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Latest Molecular dynamics Stories

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2010-10-12 12:08:47

Using large-scale computer simulations, researchers at the Georgia Institute of Technology have identified the most important factors affecting how molecules move through the crowded environment inside living cells. The findings suggest that perturbations caused by hydrodynamic interactions "“ similar to what happens when the wake from a large boat affects smaller boats on a lake "“ may be the most important factor in this intracellular diffusion. A detailed understanding of the...

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2010-10-05 08:36:57

Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life. A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life...

2010-09-21 20:56:06

The prediction of the structure and function of biological macromolecules (i.e., the machinery of life) is of foremost importance in the field of structural biology. Since the elucidation of the three-dimensional structure of DNA (the molecule that carries all genetic information) by Watson and Crick, scientists have strived to decipher the hidden code that determines the evolution of the spatial arrangement of these molecules towards their functional native state. Attempts to follow these...

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2010-03-01 07:28:03

A new technique to study protein dynamics in living cells has been created by a team of University of Illinois scientists, and evidence yielded from the new method indicates that an in vivo environment strongly modulates a protein's stability and folding rate, according to research accepted for publication in the journal Nature Methods and posted on the journal's Web site Feb. 28. Martin Gruebele, the James R. Eiszner Professor of Chemistry at Illinois and corresponding author of the paper,...

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2010-01-05 15:00:41

With the passage of a molecule through the labyrinth of a chemical system being so critical to catalysis and other important chemical processes, computer simulations are frequently used to model potential molecule/labyrinth interactions. In the past, such simulations have been expensive and time-consuming to carry out, but now researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a new algorithm that should make future simulations easier and faster to...

2009-11-04 10:08:44

A theoretical physicist at the National Institute of Standards and Technology (NIST) has developed a method for calculating the motions and forces of thousands of atoms simultaneously over a wider range of time scales than previously possible. The method overcomes a longstanding timing gap in modeling nanometer-scale materials and many other physical, chemical and biological systems at atomic and molecular levels. The new mathematical technique* can significantly improve modeling of...

2009-10-29 15:01:27

First-ever simulation of a stretching silver nanowire over a period of a millisecond Very tiny wires, called nanowires, made from such metals as silver and gold, may play a crucial role as electrical or mechanical switches in the development of future-generation ultrasmall nanodevices. Making nanodevices work will require a deep understanding of how these and other nanostructures can be engineered and fabricated as well as their resultant strengths and weaknesses. How mechanical properties...

2009-04-29 15:33:00

PITTSBURGH, April 29 /PRNewswire-USNewswire/ -- High school and undergraduate students now have a ringside seat to watch atoms and molecules in super-slow motion and vivid color, as they jostle and bump each other within the cozy environs of a human cell or a beaker on a lab bench. In "Big Numbers in Small Spaces: Simulating Atoms, Molecules and Brownian Motion," students are invited to consider how many molecules are in a single drop of water, or a single cell, and then to fly in and find...

2009-03-16 15:54:54

Using rigorous computer calculations, researchers from Carnegie Mellon University and the Carnegie Institution of Washington have established evidence that supercooled silicon experiences a liquid-liquid phase transition, where at a certain temperature two different states of liquid silicon exist. The two states each have unique properties that could be used to develop new silicon-based materials. Furthermore, the methods developed can be applied to gain a better understanding of other...

2008-08-22 03:00:15

By J, Pieter Stevens, Mark J ABSTRACT We perform atomistic simulations on a single collagen molecule to determine its intrinsic molecular strength. A tensile pull simulation to determine the tensile strength and Young's modulus is performed, and a simulation that separates two of the three helices of collagen examines the internal strength of the molecule. The magnitude of the calculated tensile forces is consistent with the strong forces of bond stretching and angle bending that are...