Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecular Dynamics Computer Simulations (molecular + dynamics_computer_simulation)
Selected AbstractsModeling H3 histone N-terminal tail and linker DNA interactionsBIOPOLYMERS, Issue 2 2006Giovanni La Penna Abstract Molecular dynamics computer simulations were performed for the 25-residue N-terminal tail of the H3 histone protein in the proximity of a DNA segment of 10 base pairs (bp), representing a model for the linker DNA in chromatin. Several least biased configurations were used as initial configurations. The secondary structure content of the protein was increased by the presence of DNA close to it, but the locations of the secondary motifs were different for different initial orientations of the DNA grooves with respect to the protein. As a common feature to all simulations, the electrostatic attraction between negatively charged DNA and positively charged protein was screened by the water solvent and counterbalanced by the intrinsic compaction of the protein due to hydrophobic effects. The protein secondary structure limited the covering of DNA by the protein to 4,5 bp. The degree of compaction and charge density of the bound protein suggests a possible role of H3 tail in a nonspecific bending and plasticity of the linker DNA when the protein is located in the crowded dense chromatin. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 135,147, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Computer simulation study on propagation of nonlinear waves through heavily defective crystalsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2004Y. Hiki Abstract A molecular dynamics computer simulation has been performed for a monatomic, anharmonic, and two-dimensional hexagonal crystal. Central forces between the nearest neighbor atoms and anharmonic forces up to the third order are considered. Pulse displacements are applied to the line of atoms at the left end of a rectangular model crystal, in the right half of which a number of light or heavy mass defects are randomly placed. Phonons or solitons propagating in the crystal and scattered by the defects are observed. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] On the direct calculation of the free energy of quantization for molecular systems in the condensed phaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Daan P. Geerke Abstract Using the path integral formalism or the Feynman-Hibbs approach, various expressions for the free energy of quantization for a molecular system in the condensed phase can be derived. These lead to alternative methods to directly compute quantization free energies from molecular dynamics computer simulations, which were investigated with an eye to their practical use. For a test system of liquid neon, two methods are shown to be most efficient for a direct evaluation of the excess free energy of quantization. One of them makes use of path integral simulations in combination with a single-step free energy perturbation approach and was previously reported in the literature. The other method employs a Feynman-Hibbs effective Hamiltonian together with the thermodynamic integration formalism. However, both methods are found to give less accurate results for the excess free energy of quantization than the estimate obtained from explicit path integral calculations on the excess free energy of the neon liquid in the classical and quantum mechanical limit. Suggestions are made to make both methods more accurate. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2001Lewis Whitehead Abstract The development of a coarse-grained reduced-representation model of the hydrocarbon region of a biological membrane is reported. The potential is based on the popular Gay,Berne model of liquid crystals, and involves the linking of individual Gay,Berne ellipsoids by harmonic springs to form each hydrocarbon chain. Diffusion coefficients and order parameters have been calculated by molecular dynamics computer simulations for a range of parameter sets. The results clearly demonstrate the presence of a phase transition from an ordered low-temperature solid phase reminiscent of the L,, phase of phospholipids, to a high-temperature disordered phase reminiscent of the L, phase. Order parameters calculated for each layer of the model are consistent with the experimental segmental order parameters reported for dipalmitoyl phosphatidylcholine. The application of this model to the study of small molecule diffusion within the membrane core is proposed. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1622,1633, 2001 [source] Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine,COMPLEXITY, Issue 4 2008Abstract It is commonly agreed that a chemical assembly of molecules can be considered alive if it can ingest resources and convert them into building blocks; has the ability to grow and self-reproduce; and can evolve. In the design proposed by Rasmussen and Chen (Science 2004, 303, 963) the assembly or protocell could be as simple as a small micellar surfactant aggregate acting as a container, anchoring an informational molecule to its exterior and incorporating a metabolism within the oily interior. We present several examples of modeling such a system with molecular dynamics computer simulations. © 2008 Wiley Periodicals, Inc. Complexity, 2008. [source] | ||||||||||