Latest Molecular dynamics Stories
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...
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,...
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...
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...
First-ever simulation of a stretching silver nanowire over a period of a millisecondVery 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...
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...
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...
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...
By Haider, Shozeb Parkinson, Gary N; Neidle, Stephen ABSTRACT Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150-200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such...
By Knee, Kelly M Dixit, Surjit B; Aitken, Colin Echeverria; Ponomarev, Sergei; Beveridge, D L; Mukerji, Ishita ABSTRACT The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG)^sub 2^, d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity....
