Projects overview - ongoing projects
(click here for expired projects)
| Dr. Vadym Aizinger | |
| Simulation of static mixer | |
| abstract : | We conduct simulations and experimental validation of static mixers using Discontinous Galerkin method. |
| M. Emal Alekozai | |
| Solvation effect on protein dynamics | |
| abstract : | The solvent efect on the protein dynamics is studied using molecular dynamcis and monte carlo simulation. In particular, the influence on surface side chain motion is studied. Furthermore, neutron scattering spectra are calculated to compare with experiments. |
| Dr. Ofir Alon | |
| Quantum Dynamics of Correlated Bosonic Systems | |
| abstract : | The dynamics of correlated bosonic systems among which Bose-Einstein condensates in traps and in optical lattices has drawn much attention in the quantum-gas community. Whereas the two basic theoretical methods -- Gross-Pitaevskii theory for general traps and Bose-Hubbard model for optical lattices -- have gained enormous popularity and are much in use, there are increasingly mounting evidences as well as physical phenomena indicating that one should go beyond these approaches. In this project we employ the essentially-exact many-body propagation theory for interacting bosons developed in Heidelberg -- the multiconfigurational time-dependent Hartree for bosons (MCTDHB) -- via its parallel implementation to explore the dynamics of bosons in traps and in optical lattices beyond the available in the literature. The MCTDHB has been very successful in unveiling novel physical phenomena of both repulsive and attractive Bose gases and much more is anticipated to come. |
| Michael Bach | |
| Phase Transition of a Polymer System | |
| abstract : | This project is located in the area of polymer physics. The polymer of interest is a hyaloronan – aggrecan – complex, which is an essential part of the extracellular matrix. One really important task of this molecule is the protection of our cells from mechanical stress. This is the motivation for us to investigate polymer brushes, which consist of simplified hyaloronan – aggrecan – complexes. Especially we are interested in the different phases of the system, and the coupled phase transition. |
| Prof. Peter Bastian | |
| DUNE | |
| abstract : | The Distributed and Unified Numerics Environment is a generic framework for the numerical solution of partial differential equations. It provides uniform access to variety of grid implementations and efficient solvers based on multigrid and domain decomposition ideas. |
| Tomasz Berezniak | |
| MOLECULAR SIMULATION ON RNA CATALYSIS | |
| abstract : | Molecular Dynamics simulations of the RNA molecules that catalyze C-C bond formation by Diels-Alder reaction. |
| Tanushree Bhattacharjee | |
| Catalytic Oxidation of Hydrocarbons | |
| abstract : | To study the CPO hydrocarbons in honey comb structure coated with rhodium. The reaction mechanisms in the gas phase and in the surface as well as their coupling will be investigated. Numerical simulation will be done which will contribute to a better understanding of the overall process. |
| Mithun Biswas | |
| Structure and Function of Histone Tails | |
| abstract : | To study the function of histone tails in chromatin folding via MD simulation. |
| Markus Blatt | |
| The Iterative Solver Template Library (ISTL) | |
| abstract : | The numerical solution of partial differential equations frequently requires solving large and sparse linear systems. When using the Finite Element Method these systems exhibit a natural block structure that is exploited for efficiency in the ``Iterative Solver Template Library\'\' (ISTL). Based on existing sequential preconditioned iterative solvers we present an abstract parallelisation approach which clearly separates the parallelisation aspects from the data structures and solver algorithms by imposing an abstract consistency model onto the building blocks of the iterative solver components. This allows for supporting overlapping and non-overlapping domain decompositions as well as data parallel implementations of standard linear solvers. |
| Cedric Bodet | |
| Non-Equilibrium Dynamics | |
| abstract : | Making far from equilibrium simulation on ultracold bose gas using the 2PI formalism |
| Manfred Bohn | |
| A random loop model for chromatin folding | |
| abstract : | Aim of this project is to study the higher-order folding motifs of chromatin. While the structure is well-known on the scale of the chromatin fiber, the packing of the fiber inside the nucleus is still an open question. We have developed a new model for chromatin folding, a random loop model, where we evaluated basic analyical results. For further development extensive molecular dynamics simulations will be performed. |
| Dr. Ana-Nicoleta Bondar | |
| Mechanism of retinal proteins | |
| abstract : | Rhodopsins are a family of widely-spread integral proteins that use the energy of light to pump cations/anions, to mediate proton flux down the electrochemical gradient, or signal transduction. To understand how specific amino-acid residues tune the function of rhodopsins we perform computer simulations on the wild-type and mutant bacteriorhodopsin embedded in a hydrated lipid bilayer. The role of internal water molecules in transmitting protein structural rearrangements is investigated by performing simulations of the recently solved structure of the squid visual rhodopsin. All computations will be performed using the charmm and namd softwares. |
| Michael Brill | |
| Molecular Dynamics with MCTDH | |
| abstract : | In this project the molecular dynamics of Kations (H_5O_2^+ and CH_5^+) is investigated. The goal is a better understanding of their dynamics, infrared spectra and the assignment of the structures in the spectrum with the different vibrational modes. |
| Fabian Brännström | |
| Evaluation of hybrid turbulence models | |
| abstract : | The evaluation of different enhanced turbulence models for 3D wall jets, 3D diffuser flows and room airflow. |
| Dr. Nicolas Calimet | |
| QM/MM simulations of anion transport in HR | |
| abstract : | Molecular Dynamics simulations using combined Quantum Mechanical/Molecular Mechanical methods will be performed to explore the light-driven anion translocation mechanism(s) of the membrane protein Halorhodopsin. |
| Mari Chikvaidze | |
| QM/MM simulations of Alkaline Phosphatase | |
| abstract : | Combined quantum mechanical/molecular mechanical simulations of enzymatic reactions using a transition network approach. The application is the calculation of reaction pathways for the enzymatically catalysed phospho-ester hydrolysis by the enzyme Alkaline phosphatase. |
| Bogdan Costescu | |
| Support, scalability tests | |
| abstract : | Not running production jobs myself, but compiling programs and offering support for the users from the Computational Molecular Biophysics (formerly Biocomputing) group. |
| Xinguang Cui Cui | |
| CFD study on the flow field and particle dispersio | |
| abstract : | Particle deposition in the human upper respiratory system has great influence on human health such as the targeted drug for treating lung disease. To improve the validity and efficiency of the drug delivery, the property of flow field and particle motion will be researched through numerical simulation. |
| Dr. Odilon da Silva | |
| Simulations of free polymers. | |
| abstract : | Our goal is to develop model based on the concept of chromatin being a polymer. The model should be able to predict that the mean square physical distance as a function of the contour length will saturates and that an ensemble of such polymers segragates into distinct domains with possible overlap. |
| Dr. Isabella Daidone | |
| Protein Folding | |
| abstract : | Multiple simulations of different peptides in solution to study their conformational thermodynamics and kinetics |
| Pedro Henrique de Almeida Konzen | |
| Diffusion flame simulations with ILDM/REDIM | |
| abstract : | The project concerns the simulation of laminar diffusion flames of hydrocarbons/air mixture. The chemical reactions are described by automatic reduced reaction mechanism generated by the ILDM and/or REDIM techniques. This allows us to reduce the number of physical/chemical variables to a few ones. The reduced model is written in axisymmetric cylindrical coordinates and discretized using Finite Element Methods. A Parallel version of the C++ Gascoigne code is used following a time depended scheme. At the end, the comparison of results with experimental and non-reduced numerical simulation data is intended to show up the advantages and/or disadvantages of the proposed strategy. |
| Prof. Olaf Deutschmann | |
| Heterogeneous Catalysis | |
| abstract : | Modeling of elementary surface reactions |
| Dr. Nadia Elghobashi-Meinhardt | |
| Conformational preference of solvated peptides | |
| abstract : | The project aims to identify preferred conformations of alanine-based peptides using long (nanosecond) MD simulations based on a hybridized quantum mechanical/molecular mechanic (QM/MM) potential. |
| Christian Engwer | |
| AdaptHydroMod | |
| abstract : | Coupling and Simulation of surface and subsurface flow in porouse media. |
| Ramona Ettig | |
| DNA loop propagation in the nucleosome | |
| abstract : | The nucleosome is the first level of DNA packaging in the cell nucleus. Due to its influence on the accessability of the DNA the nucleosome is known to take an essential role in the regulation of processes that depend on protein-DNA interaction. To accomplish this function the nucleosome needs to be highly dynamic. So called “remodeling complexes” assume the function to mobilize nucleosomes in the cell. This project focuses on the understanding of the physics behind the DNA mobility in the context of nucleosomes. In Performing long time scale molecular dynamics simulation we investigate the dynamical properties of a DNA loop inserted into the nucleosome. The aim of this study is to find a chemical and physical correct model of the mechanism of DNA motion along the nucleosomal core. |
| Jens Fleckenstein | |
| Development of a virtual MLC model | |
| abstract : | A virtual multi leaf collimator(MLC) model with condensed electron interactions to speed up calculation times of the patient dose distribution in radiotherapy treatments is being developed. Therefore Monte Carlo simulations of a medical linear accelerator are done in GEANT4 to determine a phase space proximal and distal to the MLC. |
| Miriam Fritsche | |
| Chromosome folding and kissing in the cell nucleus | |
| abstract : | Classically eukaryotic chromosomes are folded in individual territories in the cell nucleus and within these territories, they are thought to be segregated in insulated domains, allowing each gene to function independently. Recent studies have shown that genes separated by large DNA distances on the same chromosome, or even located in different chromosomes, can become co-localized in the cell nucleus, a phenomenon called "chromosome kissing". If chromosome kissing would impinge on gene expression, we would need to redefine the gene as the coding sequence of DNA and the ensemble of the remote genomic elements that affect its expression via the organization of nuclear architecture. In this project, we will develop a model based on recent experimental results capable of describing the scales of chromosome folding using polymer physics, with the goal to provide a physical basis and principle to the three dimensional chromatin organization in the cell nucleus and the origin of chromosome kissing. |
| Dennis Glass | |
| Korrelierte funktionale Bewegung in Proteinen | |
| abstract : | Biomolecular force fields are widely used to model biological systems using an explicit representation of water. Many water models exist giving a reasonable description of water under specific conditions. Most modern biomolecular force fields are parameterized for use with a specific water model (for instance CHARMM uses TIP3P). We investigate whether the substitution of the default water model has any influence on protein dynamics, by performing a series of simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models as solvent. The all-atom molecular dynamics simulation will be performed at temperatures between 20 and 300 K.It is believed that the protein dynamical transition is described almost indistinguishably for the three TIP water models investigated. |
| Viktoriya Gomilko | |
| CO Adsorption and Diffusion on Ni Surface | |
| abstract : | CO adsorption on different sites such as top, bridge and hollow and diffusion on Ni (111) and Ni (110) surface will be investigated by DFT methods. |
| Javier Gonzalez | |
| Phylogeny of avian taxa using large data sets | |
| abstract : | An increasing number of DNA sequences are available today from different organisms. From Archeobacteria to primates, hundreds of nucleotide sequences have been generated and the “Tree of Life” project demands the analysis of big data sets using algorithms which summarize the information in big “super-trees”. Disciplines such as bioinformatics and evolutionary biology are complementary to understand the evolution of organisms through phylogenetic inference. Moreover, as a consequence of multi-gene phylogenies approaches, today huge data set have been generated. Several applications based on Bayesian and maximum likelihood models are available to reconstruct the phylogenetic relationships among taxa. Today, the analysis of big data sets demands high-performance PC cluster technology. |
| Dr. Elke Goos | |
| Gas phase reaction kinetics | |
| abstract : | Modeling of elementary reactions important in combustion and soot formation |
| Dr. Alexandr Gorski | |
| DFT calculations of spectroscopic constants | |
| abstract : | Development of 2D numerical dynamic dipole-dipole coupling models based on density functional theory calculations for quantitative IR-VIS sum-frequency generation vibrational spectra analysis |
| Dr. Evgeniy Gromov | |
| Studying of the Photoactive Yellow Protein (PYP) | |
| abstract : | Calculations of the electronic structure and dynamics of the PYP chromophore aiming at the understanding of initial events in the PYP photocycle: unrevealing the mechanism of the chromophore isomerization and clarifying the role of the protein environment in the isomerization process. |
| Gerd Grünert | |
| Yeast interphase chromatin simulation | |
| abstract : | Trying to fold the yeast chromosomes in the nucleus in the interphase using brownian dynamics to generate a three-dimensional genomic map of the yeast nucleus. |
| Steffen Hau | |
| bwGRiD | |
| abstract : | Testuser fuer bwGRiD |
| Marcel Hellmann | |
| MCS of a hybrid XY-Potts model nan-Aggrecan Compl | |
| abstract : | The pericellular matrix (PCM) is a protective coat arround cells which is comprised of stretched polymer backbones with attached rigid side chains. In order to elucidate the phase behaviour of this biophysical system, a rather reductive model is studied in Monte Carlo simulations. It combines the planar rotator model (continuous degree of freedom = orientation of side chain) with a Potts model (discrete degree of freedom = height of side chain above the cell surface). First results suggest that the new hybrid model shows a phase transition distinct from its constitutents. For more detailed investigations of the phase behaviour (esp. finite size scaling analysis, studies on large systems) additional computation time is needed. |
| Dr. Marc Hemberger | |
| BQ Test | |
| abstract : | Testing of the BW-Grid Access, Usability, etc. from BioQuant perspective. |
| Paul P. Hilscher | |
| Accretion onto Kerr black holes | |
| abstract : | Numerical studies of 3D axis-symmetric general relativistic HD/MHD accretion onto Kerr black holes using the GR-I-RMHD implicit solver. |
| Xiaohu Hu | |
| MD simulation of water | |
| abstract : | MD simulation of water in external ac/dc electric fields |
| Dr. Petra Imhof | |
| Molecular Simulation of enzymatic reactions | |
| abstract : | The catalytic mechanism of specific well-characterized metalloenzymes will be modelled. Combined quantum mechanical/molecular mechanical calculations will be performed to determine the reaction mechanism in the enzymes. |
| Dr. Oliver Inderwildi | |
| Nanoparticle Synthesis | |
| abstract : | DFT simulations of nanoparticle and surface growth |
| Dr. Olaf Ippisch | |
| Parameterschätzung für Transport in Porösen Medien | |
| abstract : | Parameter Estimation for Flow and Transport in Porous Media |
| Bernhard W. Keil | |
| Algorithm for General Relativistic MHD Simulations | |
| abstract : | The efficiency and robustness of the numerical algorithm GR-I-RMHD, a 3D axi-symmetric General Relativistic - Implicit - Radiative Magneto-Hydrodynamic solver, will be tested. Specifically, we will carry out massive parallel calculations to test the performance and scaling on large parallel computer systems and compare it with well-tested parallelized simulation codes, such as PLUTO. By means of massive computations and taking into account detailed physical processes, we intend to study the formation and acceleration of ultra-relativistic multi-component plasma MHD jets from around spinning black holes and other ultra-compact objects. |
| Dr. Farooq Kiani | |
| QM/MM Simulations of ATP Hydrolysis in Myosin | |
| abstract : | Combined quantum mechanical/molecular mechanical (QM/MM) reaction path calculations will be done in order to explore the mechanism of ATP hydrolysis in Myosin. |
| Christian Kieft | |
| Simulation of the Myosin power-stroke | |
| abstract : | I will simulate the power-stroke in the myosin molecular motor. I will do both MD simulations as well as CPR calculations. Project supervisor is Dr. Fischer. |
| Prof. Meinhard Kieser | |
| Simulation of adaptive sample size calculation | |
| abstract : | The determination of sample size in clinical trials is an important part of planning a study. However, it is not possible in every study to obtain in the design stage reliable values for the parameters necessary for sample size calculation. Consequently, procedures were established for adaptive sample size recalculation during the course of the study. Using these rocedures, the type I error rate must be controlled. For special designs, the actual significance level could be determined analytically. An exact assessment is, however, not practicable for all the trial designs that are interesting for application in practice. In order to create the possibility of estimating the actual Type I error rate under adaptive sample size recalculation for a wide range of designs, a tool was developed to perform simulations. In a comprehensive Monte Carlo simulation study, the characteristics of adaprive sample size estimation will be investigated, as, for example, actual type I error rate, achieved power and expected sample size. |
| Benoit Knecht | |
| Monte-Carlo and Brownian Dynamics of chromatin | |
| abstract : | Using detailed models of the chromatin chain, the effect of local conformational changes at the level of the nucleosome (histone modification, nucleosome unrolling, changes in positioning) on the global folding of the chromatin fiber shall be investigated. |
| Dr. Markus Knodel | |
| Development and functionality of elementary networ | |
| abstract : | Project in collaboration with Prof. Christoph Schuster, IZN Heidelberg: Development and functionality of elementary networks Computational modeling of the Drosophila neuromuscular junction An important challenge in neuroscience today is understanding how networks of neurons go about processing information. Synapses are known to be important for this process however quantitative and mathematical models of the underlying physiologic processes which occur at synaptic active zones is lacking. To counteract this problem, we are developing mathematical models of synaptic vesicle dynamics at a well characterized model synapse, the Drosophila larval neuromuscular junction. This synapses simplicity, accessibility to various electrophysiological recording and imaging techniques, and the genetic malleability which is intrinsic to the Drosophila system make it ideal for computational and mathematical studies. We have employed a reductionist approach and started by modeling single presynaptic boutons. Synaptic vesicles can be divided into different \\\\\\\\\\\\\\\"pools\\\\\\\\\\\\\\\" however a quantitative understanding of their dynamics at the Drosophila neuromuscular junction is lacking. We performed biologically realistic simulations of two bouton types characterized by partial differential equations - PDEs - taking into account not only the evolution in time but moreover also the spatial structure of two dimensions (the extension to the full three dimensions will be implemented soon). These PDEs are solved using UG. UG is a program library for the calculation of multi-dimensional PDEs which are solved using a finite volume approach and implicit time stepping methods leading to extended linear equation systems which can be solved by using multi grid methods. Numerical calculations are done on multi-processor computers allowing for fast calculations using different parameters in order to asses the biological feasibility of different models. In preliminary simulations, we modeled vesicle dynamics as a diffusion process describing exocytosis as Neumann streams at synaptic active zones. The results obtained with these models are consistent with experimental results however this should be regarded as a work in progress. Further refinements will be implemented such as models of glutamate diffusion and clearance from the synaptic cleft, post synaptic receptor kinetics, and physiologically realistic whole neuromuscular junction simulations. |
| Dr. Anastasios Koukoumelis | |
| a rational expectation economic model for Ethiopia | |
| abstract : | simulations on the effects of an AIDS epidemic on the long-run economic development of Ethiopia. |
| Dr. Heinz Kredel | |
| Benchmarking and Cluster Administration | |
| abstract : | The IT Center of the University of Mannheim is partner in the BMBF project IPACS (Integrated Performance Analysis of Computer Systems). The partners develop benchmarks for distributed computer systems, a repository for the meassured benchmarks together with instanteneous Web presentation of the results and a benchmark client, which makes the downloading and running of the benchmarks easier. The projekt home page can be found at http://www.ipacs-benchmark.org/. In the testing phase of the benchmark client and the benchmark suites we use HELICS. |
| Sebastien Kreuter | |
| bwGRiD | |
| abstract : | Linpack and IPACS-Benchmarks, Integrated Performance Analysis of Computer Systems for more information visit: www.ipacs-benchmarks.org |
| Matthias Kronenwett | |
| Nonequilibrium dynamics | |
| abstract : | We compute nonequilibrium dynamics of ultracold Fermi gases based on first principles of QFT. |
| Sebastian Kuehner | |
| MyosinV conformational transitions | |
| abstract : | Calculate conformational transitioins of MyosinV dissociating from actin in an ATP dependent reaction. |
| Dr. Michael Lampe | |
| UG | |
| abstract : | UG is a software framework for the efficient solution of partial differential equations on unstructured grids. Its main features are robust multigrid solvers for unstructured, locally refined meshes, parallel multigrid methods, parallel online visualization and flexibility, which enables it to be applied to such diverse application fields like Navier-Stokes equations, elastoplasticity, density driven flow and multiphase flow in porous media. UG contains a large library of parallel solution methods for linear, nonlinear and time dependent problems and a parallel grid manager that is capable of local refinement and coarsening of unstructured meshes in two and three space dimensions. |
| Dr. Stefan Lang | |
| Scalable Simulation of Neuron Networks | |
| abstract : | Aim of this project is the simulation of realistic neuron networks with novel numerical methods. Requirements for these methods are to allow both reliable precise simulation as well as fast and efficient computation of individual cells and whole networks. and fast |
| Ernst Lexen | |
| Modelling of 3D Radiation Fields | |
| abstract : | Radiative transfer calculations are the most important tool for modelling and interpretation of spectra of astrophysical objects. Unfortunately, radiative transfer in multidimensional objects involves high dimensional calculations (three spatial, two angle, one frequency variables) and highly varying function (density, extinction coefficients) and therefore needs sophisticated numerics. For this project we want to use a state of the art finite element code that has been developed in the group of Prof. Rannacher by G. Kanschat (Ph.D. Thesis 1996) and E. Meinköhn (Ph.D. Thesis 2002). |
| Dr. Edward Xiaochuan Li | |
| Simulation of muscle-regulation proteins | |
| abstract : | Molecular Dynamics of proteins involved in the regulation of muscle contraction. |
| Dr. Aixiao Li | |
| reaction pathway simulations of hydrolase enzymes | |
| abstract : | Molecular Dynamics and reaction pathway simulation of enzymes |
| Martin Lindner | |
| Digital Embryos | |
| abstract : | Cell tracking on 4D microscope data. |
| Dr. Justo Lorenzo Bermejo | |
| Statistical genetics | |
| abstract : | Development and application of robust and adaptive methods for the analysis of genetic data |
| Xinghua Lou | |
| Digital Zebrafish | |
| abstract : | Reconstruct lineage-tree from microscopic digital zebrafish data (3D+T). |
| Prof. Thomas Ludwig | |
| High Performance Parallel Input/Output | |
| abstract : | The framework of the development of high performance parallel input/output mechanisms, conducted in the group of Prof. Ludwig, requires also testing and evaluation of concepts in production environments. Newly developed deployment and optimization techniques for parallel I/O target at their application in the Helics environment. Users of this cluster enviroment shall benefit from new results in that field. |
| Tobias Meißner | |
| Gene Expression Profiling of Multiple Myeloma | |
| abstract : | Gene Expression Profiling of Multiple Myeloma |
| Julian Merten | |
| Adaptive reconstruction of galaxy clusters | |
| abstract : | Weak and strong gravitational lensing can be combined on adaptive grids making optimal use of the available, observable information. We have developed a suitable parallel code using an adaptive grid that is able to reconstruct the distribution of dark matter in galaxy clusters on all accessible scales. The code is highly optimized for numerical performance, but its necessarily iterative nature requires execution times of 180 Opteron-CPU hours per cluster reconstruction. Extended data fields which are now routinely available thus require the execution of the code on suitably large, multi-processor machines, to which the code is already fully adapted. |
| Barmak Mostofian | |
| Analysis of the physio-chemical features of amino acids and other small biomolecules and their effect on the water environment by use of simulation and modeling techniques | |
| abstract : | Investigation of amino acids' and related compounds' physico-chemical features through analysis of simulation and modeling results. |
| Amsaveni Muruganantham | |
| Structure, reactivity of non-heme Fe-oxo complexes | |
| abstract : | Density functional and ab-initio calculations will be used to study the structure and reactivity of non-heme Fe-oxo complexes. |
| Thomas Neusius | |
| Protein Dynamics | |
| abstract : | We will perform long timescale molecular dynamics simulations of peptides in order to study their dynamical properties |
| Dr. David Nutt | |
| Molecular recognition at ice-water interfaces | |
| abstract : | Molecular dynamics simulations of biomolecules at the ice-water interface will be performed to understand the processes occurring during surface recognition and binding. |
| Jamie O'Sullivan | |
| Large-Scale Simulations of Protostellar Jets | |
| abstract : | We carry out large-scale multidimensional simulations of protostellar jet outflows using the PLUTO astrophysical HD/MHD code and a non-equilibrium molecular cooling module. We investigate the case for j-shocks as sources for molecular emission from these objects by simulating the flows with molecular chemistry. |
| Dr. Marek Orzechowski | |
| Structural simulations of troponin | |
| abstract : | Contraction of striated and cardiac muscles is regulated by a mechanism involving two major components: tropomyosin (Tm) and troponin (Tn). Tropomyosin strands that run along the actin filaments block the myosin-binding sites in resting muscle. However, when concentration of Ca2+ ions is increased, the position of tropomyosin on actin is shifted and the myosin-binding sites are unblocked. This leads to myosin-crossbridge cycling on actin and, as a result, muscle contraction. The unblocking of myosin-binding sites is triggered by troponin. Troponin is a complex of three proteins: Ca2+ binding troponin C (TnC), troponin T (TnT), and troponin I (TnI) that bind to the tropomyosin/actin filament. Despite extensive characterization, the mechanism by which troponin shifts the position of Tm on actin is still unclear. For instance, it is known from mutation studies that the lack of the C-terminus of cardiac TnI (cTnI) is associated with myocardial stunning. However, the role of this domain of cTnI is still unknown. It has been proposed in a recent “fly-casting” model that part of cTnI competes with Tm for an access to binding site on F-actin. The question of cTnI role will be addressed and investigated by molecular dynamics simulations at atomic resolution. Another objective is to determine the location and orientation of the main troponin complex on F-actin at low and high concentration of Ca2+ ions. |
| Dr. Francesco Pace | |
| Simulations of cosmologies with early dark energy | |
| abstract : | Nonlinear structure formation in cosmological models with dynamical, early dark energy will be simulated and tested for observational consequences on the counts of dark-matter halos. |
| Dr. Tobias Paul | |
| Bose-Einstein condensates in presence of disorder | |
| abstract : | We intend to study the dynamical properties of superfluid Bose-Einstein condensates in presence of defects and disorder. To that end, we will simulate the time-dependent dynamics of the condensate in the framework of the Gross-Pitaevskii Mean-Field description. In particularly we will focus on the generic insability leading to a breakdown of the superflow beyond a critical velocity. |
| Markus Petersheim | |
| Radiotherapy with external keV-photons | |
| abstract : | Unlike photons in the MeV-range, X-rays from kilovolt sources show no build-up effect in their depth-dose characteristics. Therefore it seems a priori impossible to treat below surface areas effectively with single external beams of such radiation. By introducing a large number of incident beams with different configuration parameters such as angles and distances, the energy deposit per volume to normal tissue (NT) can be reduced significantly in favor of dose application to the planning target volume (PTV). An automated algorithm (linear programming) to find the optimal configuration conditions will be developed and tested. Furthermore, the dose enhancement through Auger-electrons produced by artificially induced gold nano-particles inside the tumor volume will be analyzed. The feasibility and clinical suitability of this concept will be evaluated using Monte Carlo simulation (GEANT4) on the example of a 50 kVp X-ray source from Xoft Inc., Fremont, CA. with an additional collimator. |
| Patrick Ploetz | |
| Complex dynamics of interacting many-body systems | |
| abstract : | Solution of the time-dependent Schroedinger equation in a untruncated many-particle Hilbert space for computation of dynamical observables and spectral statistics. |
| Dr. Torsten Rathmann | |
| bwGRiD | |
| abstract : | service for grid users: consulting, documentation, software installation |
| Dr. Michael Rauch | |
| SFitter-Code | |
| abstract : | Development of the SFitter code from the LHC project of Prof. T.Plehn (ITP) |
| Dr. Thomas Richter | |
| Simulation of Fluid Structure Interaction problems | |
| abstract : | large three dimensional simulations of bio-medical flow applications |
| Georg Robbers | |
| Models of Dark Energy | |
| abstract : | Cosmological observations show that our Universe is undergoing an accelerated expansion. In order to explain this surprising fact, modern theories postulate the existence of a new form of energy with a negative pressure, called \'Dark Energy\' or \'quintessence\'. In this project, we compute the predictions of theoretical models of dark energy for the cosmic microwave background and large scale structure, and compare these predictions with observations. We are in particular investigating ways in which the specific models and quintessence in general can be either detected, constrained or ruled out via observations. |
| Kaspar Sakmann | |
| Many-body dynamics of Bose-Einstein condensates | |
| abstract : | Bose-Einstein condensates constitute controllable interacting many-body systems. Their approximate description either by mean-field equations or direct diagonalization studies has been shown to be insufficient in many interesting cases. In this project we investigate the true many-body nature of interacting Bose-Einstein condensates. In particular, the dynamics of these quantum systems is investigated by using the recently developed MCTDHB method. The method will be applied to physical problems in one and two spatial dimensions, such as Josephson junctions and interference experiments. |
| Sven Sanwald | |
| Direct numerical simulation of reactive flow | |
| abstract : | By means of direct numerical simulations all relevant scales of the fluid flow and the chemistry are resolved to gain deeper inside into the interconnection of chemical and flow scales. Due to the huge demand for computational resources different time integration methods are tested for their applicability to reactive DNS in different test cases. |
| Thomas Schubert | |
| Structural Ordering of Exotic Biomimetic Membranes | |
| abstract : | The main focus of the project is the complementary combination of structural data (obtained by specular and off-specular x-ray and neutron scattering) and molecular dynamics simulation of lipids with atomistic detail (GROMACS). For fluid lipid membranes, we are mostly interested in extracting electron density profiles and in-plane head group interactions. Extending these standard conditions, we are also interested in creating ordered gel-phase membranes to model scattering results of ordered systems and improve our current understanding of the molecular details. The effects we observe are sometimes dependent on subtle molecular differences and thus absolutely require modeling in atomistic detail. Furthermore, few atomistic computational studies so far have dealt with gel phase systems at all1-3 which imparts a fundamental impact to this project. |
| Roland Schulz | |
| INM | |
| abstract : | The Instantaneous Normal Mode (INM) theory predicts, that the diffusion constant is proportional to the number of diffusive modes. The diffusive modes are a subset of all modes with a negative eigenvalue of the Hessian matrix. This subset was computed with good agreement for simple liquids with different filtering methods. We evaluated those methods on a protein over a temperature range from 20-300K. As benchmark for the filtering methods, we compared the so computed diffusion constant with that computed from MSD. For the escape mode method we got a good agreement over two decades. This enables us, to compute temperature dependent dynamical properties of proteins from a few sampled configurations and are able to reproduce the dynamical transition. |
| Dr. Steffen Schumann | |
| LHC event simulation | |
| abstract : | LHC event simulation |
| Daniel Sellmann | |
| Simulation of Bouquet Formation in meotic prophase | |
| abstract : | Monte Carlo Simulation of a bond fluctuation model (BFM) to investigate the mechanisms leading to the so called Bouquet Formation, which is thought to be important for the pairing of homologous chromosomes, in the propahse of meosis. |
| Prof. Hans-Peter Sinn | |
| Classification of IHC breast cancer data | |
| abstract : | Several approaches have been made to establish a molecular classification for breast cancer. With the knowledge that has been gained by gene expression data, and the proposed Sorlie classification, we will try to reproduce these classification scheme using our immunohistochemistry (IHC) data on breast cancer patients. The aim is to gather a set of IHC markers that can be used for molecular classification. We will use unsupervised clustering, specifically software that was developed for unspervised clustering of gene expression data. |
| Daniel Spielmann | |
| Stochastic quantization on the lattice | |
| abstract : | The infrared behavior of Green's functions in Landau gauge QCD provides an important test of confinement scenarios such as Gribov-Zwanziger or Kugo-Ojima. However, the results for the ghost and gluon propagator obtained so far on the lattice contradict those from functional methods in the continuum. Stochastic gauge fixing in the framework of lattice gauge theory provides a new method to tackle the Gribov problem of gauge fixing. As this optimization problem is NP-hard, the numerical cost needed to obtain a useful approximation to the global maximum of the gauge fixing functional is high. Moreover, reliably determining the infrared behavior of Green's functions requires large lattices. |
| Thomas Splettstoesser | |
| Exploring structure and dynamics of actin protein | |
| abstract : | The protein actin provides the structural framework (cytoskeleton) in eukaryotic cells. It exists in two forms; As monomeric G-actin with a bound nucleotide (ATP or ADP) or as filamentous F-actin which is formed upon polymerization of ATP-bound G-actin monomers. The nature of the bound nucleotide determines the conformation of the protein and influences the properties of the filament. Our study aims at understanding the mechanism of the nucleotide dependent conformational change that takes place in the protein. |
| Dzmitry Starukhin | |
| Gas-phase surface reactions | |
| abstract : | Reactions of different gas phase molecules with molecules adsorbed on various transition metal catalyst surfaces will be investigated employing DFT calculations along with molecular dynamics simulations. |
| Dr. Alexej I. Streltsov | |
| Dynamics of Many-Boson systems | |
| abstract : | Time depandent Schrödinger equation is solved numerically for many-bosonic systems. Goal of this project is to see whether the present integration scheme can be optimized and paralellized. |
| Dr. Bogdan Tarus | |
| A study of protein folding under confinement | |
| abstract : | Classical molecular dynamics of ABeta-protein and the chicken villin headpiece subdomain (HP-36) in explicit and implicit solvent models will be performed. The dynamics and kinetics of the folding process is studied under confining conditions. Replica Exchange Molecular Dynamics method will be used to enhance the sampling. The free energy profile will be raised using geometric and kinetic clustering algorithms. |
| Ghazal Tayebirad | |
| Transport of the Bose-Einstein condensate | |
| abstract : | The main idea of this project is to study the transport of the Bose Einstein condensates in different engineered potentials (Optical Lattices) by mean-field theory based on the Gross-Pitaevskii equation, and find ways to control the decay rate of the system. |
| Lipi Thukral | |
| Molecular dynamics simulations on beta hairpin | |
| abstract : | The folding mechanism of β-hairpins, secondary structural elements in proteins, represents an issue of intense ongoing debate in current protein folding research.Until today, the rate-limiting steps of β-hairpin folding and the mechanistic role of the turn sequence are not well understood in spite of the fundamental importance of hairpins in folding and stability of proteins. Our goal is to perform molecular dynamics simulations of the experimentally investigated peptides which will elucidate conformational transitions at an atomic level. |
| Dr. Jakob Ulmschneider | |
| Simulation of Membrane Proteins | |
| abstract : | Simulation of the adsorption, folding, and insertion of membrane proteins into biological membranes |
| Dr. Oriol Vendrell Romagosa | |
| Quantum dynamics of water clusters with MCTDH | |
| abstract : | The infrared spectroscopy and dynamics of protonated water clusters in the gas phase is studied by quantum molecular dynamics with the MCTDH method. The project contemplates the extension of the parallelized version of the Heidelberg-MCTDH package . |
| Khoa Vo | |
| Parallel solver for Bandwidth Optimization Problem | |
| abstract : | The bandwidth minimization problem is a combinatorial optimization studied since about 1960. Given a graph G=(V,E)on N nodes, the task is to find a labeling l of the nodes with numbers from 1-N such that maximum difference |l(u)-l(v)|, for (u,v)in E, is minimized. It is NP-Complete, even for binary trees. The gaps between lower and upper bounds are still large for recent results. This project applies the latest methods on a parallel cluster, so that better results for the problem can be found. |
| Karine Voltz | |
| Multiscale simulation of the nucleosome | |
| abstract : | Study of the nucleosome with all-atom and coarse-grained molecular dynamics techniques. |
| Victor Vysotskiy | |
| Calculation of short-lived electronic states | |
| abstract : | 1) Calculations in parallel of non-zero elements of a target large matrix (hamiltonian); 2) Parallel multiplication of resulting sparse matrix by vector. |
| Prof. Werner Wetzel | |
| Coordination of projects from ITP | |
| abstract : | As the Computer coordinator of ITP, I will have to advice the various groups which intend to use the BW-grid facility |
| Mai Zahran | |
| study of complex DNA/EcoRV by molecular dynamic | |
| abstract : | EcoRV is a restriction enzyme produced by Escherichia Coli. The function of EcoRV is to destroy invading foreign DNA by cleaving it at a GATATC sequence. The main question is how and why the enzyme EcoRV recognizes specifically the DNA sequence GATATC? And so the aim of this work is to study the mechanism of binding and bending of the DNA in contact with EcoRV by molecular dynamics simulation |
| Yang Zhang | |
| Chromatin Structure in Interphase and Metaphase | |
| abstract : | We investigate the folding transition from interphase to metaphase based on the Dynamic Loop model developed in our group. Especially, we are interested in the changes in the loop structure of chromatin necessary to force this transition. |
Hermann Lauer, webmaster@iwr.uni-heidelberg.de
Last Update: 19.10.2009
Last Update: 19.10.2009
