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Glycosylated epidermal growth factor receptor (EGFR) in a lipid membrane. Glycans attached to glycosylation sites on the extracellular (upper) side of the membrane are rendered as stick models with transparent surfaces.

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

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.

Principal Investigator: Ilpo Vattulainen, Department of Physics, Tampere University of Technology (Finland)
HPC Platform: Hermit of HLRS - Date published: April 2015

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

On the Gating Mechanism of Ligand-Gated Ion Channels (LGICs)

On the Gating Mechanism of Ligand-Gated Ion Channels (LGICs)

Ligand-gated ion channels (LGIC) play a central role in intercellular communication in the central and peripheral nervous systems as well as in non neuronal cells. Understanding their function at an atomic level of detail will be beneficial for the development of drug therapies against a range of diseases including Alzheimer's disease, schizophrenia, pain, and depression. By capitalizing on the increasing availability of high-resolution structures of both pentameric and trimeric LGICs we aim at elucidating the molecular mechanism underlying activation/deactivation by atomistic Molecular Dynamics (MD) simulations, which is essential to rationalize the design of potent allosteric modulators.

Principal Investigator: Marco Ceccini, ISIS, University of Strasbourg (France)
HPC Platform: SuperMUC of LRZ - Date published: March 2015

More: On the Gating Mechanism of Ligand-Gated Ion Channels (LGICs) …

Nano-Gold at the Bio-Interface

Nano-Gold at the Bio-Interface

A 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.

Principal Investigator: Hannu Häkkinen, Nanoscience Center
University of Jyväskylä (Finland)
HPC Platform: Hermit of HLRS - Date published: March 2015

More: Nano-Gold at the Bio-Interface …

The Mechanisms of Vision Studied by Quantum Monte Carlo Calculations

The Mechanisms of Vision Studied by Quantum Monte Carlo Calculations

In the rod cells of the eyes of vertebrates, a special protein, named Rhodopsin, is responsible for the detection of the light and is directly involved in the activation of the signaling cascade that triggers the nervous pulses of the retina. The deep understanding of the early mechanisms of light vision goes beyond the scientific interest as it is also an important issue for the rationalization of many retina diseases.

Principal Investigator: Leonardo Guidoni, Computational Biophysics, Biochemistry, and Chemistry, University of L'Aquila (Italy)
HPC Platform: JUQUEEN of JSC - Date published: February 2015

More: The Mechanisms of Vision Studied by Quantum Monte Carlo Calculations …

The Allosteric Effect of the SH2 Domain on Abl Kinase Activation

The Allosteric Effect of the SH2 Domain on Abl Kinase Activation

Protein kinases are the key enzymes that control most cellular activities. A kinase that fails to work properly can therefore cause severe damage to the organism, causing diverse diseases including cancer. It is therefore highly desirable to develop drugs that modulate the activity of specific protein kinases.

Principal Investigator: Francesco Luigi Gervasio, Department of Chemistry and Institute of Structural Molecular Biology,University College London (UK)
HPC Platform: SuperMUC of LRZ - Date published: January 2015

More: The Allosteric Effect of the SH2 Domain on Abl Kinase Activation …

Unravelling the Influence of Protein Dynamics on Molecular Recognition

Unravelling the Influence of Protein Dynamics on Molecular Recognition

Using Petascale system SuperMUC of the Leibniz Supercomputing Centre in Garching/Munich, scientists conducted simulations of mutated proteins to quantify and understand the mechanism of the change in population of binding compatible versus non-compatible states. This resulted in a predicted change in binding affinity which is a property that can be validated experimentally.

Principal Investigator: Bert de Groot, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)
HPC Platform: SuperMUC of LRZ - Date published: January 2015
More: Unravelling the Influence of Protein Dynamics on Molecular Recognition …

Cellular Logistics Controlled by Disordered FG-Nucleoporins

From Biomolecular Structures to Thermodynamic Ensembles: Cellular Logistics Controlled by Disordered FG-Nucleoporins

The structural characterization of disordered proteins is an inherently under-determined problem: a small number of restraints are insufficient to uniquely define the conformations of a system with thousands of degrees of freedom. Molecular simulations, with their empirical force fields, can offer the additional information required to obtain conformational ensembles for disordered states of proteins. However, these simulations must contend with a massive sampling problem, which was successfully achieved by a team of scientists of the Max Planck Institute for Biophysical Chemistry in Göttingen using HPC system SuperMUC.

Principal Investigator: Helmut Grubmüller, Theoretical and Computational Biophysics, Max-Planck-Institut für biophysikalische Chemie, Göttingen (Germany)
HPC Platform: SuperMUC of LRZ - Date published: November 2014
More: From Biomolecular Structures to Thermodynamic Ensembles: Cellular Logistics Controlled by Disordered FG-Nucleoporins …

Probing Biological Water With First-Principle Simulations

Probing Biological Water With First-Principle Simulations

A team of researchers from the Johannes Gutenberg-Universität Mainz is currently investigating the structure, vibrational dynamics, and energetics of biological water at the surface of a mini-protein known as Anti-freeze protein. The Anti-freeze protein helps organisms to survive below zero degree Celsius by inhibiting ice growth.

Principal Investigator: Thomas Kühne, Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz (Germany)
HPC Platform: JUQUEEN of JSC - Date published: November 2014

More: Probing Biological Water With First-Principle Simulations …

Highly Resolved Simulations of Hemodynamics in Intracranial Aneurysms

Highly Resolved Simulations of Hemodynamics in Intracranial Aneurysms

A significant part of modern mortality is contributed by strokes, caused by the rupture of intracranial aneurysms. The deployment of a flow diverter stent in the parent artery of an aneurysm is a novel and minimally invasive treatment procedure. Numerical simulations of the complex dynamic flow can help to better understand important effects and to optimize the design of such stents.

Principal Investigator: Sabine Roller, Simulation Techniques and Scientific Computing, University of Siegen (Germany)
HPC Platform: SuperMUC of LRZ - Date published: July 2014
More: Highly Resolved Simulations of Hemodynamics in Intracranial Aneurysms …

Molecular Dynamics Simulation of Protein-Protein Complex Formation in a Crowded Environment

Molecular Dynamics Simulation of Protein-Protein Complex Formation in a Crowded Environment

A research project on HPC system SuperMUC or LRZ Garching/Munich aimed at simulating the formation of specific and non-specific protein-protein complexes and investigating the effect of additional protein molecules (crowding) on complex formation in atomic detail.

Principal Investigator: Martin Zacharias, Physik-Department T38, Technische Universität München (Germany)
HPC Platform: SuperMUC of LRZ - Date published: June 2014

More: Molecular Dynamics Simulation of Protein-Protein Complex Formation in a Crowded Environment …

Observing the Bacterial Membrane Through Molecular Modeling and Simulation

Observing the Bacterial Membrane Through Molecular Modeling and Simulation

One strategy to develop new and more efficient antibiotics that are less prone to generate resistance is to target and destabilize the bacterial membrane. In this context, investigating the physical and chemical principles governing the nature of bacterial membranes is of fundamental importance for understanding the functional role of lipid bilayers.

Principal Investigator: Matteo Dal Peraro, École Polytechnique Fédérale de Lausanne (Switzerland)
HPC Platform: JUQUEEN of JSC - Date published: March 2014
More: Observing the Bacterial Membrane Through Molecular Modeling and Simulation …

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

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


Membrane proteins are major targets for a wide range of drugs and other therapeutic agents. They play a key role in the biology of infection by pathogens, including both bacteria and viruses. Large scale computer simulations allow researchers to study the movements of membrane proteins in their native membrane environments.

Principal Investigator: Mark S. P. Sansom, University of Oxford (Great Britain)
HPC Platform: Hermit of HLRS - Date published: February 2014
More: MD Simulations of Large Membrane Systems: From Membrane Protein Arrays to the Influenza Virus …

Mesoporous silica for drug delivery: a quantum mechanical simulation

Mesoporous Silica for Drug Delivery: A Quantum Mechanical Simulation

Scientists used HPC system SuperMUC to simulate by quantum mechanical methods the features of the MCM-41 (Mobil Composition of Matter) mesoporous silica material with respect to the adsorption of ibuprofen, one of the most common anti-inflammatory drugs.

Principal Investigator: Piero Ugliengo, Department of Chemistry, University of Torino (Italy)
HPC Platform: SuperMUC of LRZ - Date published: February 2014
More: Mesoporous Silica for Drug Delivery: A Quantum Mechanical Simulation …

A Scalable Hybrid Approach to Accurately Simulate Biomolecules on SuperMUC?

A Scalable Hybrid Approach to Accurately Simulate Biomolecules on SuperMUC

A team of scientists combined an application for density functional calculations, and an in-house developed program package for molecular mechanical simulations on HPC system SuperMUC. The new approach significantly enhances the accuracy compared to conventional hybrid molecular dynamics approaches and covers interactions of the inducible dipoles from polarizable molecula mechanics with the electron density.

Principal Investigator: Gerald Mathias, Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München (Germany)
HPC Platform: SuperMUC of LRZ - Date published: January 2014
More: A Scalable Hybrid Approach to Accurately Simulate Biomolecules on SuperMUC …

Binding of a small molecule (black) ho Hsp90 (grey)

Chaperone Proteins in the Crash Test

Using high-performance computer simulations and novel ways of analysing forces within proteins, a team of scientists of the Molecular Biomechanics Group at the Heidelberg Institute of Theoretical Studies (HITS) under leadership of Dr. Frauke Gräter analysed how the heat shock protein Hsp90, a helper protein vital to any cell in any organism, is switched by the binding of a small molecule.

Principal Investigator: Frauke Gräter, Molecular Biomechanics - HITS gGmbH, Heidelberg (Germany)
HPC Platform: SuperMUC of LRZ -- Date published: November 2013

More: Chaperone Proteins in the Crash Test …

Micromechanical Behaviour of DNA

Micromechanical Behaviour of DNA

Using HPC simulations, scientists are doing research on novel single-molecule manipulation techniques in biophysics and bio-nanotechnology to analyse the dynamics of the DNA macromolecule exposed to hydrodynamic flow and complex DNA-liquid interactions by numerical simulations.

Principal Investigator: Nikolaus A. Adams, Lehrstuhl für Aerodynamik und Strömungsmechanik, Technische Universität München (Germany)
HPC Platform: HPC Systems at LRZ - Date published: July 2013

More: Micromechanical Behaviour of DNA …

Dynamics of Membrane Spanning Protein Helices

Dynamics of Membrane Spanning Protein Helices

A team of scientists from Technische Universität München conduct molecular dynamics simulations on GCS supercomputers to probe the interactions of transmembrane domains, their structural dynamics, and their impact on the surrounding membrane.

Principal Investigator: Christina Scharnagl, Physics Department and ZNN/WSI, Technische Universität München (Germany)
HPC Platform: HPC Systems of LRZ - Date published: July 2013
More: Dynamics of Membrane Spanning Protein Helices …

Background image shows pressure distribution throughout the entire airway tree. Left image shows the local strain in the lung vesicles. Right image portrays the current in the central airway.

Virtual Lung

Mechanical ventilation for patients suffering from lung diseases can lead to severe complications. Computer simulations contribute to gaining new insights into so called ventilation-induced lung injuries.

Principal Investigator: Wolfgang A. Wall, Institute for Computational Mechanics, Technische Universität München (Germany)
HPC Platform: HPC Systems at LRZ - Date published: July 2013

More: Virtual Lung …

Streamlines of the nasal cavity flow

Researchers Sniff at Computer-Aided Nasal Cavity Surgeries

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.

Principal Investigator: Andreas Lintermann, Fluid Mechanics and Institute of Aerodynamics, RWTH Aachen University (Germany)
HPC Platform: Hermit of HLRS - Date published: July 2013
More: Researchers Sniff at Computer-Aided Nasal Cavity Surgeries …

Simulating Blood Cells and Blood Flow

Simulating Blood Cells and Blood Flow

Blood performs a multitude of functions on its way through our body, from the transport of oxygen to the immune response after infections. In addition, the circulatory system may be also affected by injuries which cause bleeding, by the formation of plaques in arteries which cause coronary heart disease, and it provides the pathway for the organism invasion by bacteria or viruses. Thus, modeling of blood flow and its functions is an important challenge with many medical implications, but also with many interesting physical phenomena.

Principal Investigator: Dmitry Fedosov, Institute of Complex Systems (ICS-2), Research Center Juelich, Germany
HPC Platform: JUQUEEN of JSC - Date published: July 2013

Pressure in a bone

Leg Implant Simulations Keep Medical Field and Patients Moving Forward

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.

Principal Investigator: Ralf Schneider, HLRS Stuttgart (Germany)
HPC Platform: Hermit of HLRS - Date published: July 2013
More: Leg Implant Simulations Keep Medical Field and Patients Moving Forward …

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