Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecular Dynamics (molecular + dynamics)
Kinds of Molecular Dynamics Terms modified by Molecular Dynamics Selected AbstractsDependency of Tritium Retention in Graphite on Temperature Control of Molecular DynamicsCONTRIBUTIONS TO PLASMA PHYSICS, Issue 3-5 2010A. Ito Abstract We have investigated the carbon plasma facing material and hydrogen atom interaction by the use of molecular dynamics simulation to clarify chemical erosion processes on divertor plate. The present paper is our first try at elucidation of temperature dependence by the molecular dynamics. Temperature was controlled by using Langevin thermostat method. As a result, the retention of hydrogen atom achieve steady state, and the CH4 was generated, which was not found MD simulations without a temperature control method. About 30 percent of injected hydrogen atoms are retained. CH4 yields has a peak at 600 K, which accords with experimental results. A dominant path of CH4 generation found by the present molecular dynamics simulation is as follows: a CH is detached from eroded surface and then it grows into CH4 adsorbing hydrogen atoms via CH2 and CH3. In addition, we propose the problem that the hydrogen atom retention and CH,, yields depend on the thermal relaxation time in MD simulation using temperature control methods (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010Mahmoud Moradi Abstract Depending on their environment, polyproline peptides form chiral helices that may be either left- (PPII) or right-handed (PPI). Here, we have characterized both the structure and free energy landscapes of Ace-(Pro)n -Nme (n an integer less than 13) peptides, in vacuo and in implicit water environments. Both ab initio and classical molecular dynamics methods were used. In terms of the latter, we used a recently developed Adaptively Biased Molecular Dynamics (ABMD) method in conjunction with three different force fields (ff99, ff99SB, ff03) and two different Generalized Born models for the implicit solvent environment. Specifically, the ABMD method provides for an accurate description of the free energy landscapes in terms of a set of collective variables, which were carefully chosen as to reflect the "slow modes" of the polyproline peptides. These are primarily based on the cis - trans isomerization associated with the prolyl bonds. In agreement with recent experimental results, the peptides form not only the pure PPII or PPI structures but also a large number of stable conformers having more or less similar free energies, whose distributions we have characterized. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensorsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2004M. Belmares Abstract We introduce the Cohesive Energy Density (CED) method, a multiple sampling Molecular Dynamics computer simulation procedure that may offer higher consistency in the estimation of Hildebrand and Hansen solubility parameters. The use of a multiple sampling technique, combined with a simple but consistent molecular force field and quantum mechanically determined atomic charges, allows for the precise determination of solubility parameters in a systematic way (, = 0.4 hildebrands). The CED method yields first-principles Hildebrand parameter predictions in good agreement with experiment [root-mean-square (rms) = 1.1 hildebrands]. We apply the CED method to model the Caltech electronic nose, an array of 20 polymer sensors. Sensors are built with conducting leads connected through thin-film polymers loaded with carbon black. Odorant detection relies on a change in electric resistivity of the polymer film as function of the amount of swelling caused by the odorant compound. The amount of swelling depends upon the chemical composition of the polymer and the odorant molecule. The pattern is unique, and unambiguously identifies the compound. Experimentally determined changes in relative resistivity of seven polymer sensors upon exposure to 24 solvent vapors were modeled with the CED estimated Hansen solubility components. Predictions of polymer sensor responses result in Pearson R2 coefficients between 0.82 and 0.99. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1814,1826, 2004 [source] Molecular Dynamics of Podand Studied by Broadband Dielectric and Nuclear Magnetic Resonance Spectroscopies,,MACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 19-20 2007Bakyt Orozbaev Abstract Nuclear magnetic resonance (NMR) and broadband dielectric spectroscopies (BDS) were used to analyze the molecular dynamics in P10.3H Podand. The temperature studies of NMR line and magnetic spin,lattice relaxation times accompanied by DS investigation enabled us to distinguish three main dynamical processes connected with the motions of the P10.3H Podand chains. In the low-temperature region the magnetic relaxation was associated with fast axial C3 rotation of methyl groups. Moreover, two other independent processes were observed and interpreted as (i) segmental motion of both oxyethylene and ethylene units, and (ii) the overall motion involved in the melting process. [source] Linear and Nonlinear Viscoelasticity of a Model Unentangled Polymer Melt: Molecular Dynamics and Rouse Modes AnalysisMACROMOLECULAR THEORY AND SIMULATIONS, Issue 3 2006Mihail Vladkov Abstract Summary: Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli and viscosity, including Green-Kubo and nonequilibrium molecular dynamics (NEMD). An alternative approach, based on the use of the Rouse modes, is also discussed. This approach could be used to assess local viscoelastic properties in inhomogeneous systems. We also focus on the contributions of different interactions to the viscoelastic moduli and explain the microscopic mechanisms involved in the mechanical response of the melt to external solicitation. [source] Structures of the Chromophore Binding Sites in BLUF Domains as Studied by Molecular Dynamics and Quantum Chemical Calculations,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Kazuya Obanayama BLUF (blue-light sensing using FAD) domains constitute a new family of flavin-based blue light photoreceptors. The photocycle of BLUF is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes in the bound chromophore. The hydrogen bond rearrangements upon illumination have been inferred from spectral changes in the chromophore: ,10 nm redshift of the absorption maximum and ,16 cm,1 downshift of the C4=O stretching frequency. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. In particular, the orientation of a conserved Gln (Gln63 in AppA) is presently one of the most questioned topics in the field. Here we perform molecular dynamics simulations for the wild-type AppA, AppA1-124C20S, BlrB and T110078 and furthermore quantum chemical calculations to investigate their spectroscopic properties in the dark and signaling states. On the basis of these results, we reveal the dynamic aspect of hydrogen bonding networks at the active site and propose theoretically reasonable models for the dark and signaling states of the BLUF domains. [source] Ab Initio Molecular Dynamics.ANGEWANDTE CHEMIE, Issue 50 2009Advanced Methods., Basic Theory Cambridge University Press 2009. 578,S., geb., 45.00,£.,ISBN 978-0521898638 [source] Structure and Spectral Properties of Aqueous Hydrogen Fluoride Studied Using ab initio Molecular Dynamics.CHEMINFORM, Issue 52 2002Atte J. Sillanpaeae No abstract is available for this article. [source] Musings on ADME Predictions and Structure,Activity RelationsCHEMISTRY & BIODIVERSITY, Issue 11 2005Bernard Testa The first part of the paper examines Structure,Activity Relations (SARs) and their components from a very general point of view. The various types of interpretation emerging from statistically valid relations will be examined, namely causal (mechanistic), contextual (empirical), fortuitous, and tautological correlations. Implications for ADME predictions will be seen when discussing the diversity of interactions between active compounds (e.g., drugs) and biological systems. The second part of the paper is more specific and presents the concept of molecular-property space, an all but neglected concept in SARs. Recent results from Molecular Dynamics (MD) simulations and Molecular Interaction Fields (MIF) computations of acetylcholine will be used to illustrate not only the well-known conformational space of this molecule, but also its property space as exemplified by its lipophilicity space. It will be seen that a molecule as small as acetylcholine is able to span a relatively broad property space. Most significantly in an ADME perspective, the molecule is able, within the limits of its property space, to adapt to the medium. This is equivalent to saying that the medium constrains the molecule to resemble it as much as feasible. [source] Spectroscopic Properties in the Liquid Phase: Combining High-Level Ab Initio Calculations and Classical Molecular DynamicsCHEMPHYSCHEM, Issue 1 2006Michele Pavone Dr. Abstract We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques. [source] Binding of ciprofloxacin by humic substances: A molecular dynamics studyENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2010Ludmilla Aristilde Abstract A comprehensive assessment of the potential impacts of antimicrobials released into the environment requires an understanding of their sequestration by natural particles. Of particular interest are the strong interactions of antimicrobials with natural organic matter (NOM), which are believed to reduce their bioavailability, retard their abiotic and biotic degradation, and facilitate their persistence in soils and aquatic sediments. Molecular dynamics (MD) relaxation studies of a widely used fluoroquinolone antibiotic, ciprofloxacin (Cipro), interacting with a model humic substance (HS) in a hydrated environment, were performed to elucidate the mechanisms of these interactions. Specifically, a zwitterionic Cipro molecule, the predominant species at circumneutral pH, was reacted either with protonated HS or deprotonated HS bearing Ca, Mg, or Fe(II) cations. The HS underwent conformational changes through rearrangements of its hydrophobic and hydrophilic regions and disruption of its intramolecular H-bonds to facilitate favorable intermolecular H-bonding interactions with Cipro. Complexation of the metal cations with HS carboxylates appeared to impede binding of the positively charged amino group of Cipro with these negatively charged HS complexation sites. On the other hand, an outer-sphere complex between Cipro and the HS-bound cation led to ternary Cipro,metal,HS complexes in the case of Mg,HS and Fe(II),HS, but no such bridging interaction occurred with Ca,HS. The results suggested that the ionic potential (valence/ionic radius) of the divalent cation may be a determining factor in the formation of the ternary complex, with high ionic potential favoring the bridging interaction. Environ. Toxicol. Chem. 2010;29:90,98. © 2009 SETAC [source] Sorption kinetics of toluene in humic acid: A computational approachENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 2 2006Yang-Hsin Shih Abstract Molecular dynamics, a computational technique aiming to describe the time-dependent movement of molecules, has been applied to study the sorption kinetics of volatile organic contaminants in soil organic matter. The molecular dynamics simulation results obtain reasonably accurate estimates of diffusion rates and activation energy of the penetration of a volatile organic compound molecule into a model humic substance. The sorption rate of toluene to humic acid decreases with the density of the humic acid matrix and increases with temperature. All the present results indicate that the sorption of toluene into humic acid is mainly diffusion controlled. Finally, the present studies have shown that molecular dynamics of volatile organic compounds in humic substances yields meaningful results, which help in the understanding of diffusion at the molecular level and which facilitate the problem-solving capability for removing the contaminants from the soils. [source] Molecular dynamics of the generation process of double-walled carbon nanotubes from peapodsHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 4 2006Yasushi Shibuta Abstract The generation process of a double-walled carbon nanotube (DWNT) from a "peapod" was studied by classical molecular dynamics simulation. Starting from a peapod structure, defined by five C60 molecules inside a (10,10) single-walled carbon nanotube (SWNT), polymerized fullerenes, a peanut-like structure and an almost nanotube-like structure were obtained under suitable conditions of temperature control. The mean distance between the two layers of the DWNT agreed with an experimental report that it is larger than the interlayer spacing found in multi-walled carbon nanotubes (MWNTs). In addition, the chirality dependence of the potential energy of a DWNT on the relative chirality of its constituent tubes was examined using a 6-12 Lennard-Jones potential. It was found that the potential energy depends only on the distance between the two layers, not on the relative chiralities. © 2006 Wiley Periodicals, Inc. Heat Trans Asian Res, 35(4): 254,264, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20115 [source] Molecular dynamics in the formation process of single-walled carbon nanotubesHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 8 2003Yasushi Shibuta Abstract The mechanism of the nucleation and formation of single-walled carbon nanotubes (SWNTs) was investigated using molecular dynamics simulations. When the initial state was chosen so that carbon and nickel atoms were randomly distributed in a simulation domain, the formation of a random cage structure made up of carbon atoms, which had a few nickel atoms inside it, was observed by 6 ns. The nickel atoms, which move inside or on the surface of the cage, were seen to be preventing the complete closure of the cage and its anneal into the fullerene structure. Further, in order to observe a longer time-scale growth process, the simulation cell was artificially shrunk by the progress of simulation so that collisions between precursor clusters were promoted to comply with the limitation in the calculation time. Collisions of the imperfect random-cage clusters led to an elongated tubular cage structure, which could be regarded as an initiation of SWNTs. The simulation results were compared with FT-ICR mass spectra of the positive clusters generated by a laser-vaporization supersonic-expansion cluster beam source. © 2003 Wiley Periodicals, Inc. Heat Trans Asian Res, 32(8): 690,699, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.10123 [source] Molecular dynamics and multiscale homogenization analysis of seepage/diffusion problem in bentonite clayINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 12 2002Y. Ichikawa Abstract A scheme combining a molecular behaviour and macro-continuum phenomenon is presented for bentonite clay, which is a key component of a barrier system for disposal and containment of hazardous wastes. On designing a disposal facility we use a macro-phenomenological model. However the existing model is not sufficiently effective. Bentonite is a microinhomogeneous material. Properties of the saturated bentonite are characterized by montmorillonite and water, called montmorillonite hydrate. Since the crystalline structure of montmorillonite determines the fundamental properties of the montmorillonite hydrate, we analyse its molecular behaviour by applying a molecular dynamics simulation to enquire into the physicochemical properties of the montmorillonite hydrate such as diffusivity of chemical species. For extending the microscopic characteristics of constituent materials to a macroscopic diffusion behaviour of the microinhomogeneous material we apply a multiscale homogenization analysis, especially in order to treat micro-level of adsorption behaviour. Copyright © 2002 John Wiley & Sons, Ltd. [source] Computational study of the solvation of protoporphyrin IX and its Fe2+ complexINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008Teobaldo Cuya Guizado Abstract Molecular dynamics (MD) simulations of a well known hydrophobic structure, the heme (ferroprotoporphyrin IX) and its precursor in the heme synthesis, protoporphyrin IX (PPIX) are presented. The objective of the present study is to determine the stability of both structures in an aqueous medium, as well as the structure-solvent relation, hydration shells, and discuss their implications for biological processes. The density functional theory (DFT) is used for the electronic and structural characterization of both PPIX and its Fe2+ complex. A classical approach based on the Gromacs package is used for the MD. The radial distribution function g(r) is used to examine the allocation of water molecules around different regions of the porphyrins. The calculations demonstrate the heterogeneous character of the porphyrins with respect to the affinity with water molecules, the general hydrophobic character of the porphyrin ring bonded or not to the ion Fe, the hydrophilic character of the carboxylic oxygen that is unchanged upon iron binding, and the low hydrophilicity of Fe2+ in the heme. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Molecular dynamics of phase transitions in clusters of alkali halidesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2001Pedro C. R. Rodrigues Abstract Molecular dynamics simulations of unconstrained alkali halide clusters with 8, 64, 216, 512, 1000, 1728, 2744, 4096, 5832, and 8000 ions have been carried out using the Born,Mayer,Huggins potential. All the clusters exhibit first-order melting and freezing transitions. The melting temperature increases with the number of ions and approaches the melting temperature of the bulk. Clusters with a number of ions less than approximately 1000 present hysteresis cycles and practically do not have phase coexistence. Clusters with a number of ions over 1000 present phase coexistence during a significant part of the transition region and hysteresis is progressively eliminated as the clusters size increases. It is suggested that hysteresis is an intrinsic characteristic of small clusters. In the transition regions the calculations have been performed by fixing the total energy of the clusters. It is shown that such a technique provides a better way of analyzing the transition mechanism than the usual procedure of fixing the temperature by ad hoc rescaling the velocities or by using canonical molecular dynamics or Monte Carlo. A detailed analysis of the melting transition is presented. The effects of interfaces and impurities are discussed. A method based on the velocity autocorrelation functions is proposed, in order to determine the molar fraction of the ions present in the solid and liquid phases as well as to produce colored snapshots of the phases in coexistence. The overall agreement of the estimated melting points and enthalpies of melting with the experiment is fairly good. The estimated melting point and enthalpy of melting for KCl in particular are in excellent agreement with the experimental values. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 169,180, 2001 [source] MDLab: A molecular dynamics simulation prototyping environmentJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Trevor Cickovski Abstract Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep ,t. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] EXAFS and molecular dynamics studies of ionic solutionsJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001Paola D'Angelo This paper focuses on recent advances in the X-ray absorption spectroscopy (XAS) analysis of ionic solutions. The asymmetry of radial distribution functions associated with the solvent molecules surrounding the ions has to be taken into account to perform a reliable structural analysis. Molecular dynamics (MD) simulations provide reliable 's which can be used as starting models in the XAS data analysis. The combined MD-XAS investigation reduces meaningfully the indetermination of the structural parameters, especially for coordination numbers and Debye,Waller factors. Double-electron excitation channels can be present in the XAS spectra of ionic solutions and they have to be accounted for in the background extraction. The ability of the XAS technique to probe three-body correlation functions in ionic solutions with the aid of MD has been shown. The analysis of the low- k region of the spectra allows the detection of a weak but significant hydrogen structural signal. The XAS technique is especially well suited to determine the detailed shape of the nearest-neighbor peak in the atom,atom pair correlation functions of disordered systems. The information that they contain about the short-range atom,atom pairwise interactions can be very helpful for specifying and properly modifying model potentials used in MD simulations. [source] Molecular dynamics of the blood,testis barrier components during murine spermatogenesisMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 7 2010Masataka Chihara The blood,testis barrier (BTB) separates the seminiferous epithelium into the adluminal and basal compartments. During murine spermatogenesis, preleptotene/leptotene spermatocytes migrate from the basal to the adluminal compartment through the BTB during stages VIII,IX. In the present study, we focused on the tight junction (TJ) molecules and analyzed their spatiotemporal expression during the murine seminiferous epithelial cycle. Structural analysis revealed that the principal components of the BTB, for example, claudin-3, claudin-11, occludin, and zonula occludens-1 (ZO-1), were localized at the basal and luminal sides of the preleptotene/leptotene spermatocytes during the migration stages (VIII,IX). Although we detected claudin-11, occludin, and ZO-1 throughout spermatogenesis, claudin-3 was only detected during stages VI,IX. Quantitative PCR using dissected seminiferous tubules from three stages (Early: II,VI, Middle: VII,VIII, Late: IX,I) clarified that the mRNA levels of TJ molecules were not correlated with the histoplanimetrical protein levels during spermatogenesis. Additionally, tubulobulbar complexes, considered to be involved in the internalization of TJ, were observed at the BTB site. Furthermore, a significant reduction in the mRNA levels of genes for the degradation of occludin (Itch) and endocytic recycling (Rab13) were observed during the Late and Middle stages, respectively. Therefore, we hypothesized that the lag between mRNA and protein expression of TJ molecules may be due to posttranslational modulation, for example, tubulobulbar complexes and endocytic recycling processes. In conclusion, these findings indicate that the integrity of the BTB is maintained throughout spermatogenesis, and the stage-specific localization of claudin-3 protein plays an important role in regulating BTB permeability. Mol. Reprod. Dev. 77: 630,639, 2010. © 2010 Wiley-Liss, Inc. [source] Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenasePROTEIN SCIENCE, Issue 8 2004Swarnalatha Y. Reddy Abstract Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH, [,HC5(O,) ,C4( = O) ,] and PQQH [,HC5(OH) ,C4( = O) ,] converts to the hydroquinone PQQH2 [,C5(OH) = C4(OH) ,]. The main focus is on MD structures of MDH , PQQ , methanol, MDH , PQQH,, MDH , PQQH, sGDH , PQQ , glucose, sGDH , PQQH, (glucolactone, and sGDH , PQQH. The reaction PQQ , PQQH, occurs with Glu 171,CO2, and His 144,Im as the base species in MDH and sGDH, respectively. The general-base-catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen-bonding to the C5 = O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297,COOH would act as a proton donor for the reaction PQQH, , PQQH, if formed by transfer of the proton from Glu 171,COOH to Asp 297,CO2, in MDH. For PQQH , PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen-bonded to Glu 171,CO2, in MDH and by Wat89 in sGDH). [source] Molecular dynamics of detoxification and toxin-tolerance genes in brown planthopper (Nilaparvata lugens Stål., Homoptera: Delphacidae) feeding on resistant rice plantsARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 2 2005Zhifan Yang Abstract To investigate the molecular response of brown planthopper, Nilaparvata lugens (BPH) to BPH-resistant rice plants, we isolated cDNA fragments of the genes encoding for carboxylesterase (CAR), trypsin (TRY), cytochrome P450 monooxygenase (P450), NADH-quinone oxidoreductase (NQO), acetylcholinesterase (ACE), and Glutathione S-transferase (GST). Expression profiles of the genes were monitored on fourth instar nymphs feeding on rice varieties with different resistance levels. Northern blot hybridization showed that, compared with BPH reared on susceptible rice TN1, expression of the genes for P450 and CAR was apparently up-regulated and TRY mRNA decreased in BPH feeding on a highly resistant rice line B5 and a moderately resistant rice variety MH63, respectively. Two transcripts of GST increased in BPH feeding on B5; but in BPH feeding on MH63, this gene was inducible and its expression reached a maximum level at 24 h, and then decreased slightly. The expression of NQO gene was enhanced in BPH on B5 plants but showed a constant expression in BPH on MH63 plants. No difference in ACE gene expression among BPH on different rice plants was detected by the RT-PCR method. The results suggest these genes may play important roles in the defense response of BPH to resistant rice. Arch. Insect Biochem. Physiol. 59:59,66, 2005. © 2005 Wiley-Liss, Inc. [source] Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micellesBIOPOLYMERS, Issue 1 2009Sarah Bourbigot Abstract Topologically, platelet factor-4 kinocidins consist of distinct N-terminal extended, C-terminal helical, and interposing ,-core structural domains. The C-terminal ,-helices autonomously confer direct microbicidal activity, and the synthetic antimicrobial peptide RP-1 is modeled upon these domains. In this study, the structure of RP-1 was assessed using several complementary techniques. The high-resolution structure of RP-1 was determined by NMR in anionic sodium dodecyl sulfate (SDS) and zwitterionic dodecylphosphocholine (DPC) micelles, which approximate prokaryotic and eukaryotic membranes, respectively. NMR data indicate the peptide assumes an amphipathic ,-helical backbone conformation in both micelle environments. However, small differences were observed in the side-chain orientations of lysine, tyrosine, and phenylalanine residues in SDS versus DPC environments. NMR experiments with a paramagnetic probe indicated differences in positioning of the peptide within the two micelle types. Molecular dynamics (MD) simulations of the peptide in both micelle types were also performed to add insight into the peptide/micelle interactions and to assess the validity of this technique to predict the structure of peptides in complex with micelles. MD independently predicted RP-1 to interact only peripherally with the DPC micelle, leaving its spherical shape intact. In contrast, RP-1 entered deeply into and significantly distorted the SDS micelle. Overall, the experimental and MD results support a preferential specificity of RP-1 for anionic membranes over zwitterionic membranes. This specificity likely derives from differences in RP-1 interaction with distinct lipid systems, including subtle differences in side chain orientations, rather than gross changes in RP-1 structure in the two lipid environments. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 1,13, 2009. 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] Molecular dynamics simulations of HPr under hydrostatic pressureBIOPOLYMERS, Issue 5 2004Muriel Canalia Abstract The histidine-containing protein (HPr) plays an important role in the phosphotransferase system (PTS). The deformations induced on the protein structure at high hydrostatic pressure values (4, 50, 100, 150, and 200 MPa) were previously (H. Kalbitzer, A. Görler, H. Li, P. Dubovskii, A. Hengstenberg, C. Kowolik, H. Yamada, and K. Akasaka, Protein Science 2000, Vol. 9, pp. 693,703) analyzed by NMR experiments: the nonlinear variations of the amide chemical shifts at high pressure values were supposed to arise from induced shifts in the protein conformational equilibrium. Molecular dynamics (MD) simulations are here performed, to analyze the protein internal mobility at 0.1 MPa, and to relate the nonlinear variations of chemical shifts observed at high pressure, to variations in conformational equilibrium. The global features of the protein structure are only slightly modified along the pressure. Nevertheless, the values of the Voronoi residues volumes show that the residues of ,-helices are more compressed that those belonging to the ,-sheet. The ,-helices are also displaying the largest internal mobility and deformation in the simulations. The nonlinearity of the 1H chemical shifts, computed from the MD simulation snapshots, is in qualitative agreement with the nonlinearity of the experimentally observed chemical shifts. © 2004 Wiley Periodicals, Inc. Biopolymers 2004 [source] Coupled Navier,Stokes,Molecular dynamics simulations using a multi-physics flow simulation frameworkINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 10 2010R. Steijl Abstract Simulation of nano-scale channel flows using a coupled Navier,Stokes/Molecular Dynamics (MD) method is presented. The flow cases serve as examples of the application of a multi-physics computational framework put forward in this work. The framework employs a set of (partially) overlapping sub-domains in which different levels of physical modelling are used to describe the flow. This way, numerical simulations based on the Navier,Stokes equations can be extended to flows in which the continuum and/or Newtonian flow assumptions break down in regions of the domain, by locally increasing the level of detail in the model. Then, the use of multiple levels of physical modelling can reduce the overall computational cost for a given level of fidelity. The present work describes the structure of a parallel computational framework for such simulations, including details of a Navier,Stokes/MD coupling, the convergence behaviour of coupled simulations as well as the parallel implementation. For the cases considered here, micro-scale MD problems are constructed to provide viscous stresses for the Navier,Stokes equations. The first problem is the planar Poiseuille flow, for which the viscous fluxes on each cell face in the finite-volume discretization are evaluated using MD. The second example deals with fully developed three-dimensional channel flow, with molecular level modelling of the shear stresses in a group of cells in the domain corners. An important aspect in using shear stresses evaluated with MD in Navier,Stokes simulations is the scatter in the data due to the sampling of a finite ensemble over a limited interval. In the coupled simulations, this prevents the convergence of the system in terms of the reduction of the norm of the residual vector of the finite-volume discretization of the macro-domain. Solutions to this problem are discussed in the present work, along with an analysis of the effect of number of realizations and sample duration. The averaging of the apparent viscosity for each cell face, i.e. the ratio of the shear stress predicted from MD and the imposed velocity gradient, over a number of macro-scale time steps is shown to be a simple but effective method to reach a good level of convergence of the coupled system. Finally, the parallel efficiency of the developed method is demonstrated. Copyright © 2009 John Wiley & Sons, Ltd. [source] Implementation, performance, and science results from a 30.7 TFLOPS IBM BladeCenter clusterCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 2 2010Craig A. Stewart Abstract This paper describes Indiana University's implementation, performance testing, and use of a large high performance computing system. IU's Big Red, a 20.48 TFLOPS IBM e1350 BladeCenter cluster, appeared in the 27th Top500 list as the 23rd fastest supercomputer in the world in June 2006. In spring 2007, this computer was upgraded to 30.72 TFLOPS. The e1350 BladeCenter architecture, including two internal networks accessible to users and user applications and two networks used exclusively for system management, has enabled the system to provide good scalability on many important applications while being well manageable. Implementing a system based on the JS21 Blade and PowerPC 970MP processor within the US TeraGrid presented certain challenges, given that Intel-compatible processors dominate the TeraGrid. However, the particular characteristics of the PowerPC have enabled it to be highly popular among certain application communities, particularly users of molecular dynamics and weather forecasting codes. A critical aspect of Big Red's implementation has been a focus on Science Gateways, which provide graphical interfaces to systems supporting end-to-end scientific workflows. Several Science Gateways have been implemented that access Big Red as a computational resource,some via the TeraGrid, some not affiliated with the TeraGrid. In summary, Big Red has been successfully integrated with the TeraGrid, and is used by many researchers locally at IU via grids and Science Gateways. It has been a success in terms of enabling scientific discoveries at IU and, via the TeraGrid, across the US. Copyright © 2009 John Wiley & Sons, Ltd. [source] 369 Tflop/s molecular dynamics simulations on the petaflop hybrid supercomputer ,Roadrunner'CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 17 2009Timothy C. Germann Abstract We describe the implementation of a short-range parallel molecular dynamics (MD) code, SPaSM, on the heterogeneous general-purpose Roadrunner supercomputer. Each Roadrunner ,TriBlade' compute node consists of two AMD Opteron dual-core microprocessors and four IBM PowerXCell 8i enhanced Cell microprocessors (each consisting of one PPU and eight SPU cores), so that there are four MPI ranks per node, each with one Opteron and one Cell. We will briefly describe the Roadrunner architecture and some of the initial hybrid programming approaches that have been taken, focusing on the SPaSM application as a case study. An initial ,evolutionary' port, in which the existing legacy code runs with minor modifications on the Opterons and the Cells are only used to compute interatomic forces, achieves roughly a 2× speedup over the unaccelerated code. On the other hand, our ,revolutionary' implementation adopts a Cell-centric view, with data structures optimized for, and living on, the Cells. The Opterons are mainly used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard,Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), nearly 10× faster than the unaccelerated (Opteron-only) version. Copyright © 2009 John Wiley & Sons, Ltd. [source] Study of a highly accurate and fast protein,ligand docking method based on molecular dynamicsCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 14 2005M. Taufer Abstract Few methods use molecular dynamics simulations in concert with atomically detailed force fields to perform protein,ligand docking calculations because they are considered too time demanding, despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics which has a highly flexible computational granularity. We compare the accuracy and the time required with well-known, commonly used docking methods such as AutoDock, DOCK, FlexX, ICM, and GOLD. We show that our algorithm is accurate, fast and, because of its flexibility, applicable even to loosely coupled distributed systems such as desktop Grids for docking. Copyright © 2005 John Wiley & Sons, Ltd. [source] Parallel protein folding with STAPLCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 14 2005Shawna Thomas Abstract The protein-folding problem is a study of how a protein dynamically folds to its so-called native state,an energetically stable, three-dimensional conformation. Understanding this process is of great practical importance since some devastating diseases such as Alzheimer's and bovine spongiform encephalopathy (Mad Cow) are associated with the misfolding of proteins. We have developed a new computational technique for studying protein folding that is based on probabilistic roadmap methods for motion planning. Our technique yields an approximate map of a protein's potential energy landscape that contains thousands of feasible folding pathways. We have validated our method against known experimental results. Other simulation techniques, such as molecular dynamics or Monte Carlo methods, require many orders of magnitude more time to produce a single, partial trajectory. In this paper we report on our experiences parallelizing our method using STAPL (Standard Template Adaptive Parallel Library) that is being developed in the Parasol Lab at Texas A&M. An efficient parallel version will enable us to study larger proteins with increased accuracy. We demonstrate how STAPL enables portable efficiency across multiple platforms, ranging from small Linux clusters to massively parallel machines such as IBM's BlueGene/L, without user code modification. Copyright © 2005 John Wiley & Sons, Ltd. [source] Dependency of Tritium Retention in Graphite on Temperature Control of Molecular DynamicsCONTRIBUTIONS TO PLASMA PHYSICS, Issue 3-5 2010A. Ito Abstract We have investigated the carbon plasma facing material and hydrogen atom interaction by the use of molecular dynamics simulation to clarify chemical erosion processes on divertor plate. The present paper is our first try at elucidation of temperature dependence by the molecular dynamics. Temperature was controlled by using Langevin thermostat method. As a result, the retention of hydrogen atom achieve steady state, and the CH4 was generated, which was not found MD simulations without a temperature control method. About 30 percent of injected hydrogen atoms are retained. CH4 yields has a peak at 600 K, which accords with experimental results. A dominant path of CH4 generation found by the present molecular dynamics simulation is as follows: a CH is detached from eroded surface and then it grows into CH4 adsorbing hydrogen atoms via CH2 and CH3. In addition, we propose the problem that the hydrogen atom retention and CH,, yields depend on the thermal relaxation time in MD simulation using temperature control methods (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] | ||||||||||||||||||||||||||||||||||||||||||||||