Advanced Projects in Computational Physics 2 (CP-2)5 ECTS
(englische Bezeichnung: Advanced Projects in Computational Physics 2)
(Prüfungsordnungsmodul: Advanced lab courses and projects)

Lehrveranstaltungen:

• • Advanced Projects in Computational Physics 2
    (Praktikum, 7 SWS, Ana-Suncana Smith, Zeit und Raum nach Vereinbarung)
• Mandatory attendance

Inhalt:

Contents:
Each student will be performing one of the following mini projects for the duration of the semester. The evaluation of the work will be performed on the basis of a written report, provided in the form of a scientific paper (referenced introduction, method section, results and discussion, conclusion – 50% of the mark). Each student will deliver a 35 minutes lecture first extensively introducing the method, and then discussing the obtained results and drawn conclusion (50% of the mark).

Projects:

• 1. Molecular dynamics simulation of a dissolved nanoparticle - The aim of the project is to run a full molecular dynamics (MD) simulation of a nanoparticle in a fluid and to extract some physical quantities like the diffusion coefficient or virial coefficient. The focus lies on understanding the ingredients and physical outcomes of an MD simulation.
  

• 2. APCF – Averaged point charge field for modeling chemical reactions - Modelling of chemical reactions in solution is a large and very active field in computational quantum chemistry. The aim of the project is to write a modular program that calculates the averaged point charge field of a given solvent around a specific solute based on fully atomistic molecular dynamics simulations.
  

• 3. Following flows with Particle image velocimetry - Test the accuracy of the flow field detection using MATLAB routines. Preexisting image sequences acquired in cell motion experiments will be used for flow detection. The test will consist of evaluating the variations and errors in the flow fields with respect to different image filtering routines, interrogation window sizes, experiment time steps etc.
  

• 4. Numerical solutions for bead-based microswimmers - In this project, the student will implement the equations of motion for a microswimmer composed of spherical beads and solve them numerically. The impact of the integration method and of the time step chosen will be investigated and the results will be compared to the analytical results available. In the final presentation, the student should present the methods used as well as the results obtained and discuss them.
  

• 5. Development of a molecular superposition algorithm based on molecular graph theory - Improving upon a simple, already existing recursive algorithm, this project aims at developing molecular-graph based code capable of superimposing a molecule on top of another, and deciding whether the two match or not. You will like this project if you love programming in C++/python (your choice) and if you want to get in touch with the basics of MD code.
  

• 6. Simulations of membrane bound protein clusters - A cluster of membrane bound proteins, whose interactions are produced by coupling to the cell membrane, will be simulated using Langevin dynamics. You will produce the simulation, which involves calculating the membrane mediated forces on each protein, and analyze the output for cluster diffusion properties, stability and lifetimes.
  

• 7. Statistical analysis of the dynamics of cells within an expanding epithelial tissue – From a physical point of view, the dynamics of tissues is a many-body problem involving a large collection of cells actively crawling on a substrate, interacting with each other, dividing and dying. The resulting dynamics is complex and requires statistical tools for its investigation.
  

• 8. IMAGE PROCESSING – Segmentation of Microscopy Images - Image segmentation is important in processing microscopy data to extract features in cells, i.e. the size and shape of nuclei. The project includes the writing your own segmentation routine of microscopy images in MATLAB. It also includes the evaluation of the performance and accuracy of your segmentation. In the current case, the task will be to develop and test different numerical approaches for segmenting images of 3D polymeric networks.
  

• 9. Lattice-Boltzmann (LB) simulations of beads at interface – The project consists in studying the movement of beads at low Reynolds number at the interfaces between 2 fluids with LB3D simulations. Investigate the deformation of the interface, and thus the related capillary effects on the dynamics of the swimmer as well as the effects of the density ratio of both fluids. The project will involve developing thorough understanding of the Lattice Boltzmann simulation method, the underlying algorithms, and the development of post processing tools.
  

• 10. Monte Carlo simulations of receptor-ligand bond making and breaking - The receptors on the surface of cell membranes form many complexes with specific ligand molecules to enable the cell to sense its extracellular mechanical environment. The specific interactions between receptors and ligands essentially are stochastic and reversible chemical reactions, which work in a cooperative manner. To quantitatively understand these chemical reactions, in this project the relevant Monte Carlo simulations in statistical physics would be carried out to investigate the dynamics of the formation of bond clusters. The project will involve understanding the Monte Carlo method, and advanced sampling techniques.
  

• 11. Numerical predictions for the mixing of two liquids using the Fokker-Planck equation - Using the Fokker-Planck equation (FPE) for a system consisting of two different liquids A and B in three alternating layers ABA on top of each other, a numerical solution for the prediction of density of liquid B at the outer edge of the system should be found, assuming liquid molecules that have a finite size. Appropriate methods for solving the FPE numerically such as discretization and Euler/Runge-Kutta procedures should be applied. The stability and robustness of the solution should be analyzed and the results compared to data of molecular dynamics simulations of an equivalent system.

Lernziele und Kompetenzen:

Learning goals and competences:

Students

• acquaint themselves with special subjects and techniques in a short time

• handle complex numerical computer codes

• analsze the results and prepare illustrations

• evaluate and question the obtained results

• prepare an original report according to the standards of good scientific practice

• summarise their results in an oral presentation
  

Studien-/Prüfungsleistungen:

Advanced lab courses and projects (Prüfungsnummer: 69811)

(englischer Titel: Advanced lab courses and projects)

Prüfungsleistung, Praktikumsleistung, benotet, 5 ECTS

Anteil an der Berechnung der Modulnote: 100.0 %

weitere Erläuterungen:
Each student will be performing this mini project for the duration of the semester. The evaluation of the work will be performed on the basis of a written report, provided in the form of a scientific paper (referenced introduction, method section, results and discussion, conclusion – 50% of the mark). Each student will deliver a 35 minutes lecture first extensively introducing the method, and then discussing the obtained results and drown conclusion (50% of the mark).

Prüfungssprache: Englisch

Erstablegung: WS 2019/2020, 1. Wdh.: SS 2020

1. Prüfer:

Ana-Suncana Smith