CloseHelpPrint
Kies de Nederlandse taal
Course module: 8CB10
8CB10
Simulation of biochemical systems
Course info
Course module8CB10
Credits (ECTS)5
Category3 (Advanced)
Course typeBachelor College
Language of instructionDutch
Offered byEindhoven University of Technology; Biomedical Engineering; Computational Biology;
Is part of
Biomedical Engineering
Coherent package - Computational biology
Medical Sciences and Engineering
Contact personprof.dr. P.A.J. Hilbers
Telephone5537
E-mailp.a.j.hilbers@tue.nl
Lecturer(s)
Lecturer
dr.ir. T.F.A. de Greef
Other course modules lecturer
Responsible lecturer
prof.dr. P.A.J. Hilbers
Other course modules lecturer
Contactperson for the course
prof.dr. P.A.J. Hilbers
Other course modules lecturer
Lecturer
prof.dr.ir. N.A.W. van Riel
Other course modules lecturer
Academic year2017
Period
3  (05/02/2018 to 22/04/2018)
Starting block
3
TimeslotB: B - Mo 5-8, Tu 9-10, We 1-4
Course mode
Fulltime
Remarks-
Registration openfrom 15/11/2017 up to and including 07/01/2018
Application procedureYou apply via OSIRIS Student
Explanation-
Registration using OSIRISYes
Registration open for students from other department(s)Yes
Pre-registrationNo
Waiting listNo
Number of insufficient tests-
Number of groups of preference0
Learning objectives
After passing the course, the student has insight in:
  1. Models of simple grow processes and can set up ordinary differential equations (ode’s).
  2. Different chemical kinetics and can translating biochemical processes with given kinetics into the corresponding ode’s.
  3. Elementary solution methods, phase planes, stability analysis of ode’s, and can solve ode’s and perform a stability analysis.
  4. Different numerical methods and can solve (stiff) ode’s.
  5. Basicprinciples of molecular dynamics and is able to perform molecular simulations.
  6. Statistical mechanics, in particular microcanonic and canonic ensemble, correlation particle velocity and temperature radial distribution function and can calculate with regard to statistical mechanics.
Content
  • Modeling with differential equations: exponential growth and decay, logistic growth, mass-spring systems, Lotka-Volterra equations.
  • Reaction kineticsn: mass-action, Michaelis-Menten, Repressilator kinetics, Hill kinetics, modeling of gen regulation, cooperativity, more complicated enzyme kinetics, examples from synthetic biology.
  • Analytic solutions of differential equations: separation of variables, equations with constant coefficients.
  • Stability analysis: Phase planes, Stability of stationary points, Jacobians.
  • Numerical methods for ode's: One-stepmethods, explicite (Euler, ..., Runge-Kutta) and implicite (Cranck-Nicholson), truncation errors, numerical stability. Multi-step methods with larger stability. Praktical aspects, error estimates, ode solvers, Matlab implementation.
  • Introduction Molecular Dynamics: Newton's laws, conservative forces, potentials, dynamical equations for 1,2 and N particles.
  • Potentials: Lennard-Jones, Morse, harmonic binding potentials.
  • Numerical solutions: Special numerica methods for equations of motion (e.g. Verlet), periodic boundary conditions, truncating potentials.
  • Introduction statistical mechanics, microcanonical and canonical ensemble, relation between particle velocities and temperature, radial distribution functions.
  • Stochastics simulations: simulated annealing.
Entrance requirements
Entrance requirements tests
-
Assumed previous knowledge
Kennis van Calculus, Wiskunde II (lineaire algebra) en Toegepaste natuurwetenschappen. Basiskennis op het gebied van biochemie en moleculaire biologie.
Previous knowledge can be gained by
• 3NBB0 - Applied physical sciences
• 8RA00 - Biochemistry
• 8VB40 - Systems in time and space
• 8RB00 - Molecular cell biology
Resources for self study
-
Short promotional description of the course
Simulaties van biochemische systemen worden gebruikt om moleculaire mechanismes in de cel te begrijpen. In dit college worden basis simulatiemethoden besproken. Eerst worden modellen in termen van concentraties behandeld. Naast chemische kinetieken worden numerieke oplossingsmethoden en stochastische simulaties besproken. Daarna worden, inzoomend op individuele moleculen, Moleculaire Dynamica simulaties behandeld voor het bestuderen van de structuur en/of aggregatie van biomoleculen.
Short promotional description of the course
Simulations of biochemical systems are a basis for the unraveling of the molecular mechanisms in the cell. In this course the basic simulation methods are presented. First, models in terms of the concentrations are considered. Besides chemical kinetics also attention is given to numerical solutions and stochastic simulations. Second, zooming in to individual molecules, Molecular Dynamics simulations are treated for the prediction of structure and/or aggregation of biomolecules.
Required materials
-
Recommended materials
Collegedictaat (wordt uitgereikt)
Instructional modes
Guided selfstudy

General
-

Remark
-
Lecture

General
-

Remark
-
Tests
Assignment 2
Test weight15
Minimum grade-
Test typeInterim examination
Number of opportunities1
OpportunitiesBlock 3
Test duration in minutes-

Assessment
-

Remark
-

Assignment 1
Test weight15
Minimum grade-
Test typeInterim examination
Number of opportunities1
OpportunitiesBlock 3
Test duration in minutes-

Assessment
-

Remark
-

Written examination
Test weight70
Minimum grade5
Test typeFinal examination
Number of opportunities2
OpportunitiesBlock 3, Block 4
Test duration in minutes-

Assessment
-

Remark
-

CloseHelpPrint
Kies de Nederlandse taal