Hosts: Prof. Dr. R. Klein (FU), Prof. Dr. R. Kornhuber (FU), Prof. Dr. C. Schütte (FU/ZIB)
Location: Freie Universität Berlin, Institut für Mathematik, Arnimallee 6, 14195 Berlin-Dahlem, Room: 032 ground floor
Time: The seminar takes place on Thursday at 4:00 pm
Thursday, 20.04.2017: Colloquium
Hao Wu, Freie Universität Berlin
"What is .. WHAM/TRAM?"
Enhanced sampling is a powerful tool to study biomolecular processes with extremely large timescales, which speeds up rare events by bias potentials or higher temperatures and estimates the unbiased thermodynamics with reweighting estimators. In this talk, we will introduce two important reweighting estimation methods, the traditional weighted histogram analysis method (WHAM) based on the i.i.d assumption of simulation data, and the recently developed transition-based reweighting analysis method (TRAM) based on the Markov state modeling of data.
Thursday, 04.05.2017: Colloquium
Han Cheng Lie & Gottfried Hastermann, Freie Universität Berlin:
"What is .. data assimilation and nonequilibrium Monte Carlo rare event sampling for multiscale dynamical systems?"
The complexity of multiscale dynamical systems often calls for probabilistic or statistical approaches. For example, given a set of observations of a dynamical system, one may wish to forecast its behavior up to some time in the future. Such methods are called `data assimilation methods'. We shall present a basic data assimilation method and illustrate some problems that can arise when one applies data assimilation methods to study multiscale dynamical systems, using the simple and informative model of the double pendulum.
Alternatively, when one wishes to study a system that has explicitly random dynamics, one may face the problem that sampling from the true probability distribution of interest using simple Monte Carlo is too inefficient to be practical. This is often the case when the distribution of interest involves a rare event. We will present metastable overdamped Langevin diffusions as a class of examples that exhibit this property, and discuss a general solution strategy involving alternative probability distributions.
These two talks shall cover some of the basic ideas of SFB Projects A02 and A05.
Thursday, 18.05.2017: Colloquium
Andreas Bittracher & Péter Koltai, Freie Universität Berlin:
"What is .. a transition manifold and reaction coordinates?"
We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales, and raise the question whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics.
We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.
Thursday, 01.06.2017: Colloquium
Robert Patterson , WIAS
Stochastic Soot Simulation
One major challenge in soot simulations is that the chemical reactivity and measurement response of the soot particles is influenced by structure both on the level of interatomic bonds and on the level of aggregate shape. I will describe a two-part stochastic method, where individual molecules within soot are simulated with the Gillespie SSA and the aggregate structures are simulated separately. Time permitting I will also discuss two strategies for coupling soot simulations to reacting flow calculations. This is joint work with Edward Yapp and Markus Kraft.
This talk is given as part of the CRC 1114 Spring School and will take place at
WIAS,
Mohrenstr. 39,
10117 Berlin,
Lecture Hall Erhard-Schmidt-Hörsaal (ground floor).
Thursday, 15.06.2017: Lecture
Alexander Blum, MPI für Wissenschaftsgeschichte
Relativity after Einstein
In November 1915, Albert Einstein published his theory of gravitation, thus attaining international renown which was to last unfailingly until the present day, long after his death. The history of his general theory of relativity, however, took a different course. After the initial hype, interest in and research into the theory ebbed, resurfacing only ca. 50 years later, around 1960, in what is commonly referred to as the “renaissance” of general relativity. Only in this period did general relativity become a research field in its own right (with conferences and journals) and were essential concepts developed that we now strongly associate with Einstein’s theory, such as the black hole. In my talk, I will follow this development, asking why it took so long for Einstein’s theory to mature, what finally led to its breakthrough, and what that teaches us about scientific revolutions and theory change.
Thursday, 29.06.2017: Colloquium
Matthias Rosenau, Helmholtz Center, Potsdam: "What is .. Particle Image Velocimetry?"
Particle Image Velocimetry (PIV) is a visualization method for quantitative flow and deformation analysis. PIV is a key method used in the experiments of project B01 and, in this framework, supported by the DFG by means of a 80 k€ infrastrutural investment. PIV is based on digital image correlation and signal processing techniques. The output is basically a velocity field, in case of project B01, that of an experimentally simulated earth surface during earthquake cycles. I will give a quick overview of technical issues and applications.
Martin Heida, WIAS Berlin: "What is .. GENERIC?"
We give a short introduction into the fundamental idea of the "General Equation for the NonEquilibrium Reversible-Irreversible Coupling", called GENERIC, and apply it to gain new insights into the well-established model of rate-and-state friction in geology.
Thursday, 06.07.2017: Lecture
Giovanni Settanni, Max-Planck Graduate Center, Physics Department, University of Mainz:
Nano-bio interfaces investigated using molecular dynamics simulations
The effectiveness of drugs and, more in general, therapeutic agents (therapeutic proteins, liposomes, nanoparticles, medical implants etc.) is strongly influenced by the interface they form with the surrounding biological fluids. For example, the protein shell (corona) forming around nanoparticles in contact with blood is a major factor in determining their circulation half-time and immuno- and thrombogenicity. The composition of the layer of adsorbed proteins, their structure and orientation all play a fundamental role in the reaction of the organism to the therapeutic agent. However, the molecular factors at the base of these interactions are not yet very well understood. Classical molecular dynamics simulations can be used to evaluate the interactions of proteins with (nano-) materials. Here, I will present how we used this technique to study the adsorption on model surfaces of fibrinogen, a protein involved in blood coagulation, and the adsorption of plasma proteins on nanoparticles coated with hydrophilic polymers. In both cases, the simulations provide a molecular-level picture of the adsorption process which can then be used to build more general models of protein adsorption and compared with experimental data.
Thursday, 20.07.2017
CRC 1114 Annual Assembly and Summer Get-Together
tba: Extra Colloquium
Sabine Hittmeir, Universität Wien
Multiscale asymptotics for the convective region of tropical squall lines
We analyse the convective region of tropical squall lines by introducing a setting of several columnar clouds with small horizontal diameter 1 km, which are embedded into a larger scale area 10 km. To resolve the dynamics in these hot tower regions we have to define an appropriate small scale coordinate, which allows for each cloud tower to have its own centerline. The nonlocality of the small scale fluctuations of the horizontal velocity and the pressure components requires moreover the introduction of an intermediate scale coordinate, at which the dynamics of the individual towers can be connected. Since the overall saturated area is small, new systematic averaging procedures have to be performed, which allow to represent the effects of the cloud dynamics on the larger scale flow. The onset regime with weak precipitation moreover requires a separate analysis on the short time scale. This work is joint work with Rupert Klein.