Seminare 2013

--> NEUER ORT & ZEIT! Biozentrum, HS 102, Di. 5.3.2013, 12:30-13:30 <--

Seminar 1: Parallel Numerical Simulation of the Interaction between Three-Dimensional Incompressible Two-Phase Flows and Dynamic Rigid Bodies

Dr. Roberto Croce, Institute of Computational Science, University of Lugano

In this talk we provide an insight into some research fields concerning computational fluid dynamics (CFD). First, we present a three-dimensional Navier-Stokes solver for incompressible two-phase flow with surface tension and apply the proposed scheme to the simulation of bubble and droplet deformation. Thereafter we couple this two-phase flow model with a rigid body motion model and a large eddy turbulence model for macroscopic fluid flow simulations. Finally, we investigate an improved parallelization technique consisting of a combination of the , which enables parallel time-computation using a de-composition of the time-interval, with the well established parallel in space algorithm via domain decomposition.
We discuss the details of the proposed numerical schemes and present the results of
several numerical experiments arising from the area of bubble and droplet dynamics up to the area of real world engineering applications.


--> NEUER ORT & ZEIT! Pharmazentrum, HS 2, Di. 30.4.2013, 12:15-13:30 <--

Seminar 2: Sampling to score in molecular simulations

Prof. Chris Oostenbrink, University of Natural Resources and Life Sciences, Vienna

All molecular processes are governed by the free-energy difference associated with them. Using statistical mechanical principles, these may be estimated from molecular simulations, but this often requires extensive sampling. Particularly difficult are molecular systems that are characterized by multiple stable conformations, separated by high-energy barriers.
In this presentation, I will discuss some of our work on the calculation of free energy differences and the tricks to enhance the sampling on the one hand, or to reduce the necessary sampling on the other hand. Starting from relatively simple model compounds, I will move on to complex biomolecular systems and the calculation of binding free energies.


--> NEUER ORT & ZEIT! Pharmazentrum, HS 2, Di. 28.5.2013, 12:15-13:30 <--

Seminar 3: Simulating waves in the sun

Prof. Siddhartha Mishra, Seminar für angewandte Mathematik, ETHZ

Wave propagation in the outer solar atmosphere plays a role in many interesting phenomena e.g. chromospheric and coronal heating, generation of solar flares and prominences etc. We will present an overview of how such waves are simulated using SURYA-- a massively parallel high resolution finite volume code that solves the stratified magnetohydrodynamics (MHD) equations in a robust and efficient manner.


--> ORT & ZEIT! Bernoullistr. 16, Raum 205, Di. 01.10.2013, 12:10-13:05 <--

Seminar 4: Application challenges towards Exascale computing architectures

Dr. Marie-Christine Sawley, Intel Exascale-Lab Director, Paris (F).

Abstract: Kein Abstract verfügbar.


--> ORT & ZEIT! Bernoullistr. 16, Raum 205, Di. 05.11.2013, 12:10-13:05 <--

Seminar 5: Atomistic Calculations of Thermodynamic and Electronic Structure Properties in Chemical Compound Space

Prof. O. Anatole von Lilienfeld, Computational Chemistry, University of Basel.

The design of new compounds with specific physical, chemical, or biological properties is a central goal of much research in atomistic sciences. Unfortunately, chemical compound space, the set of all possible compositional, constitutional and conformational isomers, scales combinatorially, rendering brute-force screening for compounds with interesting properties prohibitive. Consequently, when it comes to properties and compounds that require first principles calculations, reliable optimization algorithms must not only trade-off sufficient accuracy and computational speed, but must also aim for rapid convergence in terms of number of compounds "visited".
I will first focus on underlying theory, encompassing all of chemical space in terms of interpolation parameters. Thereafter, various numerical results will be discussed for predicting molecular properties, such as electronic structure properties, interaction energies, or free energy differences, through variation of chemical composition. Finally, I will present some recent developments of machine learning methods applied to atomistic simulation in chemical space.


--> ORT & ZEIT! Bernoullistr. 16, Raum 205, Di. 03.12.2013, 12:10-13:05 <--

Seminar 6: Studying cell-to-cell heterogeneity with single-cell RNA-seq

Prof. J. Marioni, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton Cambride, UK.

Single-cell RNA-sequencing (RNA-seq) promises to yield valuable insights about variability within populations of seemingly homogeneous cells. In this talk I will describe a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. The approach allows quantification of the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. I will demonstrate the utility of the approach using data sets from A. thaliana and M. musculus before discussing new biological insights revealed by our analyses.



Prof. Friedel Thielemann

Dr. Georg Funk

Ort und Zeit der Seminare

Dept. Informatik
Bernoullistrasse 16
Seminarraum 205 (2. Stock)

Normalerweise jeden ersten Dienstag im Semester
12:10 bis ca. 13:05 Uhr