molecular Theory of Solutions.
van Kampen, N.: Stochastic Processes in Physics and Chemistry.
Syllabus
Last update: Christoph Allolio, Ph.D. (28.07.2021)
Contents:
Molecular building blocks of biology (Overview)
Water, small molecules and ions
Polymers and their monomers
Proteins, aminoacids
DNA, RNA, Nucleobases and their derivatives
Cellulose, starch and other sugars
Lipids, surfactants and self-assembled systems
Basic theory
Notions of stochastic processes
Brownian motion, Wiener process
Langevin equation, diffusion
Markov property
Remembering thermodynamics
Molecular and bulk systems
Thermodynamics of aqueous solutions
Osmotic pressure, chemical potential, ideal solutions
Thermodynamics of ions in solution
Simple polymer models
Entropic elasticity, persistence length
Polymer solutions
Introduction to molecular simulations
Molecular dynamics and statistical physics
Notion of phase space, Liouville theorem
Empirical forcefields
Potential form and parametrization
Basic algorithms of molecular dynamics
Integration of the equations of motion
Thermostats and barostats (NVT and NPT ensembles)
Monte Carlo as an alternative
Analyzing molecular simulations
Energies and their partition
Distribution functions and their interpretation
Kirkwood-Buff theory
Fluctuation-Dissipation Theorem, linear response
obtaining bulk elastic and transport properties from
molecular simulation
Microscopic stress tensor
Free energies and biased sampling
Umbrella sampling
Thermodynamic integration
Free-Energy perturbation and Bennett acceptance ratio
Simulating proteins
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 winter semester. To acquire the credits, students will need to successfully complete an exercise project at home.
Goals:
This course aims to provide a solid understanding of statistical thermodynamics and selected non-equilibrium processes, thus enabling students
to independently conduct molecular simulations of soft matter systems. Technical instructions on how to perform these simulations on current
hardware will be provided.
Molecular simulations generate a large amount of data. Their analysis by statistical methods is very instructive for
other data-driven applications. In this way, the course will increase the data literacy of the students.
Entry requirements
Last update: doc. Mgr. Petr Kaplický, Ph.D. (02.06.2020)
Basic knowledge of thermodynamics, mechanics, statistical physics and algorithms. No knowledge of chemistry or biology required.
