LIFE SCIENCES

Life Sciences

Allosteric Regulation of the Human Proteasome

Principal Investigator: Michal H. Kolář , Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry

HPC Platform used: Hazel Hen of HLRS

Local Project ID: GCS-prot

The proteasome is a large biomolecular complex responsible for protein degradation. Recent experimental data revealed that there is an allosteric communication between a core and regulatory parts of the proteasome. In the project, researchers have used atomistic simulations to study molecular details of the allosteric signal – in their study triggered by a covalent inhibitor. While the inhibitor causes only subtle structural changes, the proteasome-wide fluctuation changes may explain the self-regulation of the biomolecular machine.

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Life Sciences

Molecular Simulations of Enzymes Under Reaction Conditions

Principal Investigator: Jürgen Pleiss , Institute of Biochemistry and Technical Biochemistry, University of Stuttgart (Germany)

HPC Platform used: Hazel Hen of HLRS

Local Project ID: Biocat

The development of novel sustainable biocatalytic processes requires systematic studies of the molecular interactions between enzymes, substrates, and solvents. Based on the HLRS HPC infrastructure, comprehensive molecular simulations were performed to investigate substrate binding in enzymatic reaction systems.

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Life Sciences

NACRE - Micromechanics of Biocomposite Materials

Principal Investigator: Frauke Gräter , Heidelberg Institute for Theoretical Studies (Germany)

HPC Platform used: Hornet of HLRS

Local Project ID: PP14102332

Composite materials made up of inorganic and biological matter present remarkable properties including fracture resistance, toughness and strength. A team of scientists of the Heidelberg Institute for Theoretical Studies has been investigating the mechanical properties of nacre, a material that possesses great stability due to its elaborate hierarchical nanostructures.

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Life Sciences

Computational Modelling of a Lipase at a Hydrophobic Substrate Interface

Principal Investigator: Jürgen Pleiss , Institute of Technical Biochemistry, University of Stuttgart (Germany)

HPC Platform used: Hermit of HLRS

Local Project ID: Biocat

To gain further insight into how lipases catalyze the hydrolysis of water-insoluble triglycerides like fats and oils, scientists leveraged the computing power of the HLRS HPC infrastructure for a computational modelling of a lipase at a hydrophobic substrate interface. In total, more than 1μs of molecular dynamics simulations were performed on a system consisting of 100,000 atoms.

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Life Sciences

Unlocking the Role of Lipids in the Activation Mechanism of the Epidermal Growth Factor Receptor (EGFR)

Principal Investigator: Ilpo Vattulainen , Department of Physics, Tampere University of Technology (Finland)

HPC Platform used: Hermit of HLRS

Local Project ID: PP12071362

Scientists from the Tampere University of Technology, Finland, have shown the profound importance of glycosylation in membrane receptor conformation. The researchers used extensive atomistic simulations together with biochemical experiments to show for EGFR that receptor conformation depends in a critical manner on its glycosylation.

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Life Sciences

Nano-Gold at the Bio-Interface

Principal Investigator: Hannu Häkkinen , Nanoscience Center, University of Jyväskylä (Finland)

HPC Platform used: Hermit of HLRS

Local Project ID: PP13081629

A team of scientists of the University of Jyväskylä in Finland leveraged the computing power of HLRS supercomputer Hermit with the aim to study the structure, surface chemistry and functionalization strategies of gold nanoclusters in water - having from a few tens to a few hundreds of gold atoms - and to research their interactions with enteroviruses.

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Life Sciences

MD Simulations of Large Membrane Systems: From Membrane Protein Arrays to the Influenza Virus

Principal Investigator: Mark S.P. Sansom , University of Oxford (Great Britain)

HPC Platform used: Hermit of HLRS

Local Project ID: PP12061115

Membrane proteins are of great biomedical importance. They account for ~25% of all genes and are involved in diseases ranging from diabetes to cancer. Membrane proteins play a key role in the biology of infection by pathogens, including both bacteria and viruses. They also play an important role in signalling within and between cells. It is therefore not surprising that membrane proteins are major targets for a wide range of drugs and other therapeutic agents. Recently, the number of known structures of membrane proteins has started to increase. Large scale computer simulations allow researchers to study the movements of these proteins in their native membrane environments. 

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Life Sciences

Researchers Sniff at Computer-Aided Nasal Cavity Surgeries

Principal Investigator: Andreas Lintermann , Fluid Mechanics and Institute of Aerodynamics, RWTH Aachen University (Germany)

HPC Platform used: Hermit of HLRS

Local Project ID: nose_sim

Medical professionals want supercomputing research to answer questions related to one of humanity’s most basic needs — breathing. Luckily, Andreas Lintermann and a group of researchers at RWTH Aachen University are employing computing resources at the High-Performance Computing Center Stuttgart (HLRS) to do just that.

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Life Sciences

Leg Implant Simulations Keep Medical Field and Patients Moving Forward

Principal Investigator: Ralf Schneider , High Performance Computing Center Stuttgart (Germany)

HPC Platform used: Hermit of HLRS

Local Project ID: BoneImplant

The difference between a broken femur healing in several weeks and an entire hip replacement lies only millimeters apart. Researchers at GCS member centre HLRS (High Performance Computing Center Stuttgart) plan to use computation to make sure treating a broken leg bone in the future is not only precise, but also more personalized.

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