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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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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.

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. More: Leg Implant Simulations Keep Medical Field and Patients Moving Forward …

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