Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

Directory of Open Access Journals (Sweden)

Yue Hou

2017-02-01

Full Text Available Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM experiments, Phase Dynamics Theory and Molecular Dynamics (MD Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

Science.gov (United States)

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-02-21

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action.

Science.gov (United States)

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels-from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures.

Structure and dynamics of solvated Ba(II) in dilute aqueous solution - an ab initio QM/MM MD approach

International Nuclear Information System (INIS)

Hofer, Thomas S.; Rode, Bernd M.; Randolf, Bernhard R.

2005-01-01

Structural properties of the hydrated Ba(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double zeta HF quantum mechanical level. The first shell coordination number was found to be 9.3, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and θ-angle distributions allowed the full characterization of the hydration structure of the Ba(II) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes and rate constants were also analyzed and the ligand exchange rate constant for the first shell was determined as k = 5.3 x 10 10 s -1

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.

Science.gov (United States)

Westermaier, Yvonne; Ruiz-Carmona, Sergio; Theret, Isabelle; Perron-Sierra, Françoise; Poissonnet, Guillaume; Dacquet, Catherine; Boutin, Jean A; Ducrot, Pierre; Barril, Xavier

2017-08-01

The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.

Non-linear beam dynamics tests in the LHC: LHC dynamic aperture MD on Beam 2 (24th of June 2012)

CERN Document Server

Maclean, E H; Persson, T H B; Redaelli, S; Schmidt, F; Tomas, R; Uythoven, J

2013-01-01

This MD note summarizes measurements performed on LHC Beam 2 during the non-linear machine development (MD) of 24 June 2012. The aim of the measurement was to observe the dynamic aperture of LHC Beam 2, and obtain turn-by-turn (TbT) betatron oscillation data, enabling the study of amplitude detuning and resonance driving terms (RDTs). The regular injections required by the MD also represented an opportunity to test a new coupling feedback routine based on the analysis of injection oscillation data. Initial measurements were performed on the nominal state of the LHC at injection. On completion of this study the Landau octupoles were turned off and corrections for higher-order chromaticities were implemented to reduce the non-linearity of the machine as far as possible. A second set of measurements were then performed. All studies were performed using the LHC aperture kicker (MKA).

Harvesting graphics power for MD simulations

NARCIS (Netherlands)

van Meel, J.A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.

2008-01-01

We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a

Harvesting graphics power for MD simulations

NARCIS (Netherlands)

Meel, J.A. van; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.

We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a

Steinberg ``AUDIOMAPS'' Music Appreciation-Via-Understanding: Special-Relativity + Expectations ``Quantum-Theory'': a Quantum-ACOUSTO/MUSICO-Dynamics (QA/MD)

Science.gov (United States)

Fender, Lee; Steinberg, Russell; Siegel, Edward Carl-Ludwig

2011-03-01

Steinberg wildly popular "AUDIOMAPS" music enjoyment/appreciation-via-understanding methodology, versus art, music-dynamics evolves, telling a story in (3+1)-dimensions: trails, frames, timbres, + dynamics amplitude vs. music-score time-series (formal-inverse power-spectrum) surprisingly closely parallels (3+1)-dimensional Einstein(1905) special-relativity "+" (with its enjoyment-expectations) a manifestation of quantum-theory expectation-values, together a music quantum-ACOUSTO/MUSICO-dynamics(QA/MD). Analysis via Derrida deconstruction enabled Siegel-Baez "Category-Semantics" "FUZZYICS"="CATEGORYICS ('TRIZ") Aristotle SoO DEduction , irrespective of Boon-Klimontovich vs. Voss-Clark[PRL(77)] music power-spectrum analysis sampling-time/duration controversy: part versus whole, shows QA/MD reigns supreme as THE music appreciation-via-analysis tool for the listener in musicology!!! Connection to Deutsch-Hartmann-Levitin[This is Your Brain on Music, (06)] brain/mind-barrier brain/mind-music connection is subtle/compelling/immediate!!!

Structure, Reactivity and Dynamics

Indian Academy of Sciences (India)

Understanding structure, reactivity and dynamics is the core issue in chemical ... functional theory (DFT) calculations, molecular dynamics (MD) simulations, light- ... between water and protein oxygen atoms, the superionic conductors which ...

Steinberg ``AUDIOMAPS" Music Appreciation-Via-Understanding: Special-Relativity + Expectations "Quantum-Theory": a Quantum-ACOUSTO/MUSICO-Dynamics (QA/MD)

Science.gov (United States)

Steinberg, R.; Siegel, E.

2010-03-01

``AUDIOMAPS'' music enjoyment/appreciation-via-understanding methodology, versus art, music-dynamics evolves, telling a story in (3+1)-dimensions: trails, frames, timbres, + dynamics amplitude vs. music-score time-series (formal-inverse power- spectrum) surprisingly closely parallels (3+1)-dimensional Einstein(1905) special-relativity ``+'' (with its enjoyment- expectations) a manifestation of quantum-theory expectation- values, together a music quantum-ACOUSTO/MUSICO-dynamics (QA/MD). Analysis via Derrida deconstruction enabled Siegel- Baez ``Category-Semantics'' ``FUZZYICS''=``CATEGORYICS (``SON of 'TRIZ") classic Aristotle ``Square-of-Opposition" (SoO) DEduction-logic, irrespective of Boon-Klimontovich versus Voss- Clark[PRL(77)] music power-spectrum analysis sampling- time/duration controversy: part versus whole, shows that ``AUDIOMAPS" QA/MD reigns supreme as THE music appreciation-via- analysis tool for the listener in musicology!!! Connection to Deutsch-Hartmann-Levitin[This is Your Brain on Music,(2006)] brain/mind-barrier brain/mind-music connection is both subtle and compelling and immediate!!!

Developing improved MD codes for understanding processive cellulases

International Nuclear Information System (INIS)

Crowley, M F; Nimlos, M R; Himmel, M E; Uberbacher, E C; Iii, C L Brooks; Walker, R C

2008-01-01

The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processively depolymerize cellulose using biochemical processes that are largely not understood. Understanding the mechanisms involved and improving the efficiency of this hydrolysis process through computational models and protein engineering presents a compelling grand challenge. A detailed understanding of cellulose structure, dynamics and enzyme function at the molecular level is required to direct protein engineers to the right modifications or to understand if natural thermodynamic or kinetic limits are in play. Much can be learned about processivity by conducting carefully designed molecular dynamics (MD) simulations of the binding and catalytic domains of cellulases with various substrate configurations, solvation models and thermodynamic protocols. Most of these numerical experiments, however, will require significant modification of existing code and algorithms in order to efficiently use current (terascale) and future (petascale) hardware to the degree of parallelism necessary to simulate a system of the size proposed here. This work will develop MD codes that can efficiently use terascale and petascale systems, not just for simple classical MD simulations, but also for more advanced methods, including umbrella sampling with complex restraints and reaction coordinates, transition path sampling, steered molecular dynamics, and quantum mechanical/molecular mechanical simulations of systems the size of cellulose degrading enzymes acting on cellulose

Molecular dynamics studies of superionic conductors

International Nuclear Information System (INIS)

Rahman, A.; Vashishta, P.

1983-01-01

Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis

International Nuclear Information System (INIS)

Ramos-Alvarado, Bladimir; Kumar, Satish; Peterson, G. P.

2015-01-01

The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

Science.gov (United States)

Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

2012-01-01

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

A Molecular Dynamics (MD and Quantum Mechanics/Molecular Mechanics (QM/MM Study on Ornithine Cyclodeaminase (OCD: A Tale of Two Iminiums

Directory of Open Access Journals (Sweden)

James W. Gauld

2012-10-01

Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations

DEFF Research Database (Denmark)

Capoferri, Luigi; Leth, Rasmus; Ter Haar, Ernst

2016-01-01

of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way...... active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain...... of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD...

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

Calculating the Na⁺ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.

Science.gov (United States)

Muhammed, Zahed; Arai, Satoshi; Saijo, Shinya; Yamato, Ichiro; Murata, Takeshi; Suenaga, Atsushi

2012-07-01

Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V₁; NtpA₃-B₃-D-G) and an integral membrane domain (V₀; NtpI-K₁₀) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F). Recently nucleotide binding of catalytic NtpA monomer has been reported (Arai et al.). In the present study, we calculated the nucleotide binding affinity of NtpA by molecular dynamics (MD) simulation/free energy calculation using MM-GBSA approach based on homology modeled structure of NtpA monomer docked with ATP analogue, adenosine 5'-[β, γ-imido] triphosphate (AMP-PNP). The calculated binding free energies showed qualitatively good agreement with experimental data. The calculation was cross-validated further by the rigorous method, thermodynamic integration (TI) simulation. Finally, the interaction between NtpA and nucleotides at the atomic level was investigated by the analyses of components of free energy and the optimized model structures obtained from MD simulations, suggesting that electrostatic contribution is responsible for the difference in nucleotide binding to NtpA monomer. This is the first observation and suggestion to explain the difference of nucleotide binding properties in V-ATPase NtpA subunit, and our method can be a valuable primary step to predict nucleotide binding affinity to other subunits (NtpAB, NtpA₃B₃) and to explore subunit interactions and eventually may help to understand energy transduction mechanism of E. hirae V-ATPase. Copyright © 2012 Elsevier Inc. All rights reserved.

The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.

Science.gov (United States)

Ortiz-Suarez, Maite L; Bond, Peter J

2016-01-05

MD-1 is a member of the MD-2-related lipid-recognition (ML) family, and associates with RP105, a cell-surface protein that resembles Toll-like receptor 4 (TLR4). The RP105⋅MD-1 complex has been proposed to play a role in fine-tuning the innate immune response to endotoxin such as bacterial lipopolysaccharide (LPS) via TLR4⋅MD-2, but controversy surrounds its mechanism. We have used atomically detailed simulations to reveal the structural basis for ligand binding and consequent functional dynamics of MD-1 and the RP105 complex. We rationalize reports of endogenous phospholipid binding, by showing that they prevent collapse of the malleable MD-1 fold, before refining crystallographic models and uncovering likely binding modes for LPS analogs. Subsequent binding affinity calculations reveal that endotoxin specificity arises from the entropic cost of expanding the MD-1 cavity to accommodate bulky lipid tails, and support the role of MD-1 as a "sink" that sequesters endotoxin from TLR4 and stabilizes RP105/TLR4 interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Free-Energy Calculations. A Mathematical Perspective

Science.gov (United States)

Pohorille, Andrzej

2015-01-01

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

Science.gov (United States)

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

MD2190: Q" Stabilization during injection

CERN Document Server

Schenk, Michael; Li, Kevin Shing Bruce; Malina, Lukas; Metral, Elias; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

2018-01-01

This MD is a follow-up study of MD1831, where single bunches were stabilized against impedance-driven instabilities at 6.5 TeV in the LHC with Q''. The goals are (i) to explore whether an amplitude detuning free Q'' knob can be implemented at injection energy, and (ii) whether Q'' can provide beam stability at injection, where the beams suffer mostly from electron cloud effects. Ideally, this would relax the use of the Landau octupoles and may help in preserving the beam quality by reducing dynamic aperture limitations originating from the octupoles. The MD has been split into two parts: First, optics corrections were put in place to minimize beta-beating and linear coupling introduced by the knobs. The corrections were achieved by means of orbit bumps and skew quadrupole knobs. Machine safety was then validated with loss maps. While the betatron loss maps were approved, the off-momentum maps showed a priori unexpected losses in several arcs and the MD was stopped at this point for reasons of machine protecti...

Dopamine and Caffeine Encapsulation within Boron Nitride (14,0) Nanotubes: Classical Molecular Dynamics and First Principles Calculations.

Science.gov (United States)

García-Toral, Dolores; González-Melchor, Minerva; Rivas-Silva, Juan F; Meneses-Juárez, Efraín; Cano-Ordaz, José; H Cocoletzi, Gregorio

2018-06-07

Classical molecular dynamics (MD) and density functional theory (DFT) calculations are developed to investigate the dopamine and caffeine encapsulation within boron nitride (BN) nanotubes (NT) with (14,0) chirality. Classical MD studies are done at canonical and isobaric-isothermal conditions at 298 K and 1 bar in explicit water. Results reveal that both molecules are attracted by the nanotube; however, only dopamine is able to enter the nanotube, whereas caffeine moves in its vicinity, suggesting that both species can be transported: the first by encapsulation and the second by drag. Findings are analyzed using the dielectric behavior, pair correlation functions, diffusion of the species, and energy contributions. The DFT calculations are performed according to the BLYP approach and applying the atomic base of the divided valence 6-31g(d) orbitals. The geometry optimization uses the minimum-energy criterion, accounting for the total charge neutrality and multiplicity of 1. Adsorption energies in the dopamine encapsulation indicate physisorption, which induces the highly occupied molecular orbital-lower unoccupied molecular orbital gap reduction yielding a semiconductor behavior. The charge redistribution polarizes the BNNT/dopamine and BNNT/caffeine structures. The work function decrease and the chemical potential values suggest the proper transport properties in these systems, which may allow their use in nanobiomedicine.

MD on UFOs at MKIs and MKQs

CERN Document Server

Baer, T; Bartmann, W; Bracco, C; Carlier, E; Dehning, B; Garrel, N; Goddard, B; Jackson, S; Jimenez, M; Kain, V; Mertens, V; Misiowiec, M; Nordt, A; Papotti, G; Uythoven, J; Wenninger, J; Zerlauth, M; Zamantzas, C; Zimmermann, F

2012-01-01

UFOs ("Unidentified Falling Objects") are expected to be one of the major known performance limitation of the LHC. In this MD, the production mechanism and the dynamics of UFOs at the injection kicker magnets (MKIs) and the tune kicker magnets (MKQs) were studied. This was done by pulsing the MKIs and MKQs on a gap in the partly filled machine. During the MD, in total 58 UFO-type beam loss patterns were observed directly after pulsing the MKIs. None were observed after pulsing the MKQs, which provides important input for possible mitigation strategies. The temporal and spatial distribution of the UFO events could be determined by using a dedicated BLM Study Buffer, the implications for the UFO dynamics are discussed.

Investigation of the intermediate- and high-density forms of amorphous ice by molecular dynamics calculations and diffraction experiments

International Nuclear Information System (INIS)

Tse, John S.; Klug, Dennis D.; Guthrie, Malcolm; Benmore, Chris J.; Urquidi, Jacob; Tulk, Chris A.

2005-01-01

The lack of an 'isosbestic' point in the oxygen-oxygen atom radial distribution functions (RDFs) for the HDA→LDA ice transformation at ambient pressure derived from molecular dynamics (MD) calculations show unequivocally that intermediate phases are not equilibrium mixtures of these two amorphous forms. This is supported by x-ray structure factor data, where it is found that linear combinations of the starting and end amorphous forms do not describe intermediate forms of amorphous ice formed during the transformation. This reflects the fact that the x-ray data are heavily weighted to O-O correlations and therefore sensitive to the basic structural changes that occur during the relaxation process. The ice Ih→HDA transformation is also reexamined using MD to identify its thermodynamic nature. This apparently first-order transition induced by a mechanical instability is investigated by compression followed by decompression to negative pressures. In this study we demonstrated that the full van der Waals loop for this transition can be identified

Property Analysis of Exfoliated Graphite Nanoplatelets Modified Asphalt Model Using Molecular Dynamics (MD Method

Directory of Open Access Journals (Sweden)

Hui Yao

2017-01-01

Full Text Available This Molecular Dynamics (MD simulation paper presents a physical property comparison study between exfoliated graphite nanoplatelets (xGNP modified and control asphalt models, including density, glass transition temperature, viscosity and thermal conductivity. The three-component control asphalt model consists of asphaltenes, aromatics, and saturates based on previous references. The xGNP asphalt model was built by incorporating an xGNP and control asphalt model and controlling mass ratios to represent the laboratory prepared samples. The Amber Cornell Extension Force Field (ACEFF was used with assigned molecular electro-static potential (ESP charge from NWChem analysis. After optimization and ensemble relaxation, the properties of the control and xGNP modified asphalt models were computed and analyzed using the MD method. The MD simulated results have a similar trend as the test results. The property analysis showed that: (1 the density of the xGNP modified model is higher than that of the control model; (2 the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP asphalt binders than that of the control model; (3 the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4 the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.

Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations.

Science.gov (United States)

Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander

2015-07-01

β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become

Statistical against dynamical PLF fission as seen by the IMF-IMF correlation functions and comparisons with CoMD model

Science.gov (United States)

Pagano, E. V.; Acosta, L.; Auditore, L.; Cap, T.; Cardella, G.; Colonna, M.; De Filippo, E.; Geraci, E.; Gnoffo, B.; Lanzalone, G.; Maiolino, C.; Martorana, N.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Trifiro’, A.; Trimarchi, M.; Siwek-Wilczynska, K.

2018-05-01

In nuclear reactions at Fermi energies two and multi particles intensity interferometry correlation methods are powerful tools in order to pin down the characteristic time scale of the emission processes. In this paper we summarize an improved application of the fragment-fragment correlation function in the specific physics case of heavy projectile-like (PLF) binary massive splitting in two fragments of intermediate mass(IMF). Results are shown for the reverse kinematics reaction 124 Sn+64 Ni at 35 AMeV that has been investigated by using the forward part of CHIMERA multi-detector. The analysis was performed as a function of the charge asymmetry of the observed couples of IMF. We show a coexistence of dynamical and statistical components as a function of the charge asymmetry. Transport CoMD simulations are compared with the data in order to pin down the timescale of the fragments production and the relevant ingredients of the in medium effective interaction used in the transport calculations.

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

Science.gov (United States)

Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

2015-10-26

Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

Science.gov (United States)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

Science.gov (United States)

Gonzalez Lazo, Eduardo; Cruz Inclán, Carlos M.; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

2017-09-01

A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

Reactor dynamics calculations

International Nuclear Information System (INIS)

Devooght, J.; Lefvert, T.; Stankiewiez, J.

1981-01-01

This chapter deals with the work done in reactor dynamics within the Coordinated Research Program on Transport Theory and Advanced Reactor Calculations by three groups in Belgium, Poland, Sweden and Italy. Discretization methods in diffusion theory, collision probability methods in time-dependent neutron transport and singular perturbation method are represented in this paper

The hydration enthalpies of Md3+ and Lr3+

International Nuclear Information System (INIS)

Bruechle, W.; Schaedel, M.; Scherer, U.W.; Kratz, J.V.

1987-10-01

Lawrencium (3-min 260 Lr) and lighter actinides were produced in the bombardement of a 249 Bk target with 18 O ions and loaded onto a cation exchange column in 0.05 M α-hydroxy-isobutyrate solution at pH = 4.85 together with the radioactive lanthanide tracers 166 Ho, 171 Er, and 171 Tm. In elutions with 0.12 M α-hydroxy-isobutyrate solution (pH = 4.85) trivalent Lr was eluted exactly together with the Er tracer and Md close to Ho. Lr elutes much later than expected based on the known elution positions of the lighter actinides and the expected analogy to the elution positions of the homologous lanthanides. From the measured elution positions, ionic radii were calculated for Lr 3+ and Md 3+ . Semiempirical models allow the calculation of the heat of hydration from the ionic radii, resulting in ΔH hyd ≅ - 3654 kJ/mol for Md 3+ and ΔH hyd ≅ - 3689 kJ/mol for Lr 3+ . (orig.)

Exploration of bulk and interface behavior of gas molecules and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid using equilibrium and nonequilibrium molecular dynamics simulation and quantum chemical calculation.

Science.gov (United States)

Yang, Quan; Achenie, Luke E K

2018-04-18

Ionic liquids (ILs) show brilliant performance in separating gas impurities, but few researchers have performed an in-depth exploration of the bulk and interface behavior of penetrants and ILs thoroughly. In this research, we have performed a study on both molecular dynamics (MD) simulation and quantum chemical (QC) calculation to explore the transport of acetylene and ethylene in the bulk and interface regions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]-[BF4]). The diffusivity, solubility and permeability of gas molecules in the bulk were researched with MD simulation first. The subdiffusion behavior of gas molecules is induced by coupling between the motion of gas molecules and the ions, and the relaxation processes of the ions after the disturbance caused by gas molecules. Then, QC calculation was performed to explore the optical geometry of ions, ion pairs and complexes of ions and penetrants, and interaction potential for pairs and complexes. Finally, nonequilibrium MD simulation was performed to explore the interface structure and properties of the IL-gas system and gas molecule behavior in the interface region. The research results may be used in the design of IL separation media.

Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

Indian Academy of Sciences (India)

Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations

Science.gov (United States)

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-01

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

Polymorphic transitions in single crystals: A new molecular dynamics method

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1981-12-01

A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.

Polymorphic transitions in single crystals: A new molecular dynamics method

International Nuclear Information System (INIS)

Parrinello, M.; Rahman, A.

1981-01-01

A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas.

Science.gov (United States)

Andoh, Yoshimichi; Aoki, Noriyuki; Okazaki, Susumu

2016-02-28

Molecular dynamics (MD) calculations of lipid bilayers modeling the plasma membranes of normal mouse hepatocytes and hepatomas in water have been performed under physiological isothermal-isobaric conditions (310.15 K and 1 atm). The changes in the membrane properties induced by hepatic canceration were investigated and were compared with previous MD calculations included in our previous study of the changes in membrane properties induced by murine thymic canceration. The calculated model membranes for normal hepatocytes and hepatomas comprised 23 and 24 kinds of lipids, respectively. These included phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. We referred to previously published experimental values for the mole fraction of the lipids adopted in the present calculations. The calculated structural and dynamic properties of the membranes such as lateral structure, order parameters, lateral self-diffusion constants, and rotational correlation times all showed that hepatic canceration causes plasma membranes to become more ordered laterally and less fluid. Interestingly, this finding contrasts with the less ordered structure and increased fluidity of plasma membranes induced by thymic canceration observed in our previous MD study.

The discovery of 260Md and the decay properties of 258Fm, 258m,gMd and 259Md

International Nuclear Information System (INIS)

Lougheed, R.W.; Hulet, E.K.; Dougan, R.J.; Wild, J.F.; Dupzyk, R.J.; Henderson, C.M.; Moody, K.J.; Hahn, R.L.; Suemmerer, K.; Bethune, G.

1986-01-01

We have discovered a new neutron-rich isotope, 260 Md, from 18 O and 22 Ne bombardments of 254 Es. We observed a spontaneous-fission (SF) activity with a half-life of 32 days in electromagnetically separated fractions with mass number 260 from these bombardments and we measured the mass and kinetic energy distributions of this SF activity. The mass distribution was symmetric with the principal energy peak at a total kinetic energy (TKE) of 234 MeV, similar to previous observations for heavy fermium isotopes. Surprisingly, we also observed a smaller symmetric component with a TKE of 195 MeV. We interpret these two peaks in the TKE distribution as arising from two types of fission in the same nucleus, or bimodal fission. The observed fission activity may be either from the SF decay of 260 Md or from 260 Fm which would arise from electron-capture (EC) decay of 260 Md. We have eliminated the possible β - decay of 260 Md by measuring β - -SF time correlations for the decay of 260 Md and we plan to determine whether 260 Md decays by EC by measuring time correlations between fermium X-rays and SF events. We also measured various properties of the heavy fermium and mendelevium isotopes and obtained 1. more accurate cross-sections for the neutron-rich mendelevium isotopes which we use to predict the production rates of yet undiscovered nuclides, 2. improved half-life measurements for 258m,g Md and 259 Md, 3. confirmation of the EC decay of 258m Md by measurement of the fermium X-rays preceding the SF decay of 258 Fm and 4. very substantially improved mass and TKE distributions for the SF decay of 258 Fm and 259 Md. (orig.)

An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows

KAUST Repository

Liang, Tengfei

2013-01-01

Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.

Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair

KAUST Repository

Chawla, Mohit; Autiero, Ida; Oliva, Romina; Cavallo, Luigi

2018-01-01

the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM

Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

Science.gov (United States)

Luttmann, Edgar; Ensign, Daniel L; Vaidyanathan, Vishal; Houston, Mike; Rimon, Noam; Øland, Jeppe; Jayachandran, Guha; Friedrichs, Mark; Pande, Vijay S

2009-01-30

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors. (c) 2008 Wiley Periodicals, Inc.

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

Directory of Open Access Journals (Sweden)

Jiyoung Kang

2012-01-01

Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

Modeling shockwave deformation via molecular dynamics

International Nuclear Information System (INIS)

Holian, B.L.

1987-01-01

Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too

Md Naimuddin

Indian Academy of Sciences (India)

Home; Journals; Pramana – Journal of Physics. Md Naimuddin. Articles written in Pramana – Journal of Physics. Volume 79 Issue 5 November 2012 pp 1255-1258 Poster Presentations. Model unspecific search for new physics in collision at s = 7 TeV · Shivali Malhotra Md Naimuddin Thomas Hebbeker Arnd Meyer ...

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current knowledge of the refined structure. The MD simulations provide detailed information on the position and mobility of the hydrogen and oxygen of interlayer water, as well as its self-diffusion coefficient, through the interlayer of 14 Å tobermorite. Comparison of the MD simulation results at 100 and 300 K demonstrates that water molecules in the interlayer maintain their structure but change their mobility. The dominant configuration and self-diffusion coefficient of interlayer water are obtained in this study. Copyright © 2013 Japan Concrete Institute.

MD and FFM Electron Broadening for Warm and Dense Hydrogen Plasmas

International Nuclear Information System (INIS)

Ferri, S.; Calisti, A.; Mosse, C.; Talin, B.; Gonzalez, M. A.; Gigosos, M. A.

2006-01-01

Direct integration of the semi-classical evolution equation based on Molecular Dynamics simulations (MD) and the Frequency Fluctuation Model (FFM) have long been used to synthesize spectra accounting for ion dynamics. Cross comparisons of these approaches generally show results in good agreement. Recently, interest in low temperature (Te ∼ 1eV) and high density (Ne ∼ 1018 cm-3) hydrogen plasma spectroscopy has motivated extended applications of FFM. Arising discrepancies were found to originate in electron collision operators suggesting an improper use of impact approximations for warm and dense plasma conditions. In order to clarify this point, new useful cross comparisons between MD and FFM have been carried out for electron broadening

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes MdSAUR37, MdPP2CH and MdALMTII.

Science.gov (United States)

Jia, Dongjie; Shen, Fei; Wang, Yi; Wu, Ting; Xu, Xuefeng; Zhang, Xinzhong; Han, Zhenhai

2018-05-11

Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H + -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the physiological fundamentals of quantitative genetics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A Python tool to set up relative free energy calculations in GROMACS.

Science.gov (United States)

Klimovich, Pavel V; Mobley, David L

2015-11-01

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations.

Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

Energy Technology Data Exchange (ETDEWEB)

Jo, Ju-Yeon, E-mail: ju8879@kuchem.kyoto-u.ac.jp; Ito, Hironobu, E-mail: h.ito@kuchem.kyoto-u.ac.jp; Tanimura, Yoshitaka, E-mail: tanimura@kuchem.kyoto-u.ac.jp

2016-12-20

Frequency-domain two-dimensional (2D) Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium–nonequilibrium hybrid molecular dynamics (MD) simulation algorithm. An appropriate representation of the 2D Raman spectrum obtained from MD simulations provides an easy-to-understand depiction of structural and dynamical properties. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode–mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently. Moreover, the MD simulation results allow us to visualize the molecular structure and dynamics by comparing the accurately calculated spectrum with experimental result.

Injector MD Days 2017

CERN Document Server

Rumolo, G

2017-01-01

The Injector Machine Development (MD) days 2017 were held on 23-24 March, 2017, at CERN with thefollowing main goals:Give a chance to the MD users to present their results and show the relevant progress made in 2016 onseveral fronts.Provide the MD users and the Operation (OP) crews with a general overview on the outcome and theimpact of all ongoing MD activities.Identify the open questions and consequently define - with priorities - a list of machine studies in theinjectors for 2017 (covering the operational beams, LHC Injectors Upgrade, High Luminosity LHC,Physics Beyond Colliders, other projects).Create the opportunity to collect and document the highlights of the 2016 MDs and define the perspectivesfor 2017.Discuss how to make best use of the MD time, in particular let the main MD user express their wishesand see whether/how OP teams can contribute to their fulfilment.

Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

Science.gov (United States)

Yoshida, Norio; Higashi, Masahiro; Motoki, Hideyoshi; Hirota, Shun

2018-01-01

The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.

Molecular dynamics studies of actinide nitrides

International Nuclear Information System (INIS)

Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

2004-01-01

The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

Science.gov (United States)

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Exploring intentions of physician-scientist trainees: factors influencing MD and MD/PhD interest in research careers.

Science.gov (United States)

Kwan, Jennifer M; Daye, Dania; Schmidt, Mary Lou; Conlon, Claudia Morrissey; Kim, Hajwa; Gaonkar, Bilwaj; Payne, Aimee S; Riddle, Megan; Madera, Sharline; Adami, Alexander J; Winter, Kate Quinn

2017-07-11

Prior studies have described the career paths of physician-scientist candidates after graduation, but the factors that influence career choices at the candidate stage remain unclear. Additionally, previous work has focused on MD/PhDs, despite many physician-scientists being MDs. This study sought to identify career sector intentions, important factors in career selection, and experienced and predicted obstacles to career success that influence the career choices of MD candidates, MD candidates with research-intense career intentions (MD-RI), and MD/PhD candidates. A 70-question survey was administered to students at 5 academic medical centers with Medical Scientist Training Programs (MSTPs) and Clinical and Translational Science Awards (CTSA) from the NIH. Data were analyzed using bivariate or multivariate analyses. More MD/PhD and MD-RI candidates anticipated or had experienced obstacles related to balancing academic and family responsibilities and to balancing clinical, research, and education responsibilities, whereas more MD candidates indicated experienced and predicted obstacles related to loan repayment. MD/PhD candidates expressed higher interest in basic and translational research compared to MD-RI candidates, who indicated more interest in clinical research. Overall, MD-RI candidates displayed a profile distinct from both MD/PhD and MD candidates. MD/PhD and MD-RI candidates experience obstacles that influence their intentions to pursue academic medical careers from the earliest training stage, obstacles which differ from those of their MD peers. The differences between the aspirations of and challenges facing MD, MD-RI and MD/PhD candidates present opportunities for training programs to target curricula and support services to ensure the career development of successful physician-scientists.

Cryptanalysis of MD2

DEFF Research Database (Denmark)

Knudsen, Lars Ramkilde; Mathiassen, John Erik; Muller, Frédéric

2010-01-01

This paper considers the hash function MD2 which was developed by Ron Rivest in 1989. Despite its age, MD2 has withstood cryptanalytic attacks until recently. This paper contains the state-of-the-art cryptanalytic results on MD2, in particular collision and preimage attacks on the full hash...

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

Science.gov (United States)

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

Identification of 253Md

International Nuclear Information System (INIS)

Kadkhodayan, B.; Czerwinski, K.R.; Kreek, S.A.; Hannink, N.J.; Gregorich, K.E.; Lee, D.M.; Nurmia, M.J.; Hoffman, D.C.; Hall, H.L.

1992-01-01

We have measured the half-life and production cross section of the new isotope 253 Md, produced via the 243 Am( 13 C,3n) reaction. Isolation of Md from other activities was accomplished using elution with ammonium α-hydroxyisobutyrate from a cation exchange resin column. Experiments were performed with different irradiation time intervals, but the chemical separation always began and ended at exactly the same length of time after the end of irradiation. All separations with the same irradation lengths were combined and analyzed for growth and decay of the 3.0-d 253 Fm daughter and 20.47-d 253 Es, granddaugther of 253 Md. The amount of 253 Es in each fraction depends on the length of each irradiation and the 253 Md half-life. An increase in the length of irradiation will cause a corresponding increase in the amount of the new isotope 253 Md and hence, in the amount of 253 Es produced, provided the length of irradiations are not very long compared to the half-life of 253 Md. In this way, the Md half-life was estimated to be about 6 minutes with a production cross section of the order of 50 nb. (orig.)

Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

International Nuclear Information System (INIS)

Ribeiro, Mauro C.C.; Pádua, Agílio A.H.; Gomes, Margarida F.C.

2014-01-01

Highlights: • We compare different equation of states, EoS, for an ionic liquid under high pressure. • Molecular dynamics, MD, simulations have been used to evaluate the best EoS. • MD simulations show that a group contribution model can be extrapolated to P ∼ 1.0 GPa. • A perturbed hard-sphere EoS also fits the densities calculated by MD simulations. - Abstract: The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C 4 C 1 im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C 4 C 1 im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C 4 C 1 im][TfO] up to ∼1.0 GPa

Evaluation of melting point of UO2 by molecular dynamics simulation

International Nuclear Information System (INIS)

Arima, Tatsumi; Idemitsu, Kazuya; Inagaki, Yaohiro; Tsujita, Yuichi; Kinoshita, Motoyasu; Yakub, Eugene

2009-01-01

The melting point of UO 2 has been evaluated by molecular dynamics simulation (MD) in terms of interatomic potential, pressure and Schottky defect concentration. The Born-Mayer-Huggins potentials with or without a Morse potential were explored in the present study. Two-phase simulation whose supercell at the initial state consisted of solid and liquid phases gave the melting point comparable to the experimental data using the potential proposed by Yakub. The heat of fusion was determined by the difference in enthalpy at the melting point. In addition, MD calculations showed that the melting point increased with pressure applied to the system. Thus, the Clausius-Clapeyron equation was verified. Furthermore, MD calculations clarified that an addition of Schottky defects, which generated the local disorder in the UO 2 crystal, lowered the melting point.

MD and BCA simulations of He and H bombardment of fuzz in bcc elements

Science.gov (United States)

Klaver, T. P. C.; Zhang, S.; Nordlund, K.

2017-08-01

We present results of MD simulations of low energy He ion bombardment of low density fuzz in bcc elements. He ions can penetrate several micrometers into sparse fuzz, which allows for a sufficient He flux through it to grow the fuzz further. He kinetic energy falls off exponentially with penetration depth. A BCA code was used to carry out the same ion bombardment on the same fuzz structures as in MD simulations, but with simpler, 10 million times faster calculations. Despite the poor theoretical basis of the BCA at low ion energies, and the use of somewhat different potentials in MD and BCA calculations, the ion penetration depths predicted by BCA are only ∼12% less than those predicted by MD. The MD-BCA differences are highly systematic and trends in the results of the two methods are very similar. We have carried out more than 200 BCA calculation runs of ion bombardment of fuzz, in which parameters in the ion bombardment process were varied. For most parameters, the results show that the ion bombardment process is quite generic. The ion species (He or H), ion mass, fuzz element (W, Ta, Mo, Fe) and fuzz element lattice parameter turned out to have a modest influence on ion penetration depths at most. An off-normal angle of incidence strongly reduces the ion penetration depth. Increasing the ion energy increases the ion penetration, but the rate by which ion energy drops off at high ion energies follows the same exponential pattern as at lower energies.

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

International Nuclear Information System (INIS)

Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

2009-01-01

A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

Science.gov (United States)

Jakobtorweihen, S.; Zuniga, A. Chaides; Ingram, T.; Gerlach, T.; Keil, F. J.; Smirnova, I.

2014-07-01

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

International Nuclear Information System (INIS)

Jakobtorweihen, S.; Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.

2014-01-01

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations

Development of a model for the rational design of molecular imprinted polymer: Computational approach for combined molecular dynamics/quantum mechanics calculations

International Nuclear Information System (INIS)

Dong Cunku; Li Xin; Guo Zechong; Qi Jingyao

2009-01-01

A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and 1 H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.

Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications.

Science.gov (United States)

Stockner, Thomas; Mullen, Anna; MacMillan, Fraser

2015-10-01

ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented. © 2015 Authors; published by Portland Press Limited.

Study on high density multi-scale calculation technique

International Nuclear Information System (INIS)

Sekiguchi, S.; Tanaka, Y.; Nakada, H.; Nishikawa, T.; Yamamoto, N.; Yokokawa, M.

2004-01-01

To understand degradation of nuclear materials under irradiation, it is essential to know as much about each phenomenon observed from multi-scale points of view; they are micro-scale in atomic-level, macro-level in structural scale and intermediate level. In this study for application to meso-scale materials (100A ∼ 2μm), computer technology approaching from micro- and macro-scales was developed including modeling and computer application using computational science and technology method. And environmental condition of grid technology for multi-scale calculation was prepared. The software and MD (molecular dynamics) stencil for verifying the multi-scale calculation were improved and their movement was confirmed. (A. Hishinuma)

Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

Directory of Open Access Journals (Sweden)

Xuelu Huan

Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

MD#2183: Calibration of the IR6 B2 diamond BLMs

CERN Document Server

Valette, Matthieu; Lindstrom, Bjorn Hans Filip

2018-01-01

In case of an asynchronous beam dump with a fully filled LHC machine, causing ~40 bunches to impact on the movable dump protection absorber (TCDQ), it is expected that all standard ionisation chamber Beam Loss Monitors (IC BLM) around the LHC dumping region in IR6 will be saturated. Diamond Beam Loss Monitors (dBLM) were therefore installed next to the TCDQ downstream of the extraction kickers. These detectors allow resolving losses at a nanosecond timescale and with a dynamic range of several orders of magnitude; thus, allowing to derive the number of nominal bunches impacting the TCDQ. After a first series of calibrations using asynchronous beam dump tests, an experiment was conducted during MD#1182 to demonstrate the possibility of resolving a nominal bunch hitting the TCDQ. During this first MD only the Beam 1 dBLM was calibrated appropriately, a second calibration MD was therefore performed in 2017 for the B2 system. Results from this MD and conclusions regarding dBLM saturation with a top energy nominal...

An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

International Nuclear Information System (INIS)

Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

2008-01-01

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

Czech Academy of Sciences Publication Activity Database

Přecechtělová, J.; Munzarová, M. L.; Vaara, J.; Novotný, J.; Dračínský, Martin; Sklenář, V.

2013-01-01

Roč. 9, č. 3 (2013), s. 1641-1656 ISSN 1549-9618 Grant - others:GA MŠk(CZ) LM2010005; GA MŠk(CZ) LC06030 Program:LC Institutional support: RVO:61388963 Keywords : density-funtional calculations * molecular-dynamics simulations * phosphate group * B-DNA Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

International Nuclear Information System (INIS)

Chatterjee, A; Bhattacharya, S

2016-01-01

We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than k B T and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures. (paper)

Constant-pH molecular dynamics using stochastic titration

Science.gov (United States)

Baptista, António M.; Teixeira, Vitor H.; Soares, Cláudio M.

2002-09-01

A new method is proposed for performing constant-pH molecular dynamics (MD) simulations, that is, MD simulations where pH is one of the external thermodynamic parameters, like the temperature or the pressure. The protonation state of each titrable site in the solute is allowed to change during a molecular mechanics (MM) MD simulation, the new states being obtained from a combination of continuum electrostatics (CE) calculations and Monte Carlo (MC) simulation of protonation equilibrium. The coupling between the MM/MD and CE/MC algorithms is done in a way that ensures a proper Markov chain, sampling from the intended semigrand canonical distribution. This stochastic titration method is applied to succinic acid, aimed at illustrating the method and examining the choice of its adjustable parameters. The complete titration of succinic acid, using constant-pH MD simulations at different pH values, gives a clear picture of the coupling between the trans/gauche isomerization and the protonation process, making it possible to reconcile some apparently contradictory results of previous studies. The present constant-pH MD method is shown to require a moderate increase of computational cost when compared to the usual MD method.

A new parallel molecular dynamics algorithm for organic systems

International Nuclear Information System (INIS)

Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

1993-01-01

A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

Science.gov (United States)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Temperature dependent dynamic susceptibility calculations for itinerant ferromagnets

Energy Technology Data Exchange (ETDEWEB)

Cooke, J. F.

1980-10-01

Inelastic neutron scattering experiments have revealed a variety of interesting and unusual phenomena associated with the spin dynamics of the 3-d transition metal ferromagnets nickel and iron. An extensive series of calculations based on the itinerant electron formalism has demonstrated that the itinerant model does provide an excellent quantitative as well as qualitative description of the measured spin dynamics of both nickel and iron at low temperatures. Recent angular photo emission experiments have indicated that there is a rather strong temperature dependence of the electronic spin-splitting which, from relatively crude arguments, appears to be inconsistent with neutron scattering results. In order to investigate this point and also the origin of spin-wave renormalization, a series of calculations of the dynamic susceptibility of nickel and iron has been undertaken. The results of these calculations indicate that a discrepancy exists between the interpretations of neutron and photoemission experimental results regarding the temperature dependence of the spin-splitting of the electronic energy bands.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

Science.gov (United States)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription.

Science.gov (United States)

Li, Tong; Jiang, Zhongyu; Zhang, Lichao; Tan, Dongmei; Wei, Yun; Yuan, Hui; Li, Tianlai; Wang, Aide

2016-12-01

Ripening in climacteric fruit requires the gaseous phytohormone ethylene. Although ethylene signaling has been well studied, knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, negatively affects ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, a gene that is critical for biosynthesis of ripening-related ethylene. Expression of MdERF2 was suppressed by ethylene during ripening of apple fruit, and we observed that MdERF2 bound to the promoter of MdACS1 and directly suppressed its transcription. Moreover, MdERF2 suppressed the activity of the promoter of MdERF3, a transcription factor that we found to bind to the MdACS1 promoter, thereby increasing MdACS1 transcription. We determined that the MdERF2 and MdERF3 proteins directly interact, and this interaction suppresses the binding of MdERF3 to the MdACS1 promoter. Moreover, apple fruit with transiently downregulated MdERF2 expression showed higher ethylene production and faster ripening. Our results indicate that MdERF2 negatively affects ethylene biosynthesis and fruit ripening in apple by suppressing the transcription of MdACS1 via multiple mechanisms, thereby acting as an antagonist of positive ripening regulators. Our findings offer a deep understanding of the transcriptional regulation of ethylene biosynthesis during climacteric fruit ripening. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

Science.gov (United States)

Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

2009-07-28

Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

Science.gov (United States)

Haxhimali, Tomorr; Rudd, Robert E.; Cabot, William H.; Graziani, Frank R.

2015-11-01

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30 000-120 000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.

Dynamic Load Balancing of Parallel Monte Carlo Transport Calculations

International Nuclear Information System (INIS)

O'Brien, M; Taylor, J; Procassini, R

2004-01-01

The performance of parallel Monte Carlo transport calculations which use both spatial and particle parallelism is increased by dynamically assigning processors to the most worked domains. Since the particle work load varies over the course of the simulation, this algorithm determines each cycle if dynamic load balancing would speed up the calculation. If load balancing is required, a small number of particle communications are initiated in order to achieve load balance. This method has decreased the parallel run time by more than a factor of three for certain criticality calculations

Dynamical calculations for RHEED intensity oscillations

Science.gov (United States)

Daniluk, Andrzej

2005-03-01

A practical computing algorithm working in real time has been developed for calculating the reflection high-energy electron diffraction from the molecular beam epitaxy growing surface. The calculations are based on the use of a dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface. The results of the calculations are presented in the form of rocking curves to illustrate how the diffracted beam intensities depend on the glancing angle of the incident beam. Program summaryTitle of program: RHEED Catalogue identifier:ADUY Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUY Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Pentium-based PC Operating systems or monitors under which the program has been tested: Windows 9x, XP, NT, Linux Programming language used: Borland C++ Memory required to execute with typical data: more than 1 MB Number of bits in a word: 64 bits Number of processors used: 1 Distribution format:tar.gz Number of lines in distributed program, including test data, etc.:982 Number of bytes in distributed program, including test data, etc.: 126 051 Nature of physical problem: Reflection high-energy electron diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the molecular beam epitaxy (MBE). Nowadays, RHEED is used in many laboratories all over the world where researchers deal with the growth of materials by MBE. The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film. In most cases the interpretation of experimental results is based on the use of dynamical diffraction approaches. Such approaches are said to be quite useful in qualitative and

Analysis of quasielastic neutron scattering (QENS) data of discotic systems using different molecular dynamics (MD) models

International Nuclear Information System (INIS)

Kruglova, O.; Mulder, F.M.; Picken, S.J.; Stride, J.; Kearley, G.J.

2004-01-01

Discotic molecules are composed of an aromatic core surrounded by aliphatic chains. These molecules are of importance because they can form columns in which the π orbitals of neighbouring molecules overlap leading to conductivity along the column. These materials find applications in molecular electronics and recently--with record quantum efficiencies--in photo voltaics. Because the correlation time of the electron (or hole) hopping is in the picosecond region, molecular dynamics on this timescale is of central importance. We have recently shown that these dynamics, which is easily measured by quasielastic neutron scattering (QENS), can be understood with a rather simple 'short single-column' model via an MD simulation that reproduces the measured QENS spectra. Before progressing to the larger technologically important systems we must understand any fortuitous error cancellations that may cause the simple model to reproduce the experimental signal so well. By taking a very simple discotic, hexamethyltriphenylene (HMT), we are able to compare QENS data with three types of models: simple column, cluster and periodic. It transpires that the cluster model cannot properly accommodate inter column interactions, and a fairly modest periodic model overcomes this problem and the tendency for un-physical harmonic modes along the column

A molecular dynamics (MD simulation on tire-aggregate friction

Directory of Open Access Journals (Sweden)

Fengyan Sun

2017-07-01

Full Text Available The friction between tire and road surface is fundamentally depending on the molecular forces. In this paper, the nanoscale 3D contact model is employed to investigate the tire-aggregate friction mechanism. The tire and aggregate micro-structure are both constructed to evaluate the microscopic performance of tire-aggregate friction influence. Simulation results show for a high velocity, the energy dissipation of sliding on crystal structure is small, which results in a small friction coefficient; temperature will have influences on the friction coefficient, and with the increasing of velocity, the effect will gradually reduce. Keywords: Tire, Aggregate, Friction coefficient, Microscopic mechanism, MD simulation

Physical properties of Cu nanoparticles: A molecular dynamics study

International Nuclear Information System (INIS)

Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

2014-01-01

Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.

Science.gov (United States)

Dolenc, Jozica; Baron, Riccardo; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

2008-07-21

The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.

Molecular dynamics simulations to calculate glass transition temperature and elastic constants of novel polyethers.

Science.gov (United States)

Sarangapani, Radhakrishnan; Reddy, Sreekantha T; Sikder, Arun K

2015-04-01

Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties. Copyright © 2015 Elsevier Inc. All rights reserved.

Nuclear Research Center IRT reactor dynamics calculation

International Nuclear Information System (INIS)

Aleman Fernandez, J.R.

1990-01-01

The main features of the code DIRT, for dynamical calculations are described in the paper. With the results obtained by the program, an analysis of the dynamic behaviour of the Research Reactor IRT of the Nuclear Research Center (CIN) is performed. Different transitories were considered such as variation of the system reactivity, coolant inlet temperature variation and also variations of the coolant velocity through the reactor core. 3 refs

75 FR 47203 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-11 and MD-11F Airplanes Equipped...

Science.gov (United States)

2010-08-05

... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 11 and MD-11F Airplanes Equipped With General... Sec. 39.13 by adding the following new AD: 2010-16-03 McDonnell Douglas Corporation: Amendment 39... applies to McDonnell Douglas Corporation Model MD-11 and MD-11F airplanes, certified in any category...

Enhancement Corrosion Resistance of (γ-Glycidyloxypropyl-Silsesquioxane-Titanium Dioxide Films and Its Validation by Gas Molecule Diffusion Coefficients Using Molecular Dynamics (MD Simulation

Directory of Open Access Journals (Sweden)

Haiyan Wang

2014-01-01

Full Text Available Based on silsesquioxanes (SSO derived from the hydrolytic condensation of (γ-glycidyloxypropyltrimethoxysilane (GPMS and titanium tetrabutoxide (TTB, hybrid films on aluminum alloy (AA, film-GPMS-SSO (f-GS and f-GS-TTBi% (f-GSTT5%–25%, i = 5, 10, 15, 20 and 25 wt%, were prepared and tested by electrochemical measurements with typical potentiodynamic polarization curves. The Icorr values of the samples were significantly lower, comparing with the Icorr values of the f-GS, AA and f-GS modified tetraethoxysilane (TEOS in the previous study, which implies that the TTB5%–25% (TiO2 additions in the coatings indeed enhance the electrochemical corrosion resistance. Correlations between the film structures and anticorrosion properties were discussed. To validate the corresponding anticorrosion experiment results, different 3D-amorphous cubic unit cells were employed as models to investigate the self-diffusion coefficient (SDC for SO2, NO2 and H2O molecules by molecular dynamics (MD simulation. All of the SDCs calculated for SO2, NO2 and H2O diffusing in f-GSTT5%–25% cells were less than the SDCs in f-GS. These results validated the corresponding anticorrosion experiment results.

Pengaruh Brand Ambassador Terhadap Minat Beli Konsumen MD Clinic By Lazeta

Directory of Open Access Journals (Sweden)

Nurvita Septya Ningrum

2016-10-01

Full Text Available This research at MD Clinic by Lazeta which is in the beauty services that offer health care and facial, under of PT. Medina Global Care. MD Cilinic by Lazeta use the brand ambassador of introducing their products. The selection of brand ambassador motivated by positive image brought by the celebrities. Brand ambassadors chosen by the company as a symbol or a marker to represent the wishes and needs of prospective customers. MD Clinic by Lazeta choose Syahnaz as a brand ambassador for their products which is expected to to represent the product of MD Clinic by Lazeta, so the message can be understood by the consumer, who eventually would to lead the purchase intention. The purpose of this research was to investigate the influence of brand ambassadors on consumer purchase intention MD Clinic by Lazeta, Study on Business Administration Students year in 2103 Telkom University. Researchers used quantitative research methods. This research is population research, because all population is being respondent in this research. Populations of this research are 137 respondents. Collecting data in this research is conducted by using questionnaire distributed to all respondents, which all Students on Business Administration Telkom University who knows the MD Clinic by Lazeta. Data were analyzed using simple regression analysis and descriptive analysis.The results showed that the Brand Ambassador impact of consumer purchase intention on MD Clinic by Lazeta at the Students on Business Administration Telkom University years in 2013. Based on the calculation of the coefficient of determination (R2 can be seen the influence of brand ambassador variable (X on purchase intention (Y is 42.9%. While the remaining 57.1% is influenced by other factors which not examined in this research such as, pricing, marketing strategy and others.

Md-miR156ab and Md-miR395 Target WRKY Transcription Factors to Influence Apple Resistance to Leaf Spot Disease.

Science.gov (United States)

Zhang, Qiulei; Li, Yang; Zhang, Yi; Wu, Chuanbao; Wang, Shengnan; Hao, Li; Wang, Shengyuan; Li, Tianzhong

2017-01-01

MicroRNAs (miRNAs) are key regulators of gene expression that post-transcriptionally regulate transcription factors involved in plant physiological activities. Little is known about the effects of miRNAs in disease resistance in apple ( Malus × domestica ). We globally profiled miRNAs in the apple cultivar Golden Delicious (GD) infected or not with the apple leaf spot fungus Alternaria alternaria f. sp. mali (ALT1), and identified 58 miRNAs that exhibited more than a 2-fold upregulation upon ALT1 infection. We identified a pair of miRNAs that target protein-coding genes involved in the defense response against fungal pathogens; Md-miR156ab targets a novel WRKY transcription factor, MdWRKYN1, which harbors a TIR and a WRKY domain. Md-miR395 targets another transcription factor, MdWRKY26, which contains two WRKY domains. Real-time PCR analysis showed that Md-miR156ab and Md-miR395 levels increased, while MdWRKYN1 and MdWRKY26 expression decreased in ALT1-inoculated GD leaves; furthermore, the overexpression of Md-miR156ab and Md-miR395 resulted in a significant reduction in MdWRKYN1 and MdWRKY26 expression. To investigate whether these miRNAs and their targets play a crucial role in plant defense, we overexpressed MdWRKYN1 or knocked down Md-miR156ab activity, which in both cases enhanced the disease resistance of the plants by upregulating the expression of the WRKY-regulated pathogenesis-related (PR) protein-encoding genes MdPR3-1, MdPR3-2, MdPR4, MdPR5, MdPR10-1 , and MdPR10-2 . In a similar analysis, we overexpressed MdWRKY26 or suppressed Md-miR395 activity, and found that many PR protein-encoding genes were also regulated by MdWRKY26 . In GD, ALT-induced Md-miR156ab and Md-miR395 suppress MdWRKYN1 and MdWRKY26 expression, thereby decreasing the expression of some PR genes, and resulting in susceptibility to ALT1.

Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

Science.gov (United States)

Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

2013-10-28

End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

DMPD: Innate recognition of lipopolysaccharide by Toll-like receptor 4-MD-2. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 15051069 Innate recognition of lipopolysaccharide by Toll-like receptor 4-MD-2. Miy...ake K. Trends Microbiol. 2004 Apr;12(4):186-92. (.png) (.svg) (.html) (.csml) Show Innate recognition of lip...opolysaccharide by Toll-like receptor 4-MD-2. PubmedID 15051069 Title Innate recognition of lipopolysacchari

Biased Brownian dynamics for rate constant calculation.

OpenAIRE

Zou, G; Skeel, R D; Subramaniam, S

2000-01-01

An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampl...

Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

Science.gov (United States)

Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

2006-03-02

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to

Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

Science.gov (United States)

Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

2018-03-01

A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Stresses and elastic constants of crystalline sodium, from molecular dynamics

International Nuclear Information System (INIS)

Schiferl, S.K.

1985-02-01

The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs

75 FR 80744 - Airworthiness Directives; McDonnell Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82...

Science.gov (United States)

2010-12-23

...-1203; Directorate Identifier 2010-NM-168-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... amends Sec. 39.13 by adding the following new airworthiness directive (AD): McDonnell Douglas Corporation... Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87) and MD-88...

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

Science.gov (United States)

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

2009-01-01

and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...

An improved molecular dynamics algorithm to study thermodiffusion in binary hydrocarbon mixtures

Science.gov (United States)

Antoun, Sylvie; Saghir, M. Ziad; Srinivasan, Seshasai

2018-03-01

In multicomponent liquid mixtures, the diffusion flow of chemical species can be induced by temperature gradients, which leads to a separation of the constituent components. This cross effect between temperature and concentration is known as thermodiffusion or the Ludwig-Soret effect. The performance of boundary driven non-equilibrium molecular dynamics along with the enhanced heat exchange (eHEX) algorithm was studied by assessing the thermodiffusion process in n-pentane/n-decane (nC5-nC10) binary mixtures. The eHEX algorithm consists of an extended version of the HEX algorithm with an improved energy conservation property. In addition to this, the transferable potentials for phase equilibria-united atom force field were employed in all molecular dynamics (MD) simulations to precisely model the molecular interactions in the fluid. The Soret coefficients of the n-pentane/n-decane (nC5-nC10) mixture for three different compositions (at 300.15 K and 0.1 MPa) were calculated and compared with the experimental data and other MD results available in the literature. Results of our newly employed MD algorithm showed great agreement with experimental data and a better accuracy compared to other MD procedures.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

Science.gov (United States)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

Calculation of Transport Coefficients in Dense Plasma Mixtures

Science.gov (United States)

Haxhimali, T.; Cabot, W. H.; Caspersen, K. J.; Greenough, J.; Miller, P. L.; Rudd, R. E.; Schwegler, E. R.

2011-10-01

We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during

Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation.

Science.gov (United States)

Halonen, Roope; Zapadinsky, Evgeni; Vehkamäki, Hanna

2018-04-28

We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].

Fe IX CALCULATIONS FOR THE SOLAR DYNAMICS OBSERVATORY

International Nuclear Information System (INIS)

Foster, Adam R.; Testa, Paola

2011-01-01

New calculations of the energy levels, radiative transition rates, and collisional excitation rates of Fe IX have been carried out using the Flexible Atomic Code, paying close attention to experimentally identified levels and extending existing calculations to higher energy levels. For lower levels, R-matrix collisional excitation rates from earlier work have been used. Significant emission is predicted by these calculations in the 5f-3d transitions, which will impact analysis of Solar Dynamics Observatory Atmospheric Imaging Assembly observations using the 94 A filter.

Preparing MD-PhD students for clinical rotations: navigating the interface between PhD and MD training.

Science.gov (United States)

Goldberg, Charles; Insel, Paul A

2013-06-01

Many aspects of MD-PhD training are not optimally designed to prepare students for their future roles as translational clinician-scientists. The transition between PhD research efforts and clinical rotations is one hurdle that must be overcome. MD-PhD students have deficits in clinical skills compared with those of their MD-only colleagues at the time of this transition. Reimmersion programs (RPs) targeted to MD-PhD students have the potential to help them navigate this transition.The authors draw on their experience creating and implementing an RP that incorporates multiple types of activities (clinical exam review, objective structured clinical examination, and supervised practice in patient care settings) designed to enhance the participants' skills and readiness for clinical efforts. On the basis of this experience, they note that MD-PhD students' time away from the clinical environment negatively affects their clinical skills, causing them to feel underprepared for clinical rotations. The authors argue that participation in an RP can help students feel more comfortable speaking with and examining patients and decrease their anxiety regarding clinical encounters. The authors propose that RPs can have positive outcomes for improving the transition from PhD to clinical MD training in dual-degree programs. Identifying and addressing this and other transitions need to be considered to improve the educational experience of MD-PhD students.

Water at silica/liquid water interfaces investigated by DFT-MD simulations

Science.gov (United States)

Gaigeot, Marie-Pierre

This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

Science.gov (United States)

Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

2016-12-07

Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

Cooperativity in Molecular Dynamics Structural Models and the Dielectric Spectra of 1,2-Ethanediol

Science.gov (United States)

Usacheva, T. M.

2018-05-01

Linear relationships are established between the experimental equilibrium correlation factor and the molecular dynamics (MD) mean value of the O-H···O bond angle and the longitudinal component of the unit vector of the mean statistical dipole moment of the cluster in liquid 1,2-ethanediol (12ED). The achievements of modern MD models in describing the experimental dispersion of the permittivity of 12ED by both continuous and discrete relaxation time spectra are analyzed. The advantage computer MD experiments have over dielectric spectroscopy for calculating relaxation time and determining the molecular diffusion mechanisms of the rearrangement of the network 12ED structure, which is more complex than water, is demonstrated.

Study of shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

Science.gov (United States)

Haxhimali, Tomorr; Rudd, Robert; Cabot, William; Graziani, Frank

2015-11-01

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and Inertial Confinement Fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30000-120000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We study different mixtures with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. We introduce a model that interpolates between a screened-plasma kinetic theory at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

SU-E-T-167: Evaluation of Mobius Dose Calculation Engine Using Out of the Box Preconfigured Beam Data

Energy Technology Data Exchange (ETDEWEB)

Cardan, R [UAB University of Alabama, Birmingham, Birmingham, AL (United States); Faught, A [MD Anderson Cancer Center, Houston, TX (United States); Huang, M; Benhabib, S [University of Alabama at Birmingham, Birmingham, AL (United States); Brezovich, I; Popple, R [University of Alabama Birmingham, Birmingham, AL (United States); Followill, D [UT MD Anderson Cancer Center, Houston, TX (United States)

2014-06-01

Purpose: Determine the dose calculation accuracy of a preconfigured Mobius server for use in secondary checks of a treatment planning system. Methods: 10 plans were created for irradiation on two of the IROC (formerly RPC) accreditation phantoms: 4 for the head and neck phantom and 6 for the lung phantom. The plans each were created using one of four different photon energies (6FFF, 10 FFF, 6X, and 15X) and were varied in treatment type including VMAT, step and shoot IMRT, dynamic MLC IMRT (DMLC), and conformal RT (CRT). The TLDs in the phantoms were contoured, and each plan was sent for calculation to Mobius software (Mobius Medical Systems, Houston, TX) with a default configuration. Each plan was then irradiated on the planned phantom 3 times to create an average reading across 56 TLDs. These readings were then compared against the corresponding Mobius calculation at each TLD location. Results: The mean difference (MD) normalized to the plan prescription dose between each TLD and Mobius calculation for all measurements was 0.5 ± 3.3%, with a maximum difference of 8.4%. The MD was 0.6 ± 3.8%, − 2.0 ± 1.9%, 1.7 ± 3.7%, and 1.9 ± 1.2% across the 6FFF, 10FFF, 6X and 15X energies respectively. The MD was −1.2 ± 2.3% for lung plans and 1.8 ± 3.5% for head/neck plans. Across treatment types, the MD ranged from − 1.8 ± 1.7% for CRT to 4.3 ± 2.4 % for DMLC. Conclusion: Out of the box and preconfigured, Mobius provides accurate dose calculations with respect to beam energy, treatment type, and treatment site.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

Science.gov (United States)

Yuhara, Daisuke; Brumby, Paul E.; Wu, David T.; Sum, Amadeu K.; Yasuoka, Kenji

2018-05-01

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

Science.gov (United States)

Yuhara, Daisuke; Brumby, Paul E; Wu, David T; Sum, Amadeu K; Yasuoka, Kenji

2018-05-14

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Yesylevskyy S. O.

2010-04-01

Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

First thoughts on MD priorities for 2012

CERN Document Server

Zimmermann, F; Assmann, R

2012-01-01

In 2012, 22 days of beam time will be allocated for LHC MDs. In this paper, after recalling the 2011 LHC MD experience, the MD rrequests for 2012 are reviewed. Three primary MD themes for 2012 can be identified: 1)pushing performance in 2012, 2)preparing for 2014/15, and 3)towards maximum luminosity. Example topics include emittance growth in collision or enhanced satellites for theme 1), 25 ns operation for 2), and ATS optics for 3). Structures lists of MD requests and topics for each theme as well as some initial thoughts on the MD priorities are presented. For certain topics, "start-of-fill MDs" are proposed in order to most efficiently use of the available beam time.

Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor

Directory of Open Access Journals (Sweden)

Sandra Posch

2016-09-01

Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor

Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al.

Science.gov (United States)

Liu, Zhong-Li; Zhang, Xiu-Lu; Cai, Ling-Cang

2015-09-21

A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curve of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials.

Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al

International Nuclear Information System (INIS)

Liu, Zhong-Li; Zhang, Xiu-Lu; Cai, Ling-Cang

2015-01-01

A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curve of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials

A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

Science.gov (United States)

Danel, J.-F.; Kazandjian, L.

2018-06-01

It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

Directory of Open Access Journals (Sweden)

Aruna Rajan

2010-04-01

Full Text Available Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i they are not data driven, (ii they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA and a non-metric multidimensional scaling (nMDS method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Science.gov (United States)

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3

International Nuclear Information System (INIS)

Schie, Marcel; Marchewka, Astrid; Waser, Rainer; Müller, Thomas; De Souza, Roger A

2012-01-01

A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO 3 ). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO 3 was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.

Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.

Science.gov (United States)

Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer

2012-12-05

A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.

Equivalence of the equilibrium and the nonequilibrium molecular dynamics methods for thermal conductivity calculations: From bulk to nanowire silicon

Science.gov (United States)

Dong, Haikuan; Fan, Zheyong; Shi, Libin; Harju, Ari; Ala-Nissila, Tapio

2018-03-01

Molecular dynamics (MD) simulations play an important role in studying heat transport in complex materials. The lattice thermal conductivity can be computed either using the Green-Kubo formula in equilibrium MD (EMD) simulations or using Fourier's law in nonequilibrium MD (NEMD) simulations. These two methods have not been systematically compared for materials with different dimensions and inconsistencies between them have been occasionally reported in the literature. Here we give an in-depth comparison of them in terms of heat transport in three allotropes of Si: three-dimensional bulk silicon, two-dimensional silicene, and quasi-one-dimensional silicon nanowire. By multiplying the correlation time in the Green-Kubo formula with an appropriate effective group velocity, we can express the running thermal conductivity in the EMD method as a function of an effective length and directly compare it to the length-dependent thermal conductivity in the NEMD method. We find that the two methods quantitatively agree with each other for all the systems studied, firmly establishing their equivalence in computing thermal conductivity.

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

Science.gov (United States)

Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar

2015-01-01

Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of

Calculation of the dynamic air flow resistivity of fibre materials

DEFF Research Database (Denmark)

Tarnow, Viggo

1997-01-01

The acoustic attenuation of acoustic fiber materials is mainly determined by the dynamic resistivity to an oscillating air flow. The dynamic resistance is calculated for a model with geometry close to the geometry of real fibre material. The model constists of parallel cylinders placed randomly.......The second procedure is an extension to oscillating air flow of the Brinkman self-consistent procedure for dc flow. The procedures are valid for volume concentrations of cylinders less than 0.1. The calculations show that for the density of fibers of interest for acoustic fibre materials the simple self...

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

Science.gov (United States)

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Spontaneous fission of 259Md

International Nuclear Information System (INIS)

Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Landrum, J.H.; Dougan, R.J.; Mustafa, M.; Ghiorso, A.; Nitschke, J.M.

1979-01-01

The mass and kinetic energy distributions of fission fragments from the spontaneous fission of th newly discovered nuclide 259 Md were obtained. 259 Md was identified as the E. C. daughter of 259 No, and was found to decay entirely (> 95%) by spontaneous fission with a 95-min half-life. From the kinetic energies measured for 397 pairs of coincident fragments, a mass distribution was derived that is symmetric with sigma = 13 amu. 259 Md, together with 258 Fm and 259 Fm, form a select group of three nuclides whose mass division in spontaneous fission is highly symmetric. Unlike the total-kinetic-energy (TKE) distributions of 258 Fm and 259 Fm, which peak at approx. = to 240 MeV, this distribution for 259 Md is broad and is 50 MeV lower in energy. Analysis of the mass and energy distributions shows that events near mass symmetry also exhibit a broad TKE distribution, with one-third of the symmetric events having TKEs less than 200 MeV. The associated of low TKEs with symmetric mass division in the fission of very heavy actinides is anomalous and inconsistent with theories based upon the emergence of fragment shells near the scission point. Either three-body fragmentation or peculiar fragment shapes are assumed as the cause for the large consumption of Coulomb energy observed for a significant fraction of symmetric fissions in 259 Md. 6 figures

Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair

KAUST Repository

Chawla, Mohit

2018-01-02

The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.

Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.

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Sharad Verma

Full Text Available p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy have major contribution in binding free energy.

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

Science.gov (United States)

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Calculating evolutionary dynamics in structured populations.

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Charles G Nathanson

2009-12-01

Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

Synergistic Applications of MD and NMR for the Study of Biological Systems

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Olivier Fisette

2012-01-01

same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.

Nuclear structure calculations in the dynamic-interaction propagator approach

International Nuclear Information System (INIS)

Engelbrecht, C.A.; Hahne, F.J.W.; Heiss, W.D.

1978-01-01

The dynamic-interaction propagator approach provides a natural method for the handling of energy-dependent effective two-body interactions induced by collective excitations of a many-body system. In this work this technique is applied to the calculation of energy spectra and two-particle strengths in mass-18 nuclei. The energy dependence is induced by the dynamic exchange of the lowest 3 - octupole phonon in O 16 , which is described within a normal static particle-hole RPA. This leads to poles in the two-body self-energy, which can be calculated if other fermion lines are restricted to particle states. The two-body interaction parameters are chosen to provide the correct phonon energy and reasonable negative-parity mass-17 and positive-parity mass-18 spectra. The fermion lines must be dressed consistently with the same exchange phonon to avoid redundant solutions or ghosts. The negative-parity states are then calculated in a parameter-free way which gives good agreement with the observed spectra [af

A molecular dynamics simulation code ISIS

International Nuclear Information System (INIS)

Kambayashi, Shaw

1992-06-01

Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

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Minzhong Zhan

2015-07-01

Full Text Available The binding interaction between gallic acid (GA and lysozyme (LYS was investigated and compared by molecular dynamics (MD simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase

International Nuclear Information System (INIS)

Nagashima, Hiroki; Tokumasu, Takashi; Tsuda, Shin-ichi; Tsuboi, Nobuyuki; Koshi, Mitsuo; Hayashie, A. Koichi

2014-01-01

In this paper, the quantum effect of hydrogen molecule on its diffusivity is analyzed using Molecular Dynamics (MD) method. The path integral centroid MD (CMD) method is applied for the reproduction method of time evolution of the molecules. The diffusion coefficient of liquid hydrogen is calculated using the Green-Kubo method. The simulation is performed at wide temperature region and the temperature dependence of the quantum effect of hydrogen molecule is addressed. The calculation results are compared with those of classical MD results. As a result, it is confirmed that the diffusivity of hydrogen molecule is changed depending on temperature by the quantum effect. It is clarified that this result can be explained that the dominant factor by quantum effect on the diffusivity of hydrogen changes from the swollening the potential to the shallowing the potential well around 30 K. Moreover, it is found that this tendency is related to the temperature dependency of the ratio of the quantum kinetic energy and classical kinetic energy

Thermal conductivities of ThO{sub 2}, NpO{sub 2} and their related oxides: Molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Arima, Tatsumi, E-mail: arima@nucl.kyushu-u.ac.jp; Yoshida, Keita; Matsumoto, Taku; Inagaki, Yaohiro; Idemitsu, Kazuya

2014-02-01

The thermal conductivities of ThO{sub 2}, NpO{sub 2}, (Th, U)O{sub 2}, (Th, Pu)O{sub 2} and (U, Np)O{sub 2} have been investigated by molecular dynamics (MD) simulation up to 2000 K using the Busing–Ida potential function with partial ionic charges. In the present study, the thermal conductivity was calculated mainly by the Green–Kubo formula in the equilibrium MD scheme. The thermal conductivities of above actinide dioxides decreased with the increase of temperature due to the phonon–phonon interaction (Umklapp process). Concerning the composition of solid solutions, the decrease in thermal conductivity of (Th, Pu)O{sub 2} is great as compared to other ones. Various MD calculations elucidated that this result was caused by phonon scattering by lattice defects as additives rather than the phonon–phonon interaction, and that the lattice strain dominantly contributed to it.

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.

Science.gov (United States)

Cheng, Mary Hongying; Coalson, Rob D; Tang, Pei

2010-11-24

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.

Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens.

Science.gov (United States)

Kumar, Ashish; Kaur, Harmeet; Jain, Abha; Nair, Deepak T; Salunke, Dinakar M

2018-01-12

Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.

MD 1691: Active halo control using tune ripple at injection

CERN Document Server

Garcia Morales, Hector; Bruce, Roderik; Redaelli, Stefano; Fitterer, Miriam; Fiascaris, Maria; Nisbet, David; Thiesen, Hugues; Valentino, Gianluca; Xu, Chen; CERN. Geneva. ATS Department

2017-01-01

In this MD we performed halo excitation through tune ripple. This consists in an excitation that introduces new resonance sidebands around the existing resonance lines. In presence of sufficient detuning with amplitude, these sidebands can in principle affect only the dynamics of the halo particles at large amplitudes. Tune ripple was induced through a current modulation of the warm trim quadrupoles in IR7. This is the first time this method is experimentally tested at the LHC.

Integrating open-source software applications to build molecular dynamics systems.

Science.gov (United States)

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics.

Science.gov (United States)

Medders, Gregory R; Paesani, Francesco

2015-03-10

Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.

Calculation of the 5th AER dynamic benchmark with APROS

International Nuclear Information System (INIS)

Puska, E.K.; Kontio, H.

1998-01-01

The model used for calculation of the 5th AER dynamic benchmark with APROS code is presented. In the calculation of the 5th AER dynamic benchmark the three-dimensional neutronics model of APROS was used. The core was divided axially into 20 nodes according to the specifications of the benchmark and each six identical fuel assemblies were placed into one one-dimensional thermal hydraulic channel. The five-equation thermal hydraulic model was used in the benchmark. The plant process and automation was described with a generic VVER-440 plant model created by IVO PE. (author)

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.

Science.gov (United States)

Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto

2014-08-06

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

MdMYB9 and MdMYB11 are involved in the regulation of the JA-induced biosynthesis of anthocyanin and proanthocyanidin in apples.

Science.gov (United States)

An, Xiu-Hong; Tian, Yi; Chen, Ke-Qin; Liu, Xiao-Juan; Liu, Dan-Dan; Xie, Xing-Bin; Cheng, Cun-Gang; Cong, Pei-Hua; Hao, Yu-Jin

2015-04-01

Anthocyanin and proanthocyanidin (PA) are important secondary metabolites and beneficial to human health. Their biosynthesis is induced by jasmonate (JA) treatment and regulated by MYB transcription factors (TFs). However, which and how MYB TFs regulate this process is largely unknown in apple. In this study, MdMYB9 and MdMYB11 which were induced by methyl jasmonate (MeJA) were functionally characterized. Overexpression of MdMYB9 or MdMYB11 promoted not only anthocyanin but also PA accumulation in apple calluses, and the accumulation was further enhanced by MeJA. Subsequently, yeast two-hybrid, pull-down and bimolecular fluorescence complementation assays showed that both MYB proteins interact with MdbHLH3. Moreover, Jasmonate ZIM-domain (MdJAZ) proteins interact with MdbHLH3. Furthermore, chromatin immunoprecipitation-quantitative PCR and yeast one-hybrid assays demonstrated that both MdMYB9 and MdMYB11 bind to the promoters of ANS, ANR and LAR, whereas MdbHLH3 is recruited to the promoters of MdMYB9 and MdMYB11 and regulates their transcription. In addition, transient expression assays indicated that overexpression of MdJAZ2 inhibits the recruitment of MdbHLH3 to the promoters of MdMYB9 and MdMYB11. Our findings provide new insight into the mechanism of how MeJA regulates anthocyanin and PA accumulation in apple. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

International Nuclear Information System (INIS)

Ng, T Y; Yeak, S H; Liew, K M

2008-01-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods

Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.

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Shixiong Lua

Full Text Available T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS. Here using CD, NMR and molecular dynamics (MD simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1 unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2 Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3 T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4 EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5 As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.

Molecular dynamics study on the structure I clathrate-hydrate of methane + ethane mixture

International Nuclear Information System (INIS)

Erfan-Niya, Hamid; Modarress, Hamid; Zaminpayma, Esmaeil

2011-01-01

Molecular dynamics (MD) simulations are used to study the structure I stability of methane + ethane clathrate-hydrates at temperatures 273, 275 and 277 K. NVT- and NPT-ensembles are utilized in MD simulation, and each consists of 3 x 3 x 3 replica unit cells containing 46 water molecules which are considered as the host molecules and up to eight methane + ethane molecules considered as the guest molecules. In MD simulations for host-host interactions, the potential model used was a type of simple point charge (SPC) model, and for guest-guest and host-guest interactions the potential used was Lennard-Jones model. In the process of MD simulation, achieving equilibrium of the studied system was recognized by stability in calculated pressure for NVT-ensemble and volume for NPT-ensemble. To understand the characteristic configurations of the structure I hydrate, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules as well as other properties including kinetic energy, potential energy and total energy were calculated. The results show that guest molecules interaction with host molecules cannot decompose the hydrate structure, and these results are consistent with most previous experimental and theoretical investigations that methane + ethane mixtures form structure I hydrates over the entire mixture composition range.

The existence of a plastic phase and a solid-liquid dynamical bistability region in small fullerene cluster (C60)7: molecular dynamics simulation

International Nuclear Information System (INIS)

Piatek, A; Dawid, A; Gburski, Z

2006-01-01

We have simulated (by the molecular dymanics (MD) method) the dynamics of fullerenes (C 60 ) in an extremely small cluster composed of only as many as seven C 60 molecules. The interaction is taken to be the full 60-site pairwise additive Lennard-Jones (LJ) potential which generates both translational and anisotropic rotational motions of each molecule. Our atomically detailed MD simulations discover the plastic phase (no translations but active reorientations of fullerenes) at low energies (temperatures) of the (C 60 ) 7 cluster. We provide the in-depth evidence of the dynamical solid-liquid bistability region in the investigated cluster. Moreover, we confirm the existence of the liquid phase in (C 60 ) 7 , the finding of Gallego et al (1999 Phys. Rev. Lett. 83 5258) obtained earlier on the basis of Girifalco's model, which assumes single-site only and spherically symmetrical interaction between C 60 molecules. We have calculated the translational and angular velocity autocorrelation functions and estimated the diffusion coefficient of fullerene in the liquid phase

Muscular Dystrophy (MD)

Science.gov (United States)

... patients may need assisted ventilation to treat respiratory muscle weakness and a pacemaker for cardiac abnormalities. View Full Treatment Information Definition The muscular dystrophies (MD) are a group of more than 30 ...

Combined BC/MD approach to the evaluation of damage from fast neutrons and its implementation for beryllium irradiation in a fusion reactor

Science.gov (United States)

Borodin, V. A.; Vladimirov, P. V.

2017-12-01

The determination of primary damage production efficiency in metals irradiated with fast neutrons is a complex problem. Typically, the majority of atoms are displaced from their lattice positions not by neutrons themselves, but by energetic primary recoils, that can produce both single Frenkel pairs and dense localized cascades. Though a number of codes are available for the calculation of displacement damage from fast ions, they commonly use binary collision (BC) approximation, which is unreliable for dense cascades and thus tend to overestimate the number of created displacements. In order to amend the radiation damage predictions, this work suggests a combined approach, where the BC approximation is used for counting single Frenkel pairs only, whereas the secondary recoils able to produce localized dense cascades are stored for later processing, but not followed explicitly. The displacement production in dense cascades is then determined independently from molecular dynamics (MD) simulations. Combining contributions from different calculations, one gets the total number of displacements created by particular neutron spectrum. The approach is applied here to the case of beryllium irradiation in a fusion reactor. Using a relevant calculated energy spectrum of primary knocked-on atoms (PKAs), it is demonstrated that more than a half of the primary point defects (˜150/PKA) is produced by low-energy recoils in the form of single Frenkel pairs. The contribution to the damage from the dense cascades as predicted using the mixed BC/MD scheme, i.e. ˜110/PKA, is remarkably lower than the value deduced from uncorrected SRIM calculations (˜145/PKA), so that in the studied case SRIM tends to overpredict the total primary damage level.

Segmental dynamics in polymer electrolytes

CERN Document Server

Triolo, A; Lo Celso, F; Triolo, R; Passerini, S; Arrighi, V; Frick, B

2002-01-01

Polymer dynamics in poly(ethylene oxide) (PEO)-salt mixtures is investigated by means of quasi-elastic neutron scattering (QENS). In a previous study, we reported QENS data from the NEAT spectrometer (BENSC) that evidenced, for the first time, a dynamic heterogeneity in PEO-salt mixtures induced by salt addition. This finding is supported by molecular dynamics (MD) simulations carried out by Borodin et al. In agreement with MD simulations, our QENS data revealed two distinct processes: a fast motion corresponding to the bulk polymer and a slower relaxation, which we attribute to formation of PEO-cation complexes. In this paper we present new QENS data from the high-resolution spectrometer IN16 that further support MD simulations as well as our previous data interpretation. (orig.)

LiGRO: a graphical user interface for protein-ligand molecular dynamics.

Science.gov (United States)

Kagami, Luciano Porto; das Neves, Gustavo Machado; da Silva, Alan Wilter Sousa; Caceres, Rafael Andrade; Kawano, Daniel Fábio; Eifler-Lima, Vera Lucia

2017-10-04

To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http://www.ufrgs.br/lasomfarmacia/ligro/ .

Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

International Nuclear Information System (INIS)

Kobayashi, Kazuya; Liang, Yunfeng; Matsuoka, Toshifumi; Sakka, Tetsuo

2014-01-01

The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Kowledge-based dynamic network safety calculations. Wissensbasierte dynamische Netzsicherheitsberechnungen

Energy Technology Data Exchange (ETDEWEB)

Kulicke, B [Inst. fuer Hochspannungstechnik und Starkstromanlagen, Berlin (Germany); Schlegel, S [Inst. fuer Hochspannungstechnik und Starkstromanlagen, Berlin (Germany)

1993-06-28

An important part of network operation management is the estimation and maintenance of the security of supply. So far the control personnel has only been supported by static network analyses and safety calculations. The authors describe an expert system, which is coupled to a real time simulation program on a transputer basis, for dynamic network safety calculations. They also introduce the system concept and the most important functions of the expert system. (orig.)

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

Science.gov (United States)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of

Calculation of particle dynamics in CI-10 cyclotron

International Nuclear Information System (INIS)

Samsonov, E.V.; Karamysheva, G.A.; Vorozhtsov, S.B.

1999-01-01

The calculations of beam dynamic characteristics of High-Intensity Cyclotron-Injector CI-10 for deuteron beam of 15 MeV energy are presented. Analytical estimations of space charge effects are given. In order to increase the intensity of the accelerator beam some ideas about the cyclotron design modification are given too. (author)

Finite-temperature orbital-free DFT molecular dynamics: Coupling PROFESS and QUANTUM ESPRESSO

Science.gov (United States)

Karasiev, Valentin V.; Sjostrom, Travis; Trickey, S. B.

2014-12-01

Implementation of orbital-free free-energy functionals in the PROFESS code and the coupling of PROFESS with the QUANTUM ESPRESSO code are described. The combination enables orbital-free DFT to drive ab initio molecular dynamics simulations on the same footing (algorithms, thermostats, convergence parameters, etc.) as for Kohn-Sham (KS) DFT. All the non-interacting free-energy functionals implemented are single-point: the local density approximation (LDA; also known as finite-T Thomas-Fermi, ftTF), the second-order gradient approximation (SGA or finite-T gradient-corrected TF), and our recently introduced finite-T generalized gradient approximations (ftGGA). Elimination of the KS orbital bottleneck via orbital-free methodology enables high-T simulations on ordinary computers, whereas those simulations would be costly or even prohibitively time-consuming for KS molecular dynamics (MD) on very high-performance computer systems. Example MD simulations on H over a temperature range 2000 K ≤ T ≤4,000,000 K are reported, with timings on small clusters (16-128 cores) and even laptops. With respect to KS-driven calculations, the orbital-free calculations are between a few times through a few hundreds of times faster.

Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

Science.gov (United States)

Wu, Bin

, at neutral condition, the exterior residues folding back into interior would necessarily lead to higher entropy and equivalently lower free energy and thereby is energetically favored. As one decreases the pH condition of PAMAM dendrimers, the constituent residues would carry positive charges. The resultant inter-residue Coulomb repulsion would naturally result in conformational evolution. We found from CVSANS analysis that when dendrimers are charged by different acids, this conformational evolution is not the same. For dendrimers charged by DCl, the mass is seen to relocate from molecular interior to periphery. Nevertheless, those acidified by D 2SO4 exhibit surprisingly minor structural change under variation of molecular charge. To explain the above observation, we performed MD simulations and calculated the excess free energy of Cl- and SO 42- counterions. The binding between sulfate ions and charged amines of PAMAM dendrimers are found to be much stronger than the case for chlorides. This more energetic binding would serve as better screening effect among charged residues. Consequently, electrostatic repulsion triggered outstretching tendency is effectively diminished. In order to make direct comparison between MD simulations and neutron scattering experiments, we proposed and implemented a rigorous method, which incorporates the contribution from those invasive water molecules, to calculate scattering functions of a single PAMAM dendrimer using equilibrium MD trajectories. The bridge between neutron scattering experiments and MD simulation is successfully established. Aside from structural comparisons between MD simulations and experiments, we utilized MD simulation to decipher the previously reported QENS experimental observation that the segmental dynamics of PAMAM dendrimer would enhance with increasing molecular charge. We pursued the mechanism from the perspective of hydrocarbon component of dendrimer and solvent (water) interaction as a form similar to

Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length.

Science.gov (United States)

Reddy, M Rami; Erion, Mark D

2009-12-01

Molecular dynamics (MD) simulations in conjunction with thermodynamic perturbation approach was used to calculate relative solvation free energies of five pairs of small molecules, namely; (1) methanol to ethane, (2) acetone to acetamide, (3) phenol to benzene, (4) 1,1,1 trichloroethane to ethane, and (5) phenylalanine to isoleucine. Two studies were performed to evaluate the dependence of the convergence of these calculations on MD simulation length and starting configuration. In the first study, each transformation started from the same well-equilibrated configuration and the simulation length was varied from 230 to 2,540 ps. The results indicated that for transformations involving small structural changes, a simulation length of 860 ps is sufficient to obtain satisfactory convergence. In contrast, transformations involving relatively large structural changes, such as phenylalanine to isoleucine, require a significantly longer simulation length (>2,540 ps) to obtain satisfactory convergence. In the second study, the transformation was completed starting from three different configurations and using in each case 860 ps of MD simulation. The results from this study suggest that performing one long simulation may be better than averaging results from three different simulations using a shorter simulation length and three different starting configurations.

Molecular dynamics simulations of solutions at constant chemical potential

Science.gov (United States)

Perego, C.; Salvalaglio, M.; Parrinello, M.

2015-04-01

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

Cascade statistics in the binary collision approximation and in full molecular dynamics

International Nuclear Information System (INIS)

Hou, M.; Pan, Z.Y.

1995-01-01

The Binary Collision Approximation (BCA) and Molecular Dynamics (MD) are used to simulate low energy atomic collision cascades in solids. Results are compared and discussed on the example of copper and gold self irradiation. For MD, long range N-body potentials are built, similar to those deduced from the second moment semi-empirical tight binding model. The pair interaction contribution is splined to a Moliere screened Coulomb potential at small separation distances. The BCA calculations are performed with the MARLOWE program, using the same Moliere potential as for MD, and modelling the N-body contribution by a binding of the atoms to their equilibrium lattice sites. The scattering integrals are estimated by means of a 4 points Gauss-Mehler quadrature. In MD, the NVT equations of motion are integrated with a constant time step of 2 fs. For the NVE cascade simulations, the Newton equations of motion are solved with a dynamically adjusted time step, kept lower than 2 fs. The influence of the time step on the simulated trajectories is discussed. The mean number of moving atoms with total energy above threshold values ranging from 1 to 100 eV is estimated as a function of time over 300 fs both with MARLOWE and by MD. This estimate is repeated for external primary energies ranging from 250 eV to 1 keV. In the case of copper, the BCA results are found to be in remarkable agreement with MD over about 200 fs cascade development, provided the size of the crystallite used in MD is sufficiently large in order to account for the early mechanical response of the close environment. This agreement between the two methods is found to be the best when the binding energy of the target atoms as modelled in the BCA is adjusted to a value close to the cohesive energy. In the case of gold, the agreement between BCA and MD is reasonable and the results suggest the need of an accurate modelling of linear collision sequences in the BCA. (orig.)

Effect of surface hydrophobicity on the dynamics of water at the nanoscale confinement: A molecular dynamics simulation study

International Nuclear Information System (INIS)

Choudhury, Niharendu

2013-01-01

Highlights: • We present atomistic MD simulation of water confined between two paraffin-like plates. • Effect of plate hydrophobicity on the confined water dynamics is investigated. • Diffusivity of confined water is calculated from mean squared displacements. • Rotational dynamics of the confined water has bimodal nature of relaxation. • Monotonic dependence of translational and rotational dynamics on hydrophobicity. - Abstract: We present detailed molecular dynamics simulations of water in and around a pair of plates immersed in water to investigate the effect of degree of hydrophobicity or hydrophilicity of the plates on dynamics of water confined between the two plates. The nature of the plate has been tuned from hydrophobic to hydrophilic and vice versa by varying plate-water dispersion interaction. Analyses of the translational dynamics as performed by calculating mean squared displacements of the confined water reveal a monotonically decreasing trend of the diffusivity with increasing hydrophilicity of the plates. Orientational dynamics of the confined water also follows the same monotonic trend. Although orientational time constant almost does not change with the increase of plate-water dispersion interaction in the hydrophobic regime corresponding to the smaller plate-water attraction, it changes considerably in the hydrophilic regime corresponding to larger plate-water dispersion interactions

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

Science.gov (United States)

Prior, C; Danilāne, L; Oganesyan, V S

2018-05-16

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

The small ubiquitin-like modifier E3 ligase MdSIZ1 promotes anthocyanin accumulation by sumoylating MdMYB1 under low-temperature conditions in apple.

Science.gov (United States)

Zhou, Li-Jie; Li, Yuan-Yuan; Zhang, Rui-Fen; Zhang, Chun-Ling; Xie, Xing-Bin; Zhao, Cheng; Hao, Yu-Jin

2017-10-01

MdMYB1 acts as a crucial component of the MYB-bHLH-WD40 complex to regulate anthocyanin biosynthesis in red-skinned apples (Malus domestica), but little is known about its post-translational regulation. Here, a small ubiquitin-like modifier E3 ligase MdSIZ1 was screened out as an MdMYB1-interacting protein with a yeast two-hybridization approach. The interaction between MdSIZ1 and MdMYB1 was further verified with pull-down and CoIP assays. Furthermore, it was found that MdSIZ1 directly sumoylated MdMYB1 proteins in vivo and in vitro, especially under moderately low temperature (17 °C) conditions, and that this sumoylation was required for MdMYB1 protein stability. Moreover, the transcription level of MdSIZ1 gene was remarkably induced by low temperature and phosphorus deficiency, and MdSIZ1 overexpression exerted a large positive influence on anthocyanin accumulation and red fruit coloration, suggesting its important role in the regulation of anthocyanin biosynthesis under stress conditions. Our findings reveal an important role for a small ubiquitin-like modifier modification of MYB transcription factors in regulation of anthocyanin biosynthesis in plants. © 2017 John Wiley & Sons Ltd.

A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

Science.gov (United States)

Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

2018-05-08

Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers

Science.gov (United States)

Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun

2010-03-01

Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.

Calculation of the fifth atomic energy research dynamic benchmark with APROS

International Nuclear Information System (INIS)

Puska Eija Karita; Kontio Harii

1998-01-01

The band-out presents the model used for calculation of the fifth atomic energy research dynamic benchmark with APROS code. In the calculation of the fifth atomic energy research dynamic benchmark the three-dimensional neutronics model of APROS was used. The core was divided axially into 20 nodes according to the specifications of the benchmark and each six identical fuel assemblies were placed into one one-dimensional thermal hydraulic channel. The five-equation thermal hydraulic model was used in the benchmark. The plant process and automation was described with a generic WWER-440 plant model created by IVO Power Engineering Ltd. - Finland. (Author)

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Directory of Open Access Journals (Sweden)

Lauren Boldon

2015-02-01

Full Text Available In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS experiments, molecular dynamics (MD simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

Science.gov (United States)

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

Dynamical gluon masses in perturbative calculations at the loop level

International Nuclear Information System (INIS)

Machado, Fatima A.; Natale, Adriano A.

2013-01-01

Full text: In the phenomenology of strong interactions one always has to deal at some extent with the interplay between perturbative and non-perturbative QCD. On one hand, the former has quite developed tools, yielded by asymptotic freedom. On the other, concerning the latter, we nowadays envisage the following scenario: 1) There are strong evidences for a dynamically massive gluon propagator and infrared finite coupling constant; 2) There is an extensive and successful use of an infrared finite coupling constant in phenomenological calculations at tree level; 3) The infrared finite coupling improves the perturbative series convergence; 4) The dynamical gluon mass provides a natural infrared cutoff in the physical processes at the tree level. Considering this scenario it is natural to ask how these non-perturbative results can be used in perturbative calculations of physical observables at the loop level. Recent papers discuss how off-shell gauge and renormalization group invariant Green functions can be computed with the use of the Pinch Technique (PT), with IR divergences removed by the dynamical gluon mass, and using a well defined effective charge. In this work we improve the former results by the authors, which evaluate 1-loop corrections to some two- and three-point functions of SU(3) pure Yang-Mills, investigating the dressing of quantities that could account for an extension of loop calculations to the infrared domain of the theory, in a way applicable to phenomenological calculations. One of these improvements is maintaining the gluon propagator transverse in such a scheme. (author)

Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

International Nuclear Information System (INIS)

Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

2014-01-01

It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments

A large-scale molecular dynamics study of the divacancy defect in graphene

International Nuclear Information System (INIS)

Leyssale, Jean-Marc; Vignoles, Gerard L.

2014-01-01

We report on the dynamical behavior of single divacancy defects in large graphene sheets as studied by extensive classical molecular dynamics (MD) simulations at high temperatures and static calculations. In the first part of the paper, the ability of the used interatomic potential to properly render the stability and dynamics (energy barriers) of such defects is validated against electronic structure calculations from the literature. Then, results from MD simulations are presented. In agreement with recent TEM studies, some mobility is observed through a series of Stone-Wales-like bond rotations involving the 5-8-5, 555-777, and 5555-6-7777 reconstructions. Although these three structures are by far the most probable structures of the DV defect, not less than 18 other full reconstructions, including the experimentally observed 55-66-77 defect, were occasionally observed in the ∼1.5 μs of MD trajectories analyzed in this work. Most of these additional reconstructions have moderate formation energies and can be formed by a bond rotation mechanism from one of the aforementioned structures, with a lower activation energy than the one required to form a Stone-Wales defect in graphene. Therefore their future experimental observation is highly probable. The results presented here also suggest that the barrier to a conventional Stone-Wales transformation (the formation of two pentagon/heptagon pairs from four hexagons) can be significantly reduced in the vicinity of an existing defect, strengthening a recently proposed melting mechanism for graphene based on the aggregation of Stone-Wales defects. From a structural point of view, in addition to pentagons, heptagons, and octagons, these new DV reconstructions can also contain four- and nine-member rings and show a particularly large spatial extent of up to 13 rings (42 atoms) against three (14 atoms) for the original 5-8-5 defect. (authors)

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

Science.gov (United States)

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

Multiscale molecular dynamics using the matched interface and boundary method

International Nuclear Information System (INIS)

Geng Weihua; Wei, G.W.

2011-01-01

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.

A novel energy conversion based method for velocity correction in molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Jin, Hanhui [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 (China); Liu, Ningning [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Fan, Jianren [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)

2017-05-01

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

A novel energy conversion based method for velocity correction in molecular dynamics simulations

International Nuclear Information System (INIS)

Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren

2017-01-01

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

MdCOP1 Ubiquitin E3 Ligases Interact with MdMYB1 to Regulate Light-Induced Anthocyanin Biosynthesis and Red Fruit Coloration in Apple1[W][OA

Science.gov (United States)

Li, Yuan-Yuan; Mao, Ke; Zhao, Cheng; Zhao, Xian-Yan; Zhang, Hua-Lei; Shu, Huai-Rui; Hao, Yu-Jin

2012-01-01

MdMYB1 is a crucial regulator of light-induced anthocyanin biosynthesis and fruit coloration in apple (Malus domestica). In this study, it was found that MdMYB1 protein accumulated in the light but degraded via a ubiquitin-dependent pathway in the dark. Subsequently, the MdCOP1-1 and MdCOP1-2 genes were isolated from apple fruit peel and were functionally characterized in the Arabidopsis (Arabidopsis thaliana) cop1-4 mutant. Yeast (Saccharomyces cerevisiae) two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays showed that MdMYB1 interacts with the MdCOP1 proteins. Furthermore, in vitro and in vivo experiments indicated that MdCOP1s are necessary for the ubiquitination and degradation of MdMYB1 protein in the dark and are therefore involved in the light-controlled stability of the MdMYB1 protein. Finally, a viral vector-based transformation approach demonstrated that MdCOP1s negatively regulate the peel coloration of apple fruits by modulating the degradation of the MdMYB1 protein. Our findings provide new insight into the mechanism by which light controls anthocyanin accumulation and red fruit coloration in apple and even other plant species. PMID:22855936

The calculation of turbulence phenomena in plasma focus dynamics using REDUCE

International Nuclear Information System (INIS)

Hayd, A.; Maurer, M.; Meinke, P.; Kaeppeler, H.J.

1982-05-01

Based on previous calculations of the development of highly turbulent plasma states resulting from m=0 instabilities and the application to the turbulent development in the late stage of a plasma focus experiment, using REDUE, the treatment of plasma focus dynamics is extended to the compression stage and 'intermediate' stage between maximum density and m = o onset. For this, a two-fluid model of the magneto-fluid dynamic equations is employed. The non-linear development is again treated in ω, k-space and transformed back into r, t-space to obtain local dynamic variables as functions of time. The calculation is applied to the Stuttgart plasma focus experiment POSEIDON. It is shown that for relatively high pinch currents, neutron production also appears in the 'intermediate' phase, the life-time of which increases with increasing pinch current. (orig.)

Ensemble simulations with discrete classical dynamics

DEFF Research Database (Denmark)

Toxværd, Søren

2013-01-01

For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...

ORBIT : BEAM DYNAMICS CALCULATIONS FOR HIGH - INTENSITY RINGS

International Nuclear Information System (INIS)

HOLMES, J.A.; DANILOV, V.; GALAMBOS, J.; SHISHLO, A.; COUSINEAU, S.; CHOU, W.; MICHELOTTI, L.; OSTIGUY, F.; WEI, J.

2002-01-01

We are developing a computer code, ORBIT, specifically for beam dynamics calculations in high-intensity rings. Our approach allows detailed simulation of realistic accelerator problems. ORBIT is a particle-in-cell tracking code that transports bunches of interacting particles through a series of nodes representing elements, effects, or diagnostics that occur in the accelerator lattice. At present, ORBIT contains detailed models for strip-foil injection including painting and foil scattering; rf focusing and acceleration; transport through various magnetic elements; longitudinal and transverse impedances; longitudinal, transverse, and three-dimensional space charge forces; collimation and limiting apertures; and the calculation of many useful diagnostic quantities. ORBIT is an object-oriented code, written in C++ and utilizing a scripting interface for the convenience of the user. Ongoing improvements include the addition of a library of accelerator maps, BEAMLINE/MXYZPTLK the introduction of a treatment magnet errors and fringe fields; the conversion of the scripting interface to the standard scripting language, Python; and the parallelization of the computations using MPI. The ORBIT code is an open source, powerful, and convenient tool for studying beam dynamics in high-intensity rings

Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

Energy Technology Data Exchange (ETDEWEB)

Carr, J. K.; Roy, S.; Skinner, J. L. [Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706 (United States); Zabuga, A. V.; Rizzo, T. R. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne (Switzerland)

2014-06-14

The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

Science.gov (United States)

Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

2014-01-01

The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

International Nuclear Information System (INIS)

Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

2014-01-01

The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala) 5 -Lys-H + in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13 C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13 C 18 O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm −1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

Science.gov (United States)

Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

2013-11-07

Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

Molecular dynamics simulation of impact test

International Nuclear Information System (INIS)

Akahoshi, Y.; Schmauder, S.; Ludwig, M.

1998-01-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

Molecular dynamics simulation of impact test

Energy Technology Data Exchange (ETDEWEB)

Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

1998-11-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

The AINTEGUMENTA genes, MdANT1 and MdANT2, are associated with the regulation of cell production during fruit growth in apple (Malus × domestica Borkh.).

Science.gov (United States)

Dash, Madhumita; Malladi, Anish

2012-06-25

Fruit growth in apple (Malus × domestica Borkh.) is mediated by cell production and expansion. Genes involved in regulating these processes and thereby fruit growth, are not well characterized. We hypothesized that the apple homolog(s) of AINTEGUMENTA (ANT), an APETALA2-repeat containing transcription factor, regulates cell production during fruit growth in apple. Two ANT genes, MdANT1 and MdANT2, were isolated from apple and their expression was studied during multiple stages of fruit development. MdANT1 and MdANT2 expression was high during early fruit growth coincident with the period of cell production, rapidly declined during exit from cell production, and remained low during the rest of fruit development. The effects of increase in carbohydrate availability during fruit growth were characterized. Increase in carbohydrate availability enhanced fruit growth largely through an increase in cell production. Expression of MdANT1 and MdANT2 increased sharply by up to around 5-fold in response to an increase in carbohydrate availability. Expression of the ANT genes was compared across two apple genotypes, 'Gala' and 'Golden Delicious Smoothee' (GS), which differ in the extent of fruit growth, largely due to differences in cell production. In comparison to 'Gala', the larger fruit-size genotype, GS, displayed higher levels and a longer duration of MdANT1 and MdANT2 expression. Expression of the ANTs and cell cycle genes in the fruit core and cortex tissues isolated using laser capture microdissection was studied. During early fruit growth, expression of the MdANTs was higher within the cortex, the tissue that constitutes the majority of the fruit. Additionally, MdANT1 and MdANT2 expression was positively correlated with that of A- and B-type CYCLINS, B-type CYCLIN-DEPENDENT-KINASES (CDKBs) and MdDEL1. Multiple lines of evidence from this study suggest that MdANT1 and MdANT2 regulate cell production during fruit growth in apple. ANTs may coordinate the expression of

Ultrafast phosphate hydration dynamics in bulk H2O

Science.gov (United States)

Costard, Rene; Tyborski, Tobias; Fingerhut, Benjamin P.; Elsaesser, Thomas

2015-06-01

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H2PO4- ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric ( ν S ( PO2 - ) ) and asymmetric ( ν A S ( PO2 - ) ) PO 2- stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH)2) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν S ( PO2 - ) and ν A S ( PO2 - ) transition frequencies with larger frequency excursions for ν A S ( PO2 - ) . The calculated frequency-time correlation function is in good agreement with the experiment. The ν ( PO2 - ) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H2PO4-/H2O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Structure-dynamic model verification calculation of PWR 5 tests

International Nuclear Information System (INIS)

Engel, R.

1980-02-01

Within reactor safety research project RS 16 B of the German Federal Ministry of Research and Technology (BMFT), blowdown experiments are conducted at Battelle Institut e.V. Frankfurt/Main using a model reactor pressure vessel with a height of 11,2 m and internals corresponding to those in a PWR. In the present report the dynamic loading on the pressure vessel internals (upper perforated plate and barrel suspension) during the DWR 5 experiment are calculated by means of a vertical and horizontal dynamic model using the CESHOCK code. The equations of motion are resolved by direct integration. (orig./RW) [de

Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration.

Science.gov (United States)

Huang, Jinfeng; Zhu, Yali; Sun, Bin; Yao, Yuan; Liu, Junjun

2016-03-01

The protonation state of the Asp dyad is important as it can reveal enzymatic mechanisms, and the information this provides can be used in the development of drugs for proteins such as memapsin 2 (BACE-1), HIV-1 protease, and rennin. Conventional molecular dynamics (MD) simulations have been successfully used to determine the preferred protonation state of the Asp dyad. In the present work, we demonstrate that the results obtained from conventional MD simulations can be greatly influenced by the particular force field applied or the values used for control parameters. In principle, free-energy changes between possible protonation states can be used to determine the protonation state. We show that protonation state prediction by the thermodynamic integration (TI) method is insensitive to force field version or to the cutoff for calculating nonbonded interactions (a control parameter). In the present study, the protonation state of the Asp dyad predicted by TI calculations was the same regardless of the force field and cutoff value applied. Contrary to the intuition that conventional MD is more efficient, our results clearly show that the TI method is actually more efficient and more reliable for determining the protonation state of the Asp dyad.

An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

Directory of Open Access Journals (Sweden)

Huiding Xie

2015-11-01

Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

Science.gov (United States)

Sevgen, Emre; Giberti, Federico; Sidky, Hythem; Whitmer, Jonathan K; Galli, Giulia; Gygi, Francois; de Pablo, Juan J

2018-05-14

We present a seamless coupling of a suite of codes designed to perform advanced sampling simulations, with a first-principles molecular dynamics (MD) engine. As an illustrative example, we discuss results for the free energy and potential surfaces of the alanine dipeptide obtained using both local and hybrid density functionals (DFT), and we compare them with those of a widely used classical force field, Amber99sb. In our calculations, the efficiency of first-principles MD using hybrid functionals is augmented by hierarchical sampling, where hybrid free energy calculations are initiated using estimates obtained with local functionals. We find that the free energy surfaces obtained from classical and first-principles calculations differ. Compared to DFT results, the classical force field overestimates the internal energy contribution of high free energy states, and it underestimates the entropic contribution along the entire free energy profile. Using the string method, we illustrate how these differences lead to different transition pathways connecting the metastable minima of the alanine dipeptide. In larger peptides, those differences would lead to qualitatively different results for the equilibrium structure and conformation of these molecules.

Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea

2014-01-01

, for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained...

Hybrid classical/quantum simulation for infrared spectroscopy of water

Science.gov (United States)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

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Toofanny Rudesh D

2011-08-01

Full Text Available Abstract Background Molecular dynamics (MD simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster. For a 'full' simulation trajectory (51 ns spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster. Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36% was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

Science.gov (United States)

Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

2011-08-10

Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation

Apple MdACS6 Regulates Ethylene Biosynthesis During Fruit Development Involving Ethylene-Responsive Factor.

Science.gov (United States)

Li, Tong; Tan, Dongmei; Liu, Zhi; Jiang, Zhongyu; Wei, Yun; Zhang, Lichao; Li, Xinyue; Yuan, Hui; Wang, Aide

2015-10-01

Ethylene biosynthesis in plants involves different 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes. The regulation of each ACS gene during fruit development is unclear. Here, we characterized another apple (Malus×domestica) ACS gene, MdACS6. The transcript of MdACS6 was observed not only in fruits but also in other tissues. During fruit development, MdACS6 was initiated at a much earlier stage, whereas MdACS3a and MdACS1 began to be expressed at 35 d before harvest and immediateley after harvest, respectively. Moreover, the enzyme activity of MdACS6 was significantly lower than that of MdACS3a and MdACS1, accounting for the low ethylene biosynthesis in young fruits. Overexpression of MdACS6 (MdACS6-OE) by transient assay in apple showed enhanced ethylene production, and MdACS3a was induced in MdACS6-OE fruits but not in control fruits. In MdACS6 apple fruits silenced by the virus-induced gene silencing (VIGS) system (MdACS6-AN), neither ethylene production nor MdACS3a transcript was detectable. In order to explore the mechanism through which MdACS3a was induced in MdACS6-OE fruits, we investigated the expression of apple ethylene-responsive factor (ERF) genes. The results showed that the expression of MdERF2 was induced in MdACS6-OE fruits and inhibited in MdACS6-AN fruits. Yeast one-hybrid assay showed that MdERF2 protein could bind to the promoter of MdACS3a. Moreover, down-regulation of MdERF2 in apple flesh callus led to a decrease of MdACS3a expression, demonstrating the regulation of MdERF2 on MdACS3a. The mechanism through which MdACS6 regulates the action of MdACS3a was discussed. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Detailed regulatory mechanism of the interaction between ZO-1 PDZ2 and connexin43 revealed by MD simulations.

Directory of Open Access Journals (Sweden)

Fei Xiao

Full Text Available The gap junction protein connexin43 (Cx43 binds to the second PDZ domain of Zonula occludens-1 (ZO-1 through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9 and Ser (-10 of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9 significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation.

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

International Nuclear Information System (INIS)

Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

2014-01-01

Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

Dynamical optimization techniques for the calculation of electronic structure in solids

International Nuclear Information System (INIS)

Benedek, R.; Min, B.I.; Garner, J.

1989-01-01

The method of dynamical simulated annealing, recently introduced by Car and Parrinello, provides a new tool for electronic structure computation as well as for molecular dynamics simulation. In this paper, we explore an optimization technique that is complementary to dynamical simulated annealing, the method of steepest descents (SD). As an illustration, SD is applied to calculate the total energy of diamond-Si, a system previously treated by Car and Parrinello. The adaptation of SD to treat metallic systems is discussed and a numerical application is presented. (author) 18 refs., 3 figs

Infrared microspectroscopy of live cells in microfluidic devices (MD-IRMS): toward a powerful label-free cell-based assay.

Science.gov (United States)

Vaccari, L; Birarda, G; Businaro, L; Pacor, S; Grenci, G

2012-06-05

Until nowadays most infrared microspectroscopy (IRMS) experiments on biological specimens (i.e., tissues or cells) have been routinely carried out on fixed or dried samples in order to circumvent water absorption problems. In this paper, we demonstrate the possibility to widen the range of in-vitro IRMS experiments to vibrational analysis of live cellular samples, thanks to the development of novel biocompatible IR-visible transparent microfluidic devices (MD). In order to highlight the biological relevance of IRMS in MD (MD-IRMS), we performed a systematic exploration of the biochemical alterations induced by different fixation protocols, ethanol 70% and formaldehyde solution 4%, as well as air-drying on U937 leukemic monocytes by comparing their IR vibrational features with the live U937 counterpart. Both fixation and air-drying procedures affected lipid composition and order as well as protein structure at a different extent while they both induced structural alterations in nucleic acids. Therefore, only IRMS of live cells can provide reliable information on both DNA and RNA structure and on their cellular dynamic. In summary, we show that MD-IRMS of live cells is feasible, reliable, and biologically relevant to be recognized as a label-free cell-based assay.

Quasielastic neutron scattering and molecular dynamics simulation studies of the melting transition in butane and hexane monolayers adsorbed on graphite

DEFF Research Database (Denmark)

Hervig, K.W.; Wu, Z.; Dai, P.

1997-01-01

Quasielastic neutron scattering experiments and molecular dynamics (MD) simulations have been used to investigate molecular diffusive motion near the melting transition of monolayers of flexible rod-shaped molecules. The experiments were conducted on butane and hexane monolayers adsorbed...... comparison with experiment, quasielastic spectra calculated from the MD simulations were analyzed using the same models and fitting algorithms as for the neutron spectra. This combination of techniques gives a microscopic picture of the melting process in these two monolayers which is consistent with earlier...... neutron diffraction experiments. Butane melts abruptly to a liquid phase where the molecules in the trans conformation translationally diffuse while rotating about their center of mass. In the case of the hexane monolayer, the MD simulations show that the appearance of quasielastic scattering below T...

Calculation of dynamic hydraulic forces in nuclear plant piping systems

International Nuclear Information System (INIS)

Choi, D.K.

1982-01-01

A computer code was developed as one of the tools needed for analysis of piping dynamic loading on nuclear power plant high energy piping systems, including reactor safety and relief value upstream and discharge piping systems. The code calculates the transient hydraulic data and dynamic forces within the one-dimensional system, caused by a pipe rupture or sudden value motion, using a fixed space and varying time grid-method of characteristics. Subcooled, superheated, homogeneous two-phase and transition flow regimes are considered. A non-equilibrium effect is also considered in computing the fluid specific volume and fluid local sonic velocity in the two-phase mixture. Various hydraulic components such as a spring loaded or power operated value, enlarger, orifice, pressurized tank, multiple pipe junction (tee), etc. are considered as boundary conditions. Comparisons of calculated results with available experimental data shows a good agreement. (Author)

New Systematic CFD Methods to Calculate Static and Single Dynamic Stability Derivatives of Aircraft

Directory of Open Access Journals (Sweden)

Bai-gang Mi

2017-01-01

Full Text Available Several new systematic methods for high fidelity and reliability calculation of static and single dynamic derivatives are proposed in this paper. Angle of attack step response is used to obtain static derivative directly; then translation acceleration dynamic derivative and rotary dynamic derivative can be calculated by employing the step response motion of rate of the angle of attack and unsteady motion of pitching angular velocity step response, respectively. Longitudinal stability derivative calculations of SACCON UCAV are taken as test cases for validation. Numerical results of all cases achieve good agreement with reference values or experiments data from wind tunnel, which indicate that the proposed methods can be considered as new tools in the process of design and production of advanced aircrafts for their high efficiency and precision.

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

International Nuclear Information System (INIS)

Mori, Yukie; Masuda, Yuichi

2015-01-01

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

Energy Technology Data Exchange (ETDEWEB)

Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

2015-09-08

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

Science.gov (United States)

Moktan, Hem; Pezza, Roberto; Zhou, Donghua

2015-03-01

The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

A New Calculation Method of Dynamic Kill Fluid Density Variation during Deep Water Drilling

Directory of Open Access Journals (Sweden)

Honghai Fan

2017-01-01

Full Text Available There are plenty of uncertainties and enormous challenges in deep water drilling due to complicated shallow flow and deep strata of high temperature and pressure. This paper investigates density of dynamic kill fluid and optimum density during the kill operation process in which dynamic kill process can be divided into two stages, that is, dynamic stable stage and static stable stage. The dynamic kill fluid consists of a single liquid phase and different solid phases. In addition, liquid phase is a mixture of water and oil. Therefore, a new method in calculating the temperature and pressure field of deep water wellbore is proposed. The paper calculates the changing trend of kill fluid density under different temperature and pressure by means of superposition method, nonlinear regression, and segment processing technique. By employing the improved model of kill fluid density, deep water kill operation in a well is investigated. By comparison, the calculated density results are in line with the field data. The model proposed in this paper proves to be satisfactory in optimizing dynamic kill operations to ensure the safety in deep water.

Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics

Energy Technology Data Exchange (ETDEWEB)

Alekseeva, Uliana, E-mail: Alekseeva@itc.rwth-aachen.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Winkler, Roland G., E-mail: r.winkler@fz-juelich.de [Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Sutmann, Godehard, E-mail: g.sutmann@fz-juelich.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); ICAMS, Ruhr-University Bochum, D-44801 Bochum (Germany)

2016-06-01

A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.

Development of Dynamic Environmental Effect Calculation Model

International Nuclear Information System (INIS)

Jeong, Chang Joon; Ko, Won Il

2010-01-01

The short-term, long-term decay heat, and radioactivity are considered as main environmental parameters of SF and HLA. In this study, the dynamic calculation models for radioactivity, short-term decay heat, and long-term heat load of the SF are developed and incorporated into the Doneness code. The spent fuel accumulation has become a major issue for sustainable operation of nuclear power plants. If a once-through fuel cycle is selected, the SF will be disposed into the repository. Otherwise, in case of fast reactor or reuse cycle, the SF will be reprocessed and the high level waste will be disposed

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

Science.gov (United States)

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

International Nuclear Information System (INIS)

Nangia, Shivangi; Garrison, Barbara J.

2011-01-01

There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

Prediction and analysis of the structure of hydrated Mn2+, V2+, Ti3 and Cr3 ions by means of the MD simulation methods

International Nuclear Information System (INIS)

Iglesias, Y.J.

2002-01-01

Classical Molecular dynamics (MD) and hybrid Quantum/Molecular Mechanics-Molecular Dynamics (QM/MM-MD) simulations have been performed to investigate structural properties of Mn(II), V(II), Cr(III) and Ti(III) cations in aqueous solution. The first hydration sphere in QM/MM-MD simulations is treated quantum mechanically, while the rest of the system is described by classical analytical two- and three-body potentials. The results obtained for the first hydration shell from this method are in agreement with experimental data, showing 100 % of 6 fold coordination around the ion in all cases. The results prove that non/additive contributions are mandatory for an accurate description of ion hydration. Within the QM/MM method, the inclusion of a perturbation field describing the remaining system was shown to be an accurate tool for evaluating the first shell structure, and thus to be a good alternative for systems, where the construction of a three-body correction function is difficult or too time-consuming. (author)

The effect of walking speed on local dynamic stability is sensitive to calculation methods

DEFF Research Database (Denmark)

Stenum, Jan; Bruijn, Sjoerd M; Jensen, Bente Rona

2014-01-01

Local dynamic stability has been assessed by the short-term local divergence exponent (λS), which quantifies the average rate of logarithmic divergence of infinitesimally close trajectories in state space. Both increased and decreased local dynamic stability at faster walking speeds have been...... reported. This might pertain to methodological differences in calculating λS. Therefore, the aim was to test if different calculation methods would induce different effects of walking speed on local dynamic stability. Ten young healthy participants walked on a treadmill at five speeds (60%, 80%, 100%, 120......% and 140% of preferred walking speed) for 3min each, while upper body accelerations in three directions were sampled. From these time-series, λS was calculated by three different methods using: (a) a fixed time interval and expressed as logarithmic divergence per stride-time (λS-a), (b) a fixed number...

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Science.gov (United States)

Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

MD290: Q4 IP6 Quench Level

CERN Document Server

Bednarek, Mateusz Jakub; Lechner, Anton; CERN. Geneva. ATS Department

2016-01-01

The detailed program proposed for the LHC Machine Development concerning a quench induced by fast losses on the MQY.4L6 quadrupole is presented. The merit of the MD, the necessary modifications of the machine protection systems are presented together with a preliminary analysis of the MD results.

Chosen-Prefix Collisions for MD5 and Applications

NARCIS (Netherlands)

M.M.J. Stevens (Marc); A.K. Lenstra (Arjen); B. de Weger (Benne)

2012-01-01

textabstractWe present a novel, automated way to find differential paths for MD5. Its main application is in the construction of \\emph{chosen-prefix collisions}. We have shown how, at an approximate expected cost of $2^{39}$ calls to the MD5 compression function, for any two chosen

Investigation on single carbon atom transporting through the single-walled carbon nanotube by MD simulation

International Nuclear Information System (INIS)

Ding Yinfeng; Zhang Zhibin; Ke Xuezhi; Zhu Zhiyuan; Zhu Dezhang; Wang Zhenxia; Xu Hongjie

2005-01-01

The single carbon atom transporting through the single-walled carbon nanotube has been studied by molecular-dynamics (MD) simulation. We got different trajectories of the carbon atom by changing the input parameters. The simulation results indicate that the single carbon atom with low energy can transport through the carbon nanotube under some input conditions and result in different trajectories being straight line or 'rosette' or circular. (authors)

Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Directory of Open Access Journals (Sweden)

Ji-Long Zhang

Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus

Science.gov (United States)

Dougherty, Laura; Zhu, Yuandi; Xu, Kenong

2016-01-01

Phytohormone ethylene largely determines apple fruit shelf life and storability. Previous studies demonstrated that MdACS1 and MdACS3a, which encode 1-aminocyclopropane-1-carboxylic acid synthases (ACS), are crucial in apple fruit ethylene production. MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening, while MdACS3a has been regarded a main regulator for ethylene production transition from system 1 (during fruit development) to system 2 (during fruit ripening). However, MdACS3a was also shown to have limited roles in initiating the ripening process lately. To better assess their roles, fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses. Allelotyping was accomplished using an existing marker (ACS1) for MdACS1 and two markers (CAPS866 and CAPS870) developed here to specifically detect the two null alleles (ACS3a-G289V and Mdacs3a) of MdACS3a. In total, 952 Malus accessions were allelotyped with the three markers. The major findings included: The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable; allele MdACS1–2 was significantly associated with low ethylene and slow softening; under the same background of the MdACS1 allelotypes, null allele Mdacs3a (not ACS3a-G289V) could confer a significant delay of ethylene peak; alleles MdACS1–2 and Mdacs3a (excluding ACS3a-G289V) were highly enriched in M. domestica and M. hybrid when compared with those in M. sieversii. These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a. PMID:27231553

Advanced Dynamics Analytical and Numerical Calculations with MATLAB

CERN Document Server

Marghitu, Dan B

2012-01-01

Advanced Dynamics: Analytical and Numerical Calculations with MATLAB provides a thorough, rigorous presentation of kinematics and dynamics while using MATLAB as an integrated tool to solve problems. Topics presented are explained thoroughly and directly, allowing fundamental principles to emerge through applications from areas such as multibody systems, robotics, spacecraft and design of complex mechanical devices. This book differs from others in that it uses symbolic MATLAB for both theory and applications. Special attention is given to solutions that are solved analytically and numerically using MATLAB. The illustrations and figures generated with MATLAB reinforce visual learning while an abundance of examples offer additional support. This book also: Provides solutions analytically and numerically using MATLAB Illustrations and graphs generated with MATLAB reinforce visual learning for students as they study Covers modern technical advancements in areas like multibody systems, robotics, spacecraft and des...

Ultrafast phosphate hydration dynamics in bulk H2O

International Nuclear Information System (INIS)

Costard, Rene; Tyborski, Tobias; Fingerhut, Benjamin P.; Elsaesser, Thomas

2015-01-01

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H 2 PO 4 − ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (ν S (PO 2 − )) and asymmetric (ν AS (PO 2 − )) PO 2 − stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH) 2 ) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν S (PO 2 − ) and ν AS (PO 2 − ) transition frequencies with larger frequency excursions for ν AS (PO 2 − ). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO 2 − ) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H 2 PO 4 − /H 2 O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water

Swiss national MD-PhD-program: an outcome analysis.

Science.gov (United States)

Kuehnle, Katrin; Winkler, David T; Meier-Abt, Peter J

2009-09-19

This study aims at a first evaluation of the outcome of the Swiss national MD-PhD program during the last 16 years. One hundred and twenty six former and current students in the Swiss national MD-PhD program were surveyed via a Web-based questionnaire in September 2007. Twenty-four questions assessed information regarding participant demographics, information on the PhD thesis and publication activity, current positions and research activity, as well as participant's opinions, attitudes and career goals. Eighty questionnaires were received from 126 MD-PhD students and graduates (63.5% response rate). The responders consisted of present students (36%), former graduates (56%), and dropouts (8%). The percentage of women in the program was 23%, and the average duration of the program was 4.2 +/- 1.4 years. Research interests were predominantly in the fields of neuroscience, immunology, molecular biology and cancer research. A considerable portion of the MD-PhD graduates had an excellent publication record stemming from their PhD research work, and 89% were planning to continue a research-orientated career. Over 50% of those MD-PhD graduates completing their thesis before 2002 had already reached an assistant or full professor position at the time of the survey. Nearly all participants considered the MD-PhD training helpful to their career and high quality standards were assigned to the acquired practical and intellectual skills. However, criticism was expressed concerning the general mentoring and the career related mentoring. Moreover, general mentoring and career related mentoring were significantly less well perceived in research groups employing more than seven PhD students at the same time. The MD-PhD students and graduates surveyed were satisfied with their education and most of them continued a research-orientated career. Regarding the overall positive evaluation, this study supports the view that MD-PhD graduates are well qualified for a successful career in

MD-11 PCA - Research flight team photo

Science.gov (United States)

1995-01-01

On Aug. 30, 1995, a the McDonnell Douglas MD-11 transport aircraft landed equipped with a computer-assisted engine control system that has the potential to increase flight safety. In landings at NASA Dryden Flight Research Center, Edwards, California, on August 29 and 30, the aircraft demonstrated software used in the aircraft's flight control computer that essentially landed the MD-11 without a need for the pilot to manipulate the flight controls significantly. In partnership with McDonnell Douglas Aerospace (MDA), with Pratt & Whitney and Honeywell helping to design the software, NASA developed this propulsion-controlled aircraft (PCA) system following a series of incidents in which hydraulic failures resulted in the loss of flight controls. This new system enables a pilot to operate and land the aircraft safely when its normal, hydraulically-activated control surfaces are disabled. This August 29, 1995, photo shows the MD-11 team. Back row, left to right: Tim Dingen, MDA pilot; John Miller, MD-11 Chief pilot (MDA); Wayne Anselmo, MD-11 Flight Test Engineer (MDA); Gordon Fullerton, PCA Project pilot; Bill Burcham, PCA Chief Engineer; Rudey Duran, PCA Controls Engineer (MDA); John Feather, PCA Controls Engineer (MDA); Daryl Townsend, Crew Chief; Henry Hernandez, aircraft mechanic; Bob Baron, PCA Project Manager; Don Hermann, aircraft mechanic; Jerry Cousins, aircraft mechanic; Eric Petersen, PCA Manager (Honeywell); Trindel Maine, PCA Data Engineer; Jeff Kahler, PCA Software Engineer (Honeywell); Steve Goldthorpe, PCA Controls Engineer (MDA). Front row, left to right: Teresa Hass, Senior Project Management Analyst; Hollie Allingham (Aguilera), Senior Project Management Analyst; Taher Zeglum, PCA Data Engineer (MDA); Drew Pappas, PCA Project Manager (MDA); John Burken, PCA Control Engineer.

Influence of inverse dynamics methods on the calculation of inter-segmental moments in vertical jumping and weightlifting

Directory of Open Access Journals (Sweden)

Cleather Daniel J

2010-11-01

Full Text Available Abstract Background A vast number of biomechanical studies have employed inverse dynamics methods to calculate inter-segmental moments during movement. Although all inverse dynamics methods are rooted in classical mechanics and thus theoretically the same, there exist a number of distinct computational methods. Recent research has demonstrated a key influence of the dynamics computation of the inverse dynamics method on the calculated moments, despite the theoretical equivalence of the methods. The purpose of this study was therefore to explore the influence of the choice of inverse dynamics on the calculation of inter-segmental moments. Methods An inverse dynamics analysis was performed to analyse vertical jumping and weightlifting movements using two distinct methods. The first method was the traditional inverse dynamics approach, in this study characterized as the 3 step method, where inter-segmental moments were calculated in the local coordinate system of each segment, thus requiring multiple coordinate system transformations. The second method (the 1 step method was the recently proposed approach based on wrench notation that allows all calculations to be performed in the global coordinate system. In order to best compare the effect of the inverse dynamics computation a number of the key assumptions and methods were harmonized, in particular unit quaternions were used to parameterize rotation in both methods in order to standardize the kinematics. Results Mean peak inter-segmental moments calculated by the two methods were found to agree to 2 decimal places in all cases and were not significantly different (p > 0.05. Equally the normalized dispersions of the two methods were small. Conclusions In contrast to previously documented research the difference between the two methods was found to be negligible. This study demonstrates that the 1 and 3 step method are computationally equivalent and can thus be used interchangeably in

Ab initio calculation of the electronic absorption spectrum of liquid water

International Nuclear Information System (INIS)

Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa

2014-01-01

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

Science.gov (United States)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

Science.gov (United States)

Huang, Jiayu; Liu, Shu; Zhang, Dong H.; Krems, Roman V.

2018-04-01

Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Science.gov (United States)

Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

2017-06-13

λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

Molecular theory of mass transfer kinetics and dynamics at gas-water interface

International Nuclear Information System (INIS)

Morita, Akihiro; Garrett, Bruce C

2008-01-01

The mass transfer mechanism across gas-water interface is studied with molecular dynamics (MD) simulation. The MD results provide a robust and qualitatively consistent picture to previous studies about microscopic aspects of mass transfer, including interface structure, free energy profiles for the uptake, scattering dynamics and energy relaxation of impinging molecules. These MD results are quantitatively compared with experimental uptake measurements, and we find that the apparent inconsistency between MD and experiment could be partly resolved by precise decomposition of the observed kinetics into elemental steps. Remaining issues and future perspectives toward constructing a comprehensive multi-scale description of interfacial mass transfer are summarized.

Analysis of direct contact membrane distillation based on a lumped-parameter dynamic predictive model

KAUST Repository

Karam, Ayman M.; Alsaadi, Ahmad Salem; Ghaffour, NorEddine; Laleg-Kirati, Taous-Meriem

2016-01-01

Membrane distillation (MD) is an emerging technology that has a great potential for sustainable water desalination. In order to pave the way for successful commercialization of MD-based water desalination techniques, adequate and accurate dynamical models of the process are essential. This paper presents the predictive capabilities of a lumped-parameter dynamic model for direct contact membrane distillation (DCMD) and discusses the results under wide range of steady-state and dynamic conditions. Unlike previous studies, the proposed model captures the time response of the spacial temperature distribution along the flow direction. It also directly solves for the local temperatures at the membrane interfaces, which allows to accurately model and calculate local flux values along with other intrinsic variables of great influence on the process, like the temperature polarization coefficient (TPC). The proposed model is based on energy and mass conservation principles and analogy between thermal and electrical systems. Experimental data was collected to validated the steady-state and dynamic responses of the model. The obtained results shows great agreement with the experimental data. The paper discusses the results of several simulations under various conditions to optimize the DCMD process efficiency and analyze its response. This demonstrates some potential applications of the proposed model to carry out scale up and design studies. © 2016

Analysis of direct contact membrane distillation based on a lumped-parameter dynamic predictive model

KAUST Repository

Karam, Ayman M.

2016-10-03

Membrane distillation (MD) is an emerging technology that has a great potential for sustainable water desalination. In order to pave the way for successful commercialization of MD-based water desalination techniques, adequate and accurate dynamical models of the process are essential. This paper presents the predictive capabilities of a lumped-parameter dynamic model for direct contact membrane distillation (DCMD) and discusses the results under wide range of steady-state and dynamic conditions. Unlike previous studies, the proposed model captures the time response of the spacial temperature distribution along the flow direction. It also directly solves for the local temperatures at the membrane interfaces, which allows to accurately model and calculate local flux values along with other intrinsic variables of great influence on the process, like the temperature polarization coefficient (TPC). The proposed model is based on energy and mass conservation principles and analogy between thermal and electrical systems. Experimental data was collected to validated the steady-state and dynamic responses of the model. The obtained results shows great agreement with the experimental data. The paper discusses the results of several simulations under various conditions to optimize the DCMD process efficiency and analyze its response. This demonstrates some potential applications of the proposed model to carry out scale up and design studies. © 2016

The fifth Atomic Energy Research dynamic benchmark calculation with HEXTRAN-SMABRE

International Nuclear Information System (INIS)

Haenaelaeinen, Anitta

1998-01-01

The fifth Atomic Energy Research dynamic benchmark is the first Atomic Energy Research benchmark for coupling of the thermohydraulic codes and three-dimensional reactor dynamic core models. In VTT HEXTRAN 2.7 is used for the core dynamics and SMABRE 4.6 as a thermohydraulic model for the primary and secondary loops. The plant model for SMABRE is based mainly on two input models. the Loviisa model and standard WWER-440/213 plant model. The primary circuit includes six separate loops, totally 505 nodes and 652 junctions. The reactor pressure vessel is divided into six parallel channels. In HEXTRAN calculation 176 symmetry is used in the core. In the sequence of main steam header break at the hot standby state, the liquid temperature is decreased symmetrically in the core inlet which leads to return to power. In the benchmark, no isolations of the steam generators are assumed and the maximum core power is about 38 % of the nominal power at four minutes after the break opening in the HEXTRAN-SMABRE calculation. Due to boric acid in the high pressure safety injection water, the power finally starts to decrease. The break flow is pure steam in the HEXTRAN-SMABRE calculation during the whole transient even in the swell levels in the steam generators are very high due to flashing. Because of sudden peaks in the preliminary results of the steam generator heat transfer, the SMABRE drift-flux model was modified. The new model is a simplified version of the EPRI correlation based on test data. The modified correlation behaves smoothly. In the calculations nuclear data is based on the ENDF/B-IV library and it has been evaluated with the CASMO-HEX code. The importance of the nuclear data was illustrated by repeating the benchmark calculation with using three different data sets. Optimal extensive data valid from hot to cold conditions were not available for all types of fuel enrichments needed in this benchmark.(Author)

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

Science.gov (United States)

Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

2018-02-06

Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society

Comparative classical and 'ab initio' molecular dynamics study of molten and glassy germanium dioxide

International Nuclear Information System (INIS)

Hawlitzky, M; Horbach, J; Binder, K; Ispas, S; Krack, M

2008-01-01

A molecular dynamics (MD) study of the static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modeled by the classical pair potential proposed by Oeffner and Elliott (OE) (1998 Phys. Rev. B 58 14791). We compare our results to experiments and previous simulations. In addition, an 'ab initio' method, the so-called Car-Parrinello molecular dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO 2 , the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO 2 , for high temperatures the dynamics of molten GeO 2 is compatible with a description in terms of mode coupling theory

Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

International Nuclear Information System (INIS)

Chattaraj, D.; Dash, Smruti

2013-01-01

The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

Dislocation-cavity interaction in Fe: a comparison between molecular dynamics and dislocation dynamics

International Nuclear Information System (INIS)

Hafez Haghighat, S.M.; Schaeublin, R.; Fivel, M.C.

2007-01-01

Full text of publication follows: multi-scale modeling, including molecular dynamics (MD) and discrete dislocation dynamics (DDD) methods, appears as a significant tool for the description of plasticity and mechanical properties of materials. This research is on the investigation of the subsequence effects of irradiation on the plasticity of pure Fe and focuses on the interaction of a single dislocation and a spherical cavity, as void or He bubble. Extensive MD simulations of the interaction under imposed strain rate [1, 2] have shown that various temperatures and cavity sizes result in different release stresses depending on dislocation bow out. It appears that a temperature increase and cavity size decrease reduce the cavity strength. MD simulation shows that the elastic field around the cavity is largely anisotropic. This anisotropy may influence the way the dislocation unpins from the cavity. Following the MD simulations, the interaction of a single dislocation and a spherical cavity is now simulated using a DDD discrete dislocation dynamics model. The simulation accounts for the non-Schmidt effect induced by the bcc structure of Fe through local rules derived from MD simulations [3]. The cavity is introduced in the simulation by computing the image forces using a finite element technique. The effective stress applied on the dislocation is then obtained as the superimposition of the applied stress field, the image stress field and the internal stresses. Note that such a model only uses elasticity theory and no core effect of dislocations is taken into account. One of the objectives of this work is to check whether elasticity is responsible of the behaviour observed by MD. Several cases are tested. First an edge dislocation in a (110) plane is pushed against the cavity under a pure shear loading. The local reaction of the dislocations and the cavity are compared to the MD simulations. Then, the case of a screw dislocation is studied. Finally, other loading

Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

Dynamic transition in the structure of an energetic crystal during chemical reactions at shock front prior to detonation.

Science.gov (United States)

Nomura, Ken-Ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya; van Duin, Adri C T; Goddard, William A

2007-10-05

Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front.

Implementation of random set-up errors in Monte Carlo calculated dynamic IMRT treatment plans

International Nuclear Information System (INIS)

Stapleton, S; Zavgorodni, S; Popescu, I A; Beckham, W A

2005-01-01

The fluence-convolution method for incorporating random set-up errors (RSE) into the Monte Carlo treatment planning dose calculations was previously proposed by Beckham et al, and it was validated for open field radiotherapy treatments. This study confirms the applicability of the fluence-convolution method for dynamic intensity modulated radiotherapy (IMRT) dose calculations and evaluates the impact of set-up uncertainties on a clinical IMRT dose distribution. BEAMnrc and DOSXYZnrc codes were used for Monte Carlo calculations. A sliding window IMRT delivery was simulated using a dynamic multi-leaf collimator (DMLC) transport model developed by Keall et al. The dose distributions were benchmarked for dynamic IMRT fields using extended dose range (EDR) film, accumulating the dose from 16 subsequent fractions shifted randomly. Agreement of calculated and measured relative dose values was well within statistical uncertainty. A clinical seven field sliding window IMRT head and neck treatment was then simulated and the effects of random set-up errors (standard deviation of 2 mm) were evaluated. The dose-volume histograms calculated in the PTV with and without corrections for RSE showed only small differences indicating a reduction of the volume of high dose region due to set-up errors. As well, it showed that adequate coverage of the PTV was maintained when RSE was incorporated. Slice-by-slice comparison of the dose distributions revealed differences of up to 5.6%. The incorporation of set-up errors altered the position of the hot spot in the plan. This work demonstrated validity of implementation of the fluence-convolution method to dynamic IMRT Monte Carlo dose calculations. It also showed that accounting for the set-up errors could be essential for correct identification of the value and position of the hot spot

Implementation of random set-up errors in Monte Carlo calculated dynamic IMRT treatment plans

Science.gov (United States)

Stapleton, S.; Zavgorodni, S.; Popescu, I. A.; Beckham, W. A.

2005-02-01

The fluence-convolution method for incorporating random set-up errors (RSE) into the Monte Carlo treatment planning dose calculations was previously proposed by Beckham et al, and it was validated for open field radiotherapy treatments. This study confirms the applicability of the fluence-convolution method for dynamic intensity modulated radiotherapy (IMRT) dose calculations and evaluates the impact of set-up uncertainties on a clinical IMRT dose distribution. BEAMnrc and DOSXYZnrc codes were used for Monte Carlo calculations. A sliding window IMRT delivery was simulated using a dynamic multi-leaf collimator (DMLC) transport model developed by Keall et al. The dose distributions were benchmarked for dynamic IMRT fields using extended dose range (EDR) film, accumulating the dose from 16 subsequent fractions shifted randomly. Agreement of calculated and measured relative dose values was well within statistical uncertainty. A clinical seven field sliding window IMRT head and neck treatment was then simulated and the effects of random set-up errors (standard deviation of 2 mm) were evaluated. The dose-volume histograms calculated in the PTV with and without corrections for RSE showed only small differences indicating a reduction of the volume of high dose region due to set-up errors. As well, it showed that adequate coverage of the PTV was maintained when RSE was incorporated. Slice-by-slice comparison of the dose distributions revealed differences of up to 5.6%. The incorporation of set-up errors altered the position of the hot spot in the plan. This work demonstrated validity of implementation of the fluence-convolution method to dynamic IMRT Monte Carlo dose calculations. It also showed that accounting for the set-up errors could be essential for correct identification of the value and position of the hot spot.

Modeling Dynamic Objects in Monte Carlo Particle Transport Calculations

International Nuclear Information System (INIS)

Yegin, G.

2008-01-01

In this study, the Multi-Geometry geometry modeling technique was improved in order to handle moving objects in a Monte Carlo particle transport calculation. In the Multi-Geometry technique, the geometry is a superposition of objects not surfaces. By using this feature, we developed a new algorithm which allows a user to make enable or disable geometry elements during particle transport. A disabled object can be ignored at a certain stage of a calculation and switching among identical copies of the same object located adjacent poins during a particle simulation corresponds to the movement of that object in space. We called this powerfull feature as Dynamic Multi-Geometry technique (DMG) which is used for the first time in Brachy Dose Monte Carlo code to simulate HDR brachytherapy treatment systems. Our results showed that having disabled objects in a geometry does not effect calculated dose values. This technique is also suitable to be used in other areas such as IMRT treatment planning systems

The fifth AER dynamic benchmark calculation with hextran-smabre

International Nuclear Information System (INIS)

Haemaelaeinen, A.; Kyrki-Rajamaeki, R.

1998-01-01

The first AER benchmark for coupling of the thermohydraulic codes and three-dimensional reactordynamic core models is discussed. HEXTRAN 2.7 is used for the core dynamics and SMABRE 4.6 as a thermohydraulic model for the primary and secondary loops. The plant model for SMABRE is based mainly on two input models, the Loviisa model and standard VVER-440/213 plant model. The primary circuit includes six separate loops, totally 505 nodes and 652 junctions. The reactor pressure vessel is divided into six parallel channels. In HEXTRAN calculation 1/6 symmetry is used in the core. In the calculations nuclear data is based on the ENDF/B-IV library and it has been evaluated with the CASMO-HEX code. The importance of the nuclear data was illustrated by repeating the benchmark calculation with using three different data sets. Optimal extensive data valid from hot to cold conditions were not available for all types of fuel enrichments needed in this benchmark. (author)

Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation

International Nuclear Information System (INIS)

Higuchi, Yuji; Ishikawa, Takeshi; Ozawa, Nobuki; Chazeau, Laurent; Cavaillé, Jean-Yves; Kubo, Momoji

2015-01-01

Highlights: • We study the different dynamics of dissociation and recombination processes. • Hydrogen at the chain ends collides each other in the recombination process. • Dissociation and recombination processes take different pathway. - Abstract: We investigate the different dynamics of the stress-induced dissociation and recombination reactions in a model of polyethylene by a first-principles molecular dynamics simulation at the B3LYP/6-31g(d) level. The dissociation under external forces acting on the chemical reaction site at 300 K follows the same pathway as the one calculated by the static first-principles method because it has a similar activation barrier to that of the static first-principles calculation. On the other hand, in the recombination process, thermal fluctuations causes collisions between hydrogen atoms at the chain ends. Furthermore, when external forces do not directly act on the chemical reaction site, two different dissociation processes are observed. On the other hand, recombination process is not observed due to rarely contact of the radical carbon. These results indicate that dissociation and recombination dynamics are very different, showing the importance of the dynamic calculation.

Structure and dynamics of mica-confined films of [C10C1Pyrr][NTf2] ionic liquid

Science.gov (United States)

Freitas, Adilson Alves de; Shimizu, Karina; Smith, Alexander M.; Perkin, Susan; Canongia Lopes, José Nuno

2018-05-01

The structure of the ionic liquid 1-decyl-1-methylpyrrolidinium bis[(trifluoromethane)sulfonyl]imide, [C10C1Pyrr][NTf2], has been probed using Molecular Dynamics (MD) simulations. The simulations endeavour to model the behaviour of the ionic liquid in bulk isotropic conditions and also at interfaces and in confinement. The MD results have been confronted and validated with scattering and surface force experiments reported in the literature. The calculated structure factors, distribution functions, and density profiles were able to provide molecular and mechanistic insights into the properties of these long chain ionic liquids under different conditions, in particular those that lead to the formation of multi-layered ionic liquid films in confinement. Other properties inaccessible to experiment such as in-plane structures and relaxation rates within the films have also been analysed. Overall the work contributes structural and dynamic information relevant to many applications of ionic liquids with long alkyl chains, ranging from nanoparticle synthesis to lubrication.

76 FR 5686 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

Science.gov (United States)

2011-02-02

... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to.... The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke City MD, has a vertical clearance in...

76 FR 48898 - Robert Leigh Kale, M.D., Decision and Order

Science.gov (United States)

2011-08-09

... DEPARTMENT OF JUSTICE Drug Enforcement Administration Robert Leigh Kale, M.D., Decision and Order... Enforcement Administration, issued an Order to Show Cause to Robert Leigh Kale, M.D. (Registrant), of Fort... Certificate of Registration, BK9514375, issued to Robert Leigh Kale, M.D., be, and it hereby is, revoked. I...

Accelerating convergence of molecular dynamics-based structural relaxation

DEFF Research Database (Denmark)

Christensen, Asbjørn

2005-01-01

We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

Transport coefficients of dense fluids composed of globular molecules. Equilibrium molecular dynamics investigations using more-center Lennard-Jones potentials

Science.gov (United States)

Hoheisel, C.

1988-09-01

Equilibrium molecular dynamics calculations with constraints have been performed for model liquids SF6 and CF4. The computations were carried out with four- and six-center Lennard-Jones potentials and up to 2×105 integration steps. Shear, bulk viscosity and the thermal conductivity have been calculated with use of Green-Kubo relations in the formulation of ``molecule variables.'' Various thermodynamic states were investigated. For SF6, a detailed comparison with experimental data was possible. For CF4, the MD results could only be compared with experiment for one liquid state. For the latter liquid, a complementary comparison was performed using MD results obtained with a one-center Lennard-Jones potential. A limited test of the particle number dependence of the results is presented. Partial and total correlations functions are shown and discussed with respect to findings obtained for the one-center Lennard-Jones liquid.

MD1405: Demonstration of forced dynamic aperture measurements at injection

CERN Document Server

Carlier, Felix Simon; Persson, Tobias Hakan Bjorn; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

2017-01-01

Accurate measurements of dynamic aperture become more important for the LHC as it advances into increasingly nonlinear regimes of operations, as well as for the High Luminosity LHC where machine nonlinearities will have a significantly larger impact. Direct dynamic aperture measurements at top energy in the LHC are challenging, and conventional single kick methods are not viable. Dynamic aperture measurements under forced oscillation of AC dipoles have been proposed as s possible alternative observable. A first demonstration of forced DA measurements at injections energy is presented.

Molecular dynamics simulation based on the multi-component molecular orbital method: Application to H5O2+,D5O2+,andT5O2+

International Nuclear Information System (INIS)

Ishimoto, Takayoshi; Koyama, Michihisa

2012-01-01

Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H 5 O 2 + , and its isotopomers (D 5 O 2 + andT 5 O 2 + ). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H 5 O 2 + , and isotopomers. ► O ⋯ O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC M O) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC M O based MD (MC M O-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers (D 5 O 2 + andT 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC M O-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.

76 FR 20032 - Thomas E. Mitchell, M.D.; Dismissal of Proceeding

Science.gov (United States)

2011-04-11

... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 10-7] Thomas E. Mitchell, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Thomas E. Mitchell, M.D....100(b) and 0.104, I hereby order that the Order to Show Cause issued to Thomas E. Mitchell, M.D., be...

A study of internal energy relaxation in shocks using molecular dynamics based models

International Nuclear Information System (INIS)

Li, Zheng; Parsons, Neal; Levin, Deborah A.

2015-01-01

Recent potential energy surfaces (PESs) for the N 2 + N and N 2 + N 2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N 2 + N 2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N 2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available

Calculating the Maximum Density of the Surface Packing of Ions in Ionic Liquids

Science.gov (United States)

Kislenko, S. A.; Moroz, Yu. O.; Karu, K.; Ivaništšev, V. B.; Fedorov, M. V.

2018-05-01

The maximum density of monolayer packing on a graphene surface is calculated by means of molecular dynamics (MD) for ions of characteristic size and symmetry: 1-butyl-3-methylimidazolium [BMIM]+, tetrabutylammonium [TBA]+, tetrafluoroborate [BF4]-, dicyanamide [DCA]-, and bis(trifluoromethane) sulfonimide [TFSI]-. The characteristic orientations of ions in a closely packed monolayer are found. It is shown that the formation of a closely packed monolayer is possible for [DCA]- and [BF4]- anions only at surface charges that exceed the limit of the electrochemical stability of the corresponding ionic liquids. For the [TBA]+ cation, a monolayer structure can be observed at the charge of nearly 30 μC/cm2 attainable in electrochemical experiment.

77 FR 7182 - Scott W. Houghton, M.D.; Decision and Order

Science.gov (United States)

2012-02-10

... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 12-09] Scott W. Houghton, M.D... CFR 0.100(b), I order that DEA Certificate of Registration BH8796077, issued to Scott W. Houghton, M.D., be, and it hereby is, revoked. I further order that any pending application of Scott W. Houghton, M.D...

Viscosity of magnetic fluids must be modified in calculations of dynamic susceptibility

Energy Technology Data Exchange (ETDEWEB)

Lebedev, A.V., E-mail: lav@icmm.ru

2017-06-01

The frequency dependences of dynamic susceptibility were measured for a series of magnetic fluid samples with the same dispersed composition at different temperatures. Coincidence of normalized dynamic susceptibility curves plotted for different concentrations was obtained only after introducing correction for the value of dynamic viscosity of the magnetic fluid. The value of the correction coefficient doesn’t depend on temperature and is the universal function of the hydrodynamic concentration of particles. - Highlights: • Dynamic susceptibility was measured at different temperatures and concentrations. • Coincidence of curves requires a correction of value of viscosity in calculations. • This correction is function of the hydrodynamic concentration of particles. • With this function the rotation of particles are described correctly.

Trends in MD/PhD Graduates Entering Psychiatry: Assessing the Physician-Scientist Pipeline.

Science.gov (United States)

Arbuckle, Melissa R; Luo, Sean X; Pincus, Harold Alan; Gordon, Joshua A; Chung, Joyce Y; Chavez, Mark; Oquendo, Maria A

2018-06-01

The goal of this study was to identify trends in MD/PhD graduates entering psychiatry, to compare these trends with other specialties, and to review strategies for enhancing the physician-scientist pipeline. Data on 226,588 medical students graduating from Liaison Committee on Medical Education accredited programs between 1999 and 2012 (6626 MD/PhDs) were used to evaluate the number, percentage, and proportion of MD/PhDs entering psychiatry in comparison with other specialties (neurology, neurosurgery, internal medicine, family medicine, and radiation oncology). Linear regression and multiple linear regression determined whether these values increased over time and varied by sex. Over 14 years, an average of 18 MD/PhDs (range 13-29) enrolled in psychiatry each year. The number of MD/PhDs going into psychiatry significantly increased, although these gains were modest (less than one additional MD/PhD per year). The proportion of students entering psychiatry who were MD/PhDs varied between 2.9 and 5.9 per 100 residents, with no significant change over time. There was also no change in the percentage of MD/PhDs entering psychiatry from among all MD/PhD graduates. The rate of increase in the number of MD/PhDs going into psychiatry did not differ significantly from other specialties except for family medicine, which is decreasing. The rate of MD/PhDs going into psychiatry was higher for women, suggesting closure of the sex gap in 17 years. Despite the increase in the number of MD/PhDs entering psychiatry, these numbers remain low. Expanding the cohort of physician-scientists dedicated to translational research in psychiatry will require a multipronged approach.

Characterization of an Autophagy-related Gene MdATG8i from apple

Directory of Open Access Journals (Sweden)

Ping eWang

2016-05-01

Full Text Available Nutrient deficiencies restrict apple (Malus sp. tree growth and productivity in Northwest China. The process of autophagy, a conserved degradation pathway in eukaryotic cells, has important roles in nutrient-recycling and helps improve plant performance during periods of nutrient-starvation. Little is known about the functioning of autophagy-related genes (ATGs in apple. In this study, one of the ATG8 gene family members MdATG8i was isolated from M. domestica. MdATG8i has conserved putative tubulin binding sites and ATG7 interaction domains. A 1865-bp promoter region cloned from apple genome DNA was predicated to have cis-regulatory elements responsive to light, environmental stresses and hormones. MdATG8i transcriptions were induced in response to leaf senescence, nitrogen depletion, and oxidative stress. At cellular level, MdATG8i protein was expressed in the nucleus and cytoplasm of onion epidermal cells. Yeast two-hybrid tests showed that MdATG8i could interact with MdATG7a and MdATG7b. In Arabidopsis, its heterologous expression was associated with enhanced vegetative growth, leaf senescence, and tolerance to nitrogen- and carbon-starvation. MdATG8i-overexpressing ‘Orin’ apple callus lines also displayed improved tolerance to nutrient-limited conditions. Our results demonstrate that MdATG8i protein could function in autophagy in a conserved way, as a positive regulator in the response to nutrient-starvation.

[MD PhD programs: Providing basic science education for ophthalmologists].

Science.gov (United States)

Spaniol, K; Geerling, G

2015-06-01

Enrollment in MD PhD programs offers the opportunity of a basic science education for medical students and doctors. These programs originated in the USA where structured programs have been offered for many years, but now German universities also run MD PhD programs. The MD PhD programs provided by German universities were investigated regarding entrance requirements, structure and financing modalities. An internet and telephone-based search was carried out. Out of 34 German universities 22 offered MD PhD programs. At 15 of the 22 universities a successfully completed course of studies in medicine was required for enrollment, 7 programs admitted medical students in training and 7 programs required a medical doctoral thesis, which had to be completed with at least a grade of magna cum laude in 3 cases. Financing required scholarships in many cases. Several German universities currently offer MD PhD programs; however, these differ considerably regarding entrance requirements, structure and financing. A detailed analysis investigating the success rates of these programs (e.g. successful completion and career paths of graduates) would be of benefit.

Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Erpenbeck, J.J.; Kincaid, J.M.

1986-01-01

A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure, which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo timecorrelation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau

Assessment of hydrogen bonding effect on ionization of water from ambient to supercritical region–MD simulation approach

International Nuclear Information System (INIS)

Swiatla-Wojcik, D.; Mozumder, A.

2014-01-01

We present a novel, molecular dynamics (MD) simulation based, strategy to analyze how the degree of hydrogen bonding may influence the ionization and dissociation of water upon heating from ambient to supercritical temperatures. Calculations show a negligible change in the ionization energy up to 200 °C. At higher temperatures the ionization energy increases due to the decreasing degree of hydrogen bonding. The influence of density (pressure) is pronounced in the supercritical region. The ionization is more energy consuming in the less dense fluid. We also show that high temperature and low density may promote dissociation of the electronically excited water molecules. Implications on the initial radiation chemical yields of the hydrated electron, hydrogen atom and hydroxyl radical are discussed. - Highlights: • Up to 200 °C changes in the vertical and adiabatic ionization potentials are negligible. • At higher temperatures ionization is more energy consuming. • Ionization potential increases with decreasing density of supercritical water. • High temperature and low density promote dissociation of the excited molecules

Ab initio molecular dynamics: basic concepts, current trends and novel applications

International Nuclear Information System (INIS)

Tuckerman, Mark E

2002-01-01

The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car-Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed. (topical review)

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

International Nuclear Information System (INIS)

Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

2015-01-01

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

Simultaneous ion and neutral evaporation in aqueous nanodrops: experiment, theory, and molecular dynamics simulations.

Science.gov (United States)

Higashi, Hidenori; Tokumi, Takuya; Hogan, Christopher J; Suda, Hiroshi; Seto, Takafumi; Otani, Yoshio

2015-06-28

We use a combination of tandem ion mobility spectrometry (IMS-IMS, with differential mobility analyzers), molecular dynamics (MD) simulations, and analytical models to examine both neutral solvent (H2O) and ion (solvated Na(+)) evaporation from aqueous sodium chloride nanodrops. For experiments, nanodrops were produced via electrospray ionization (ESI) of an aqueous sodium chloride solution. Two nanodrops were examined in MD simulations: a 2500 water molecule nanodrop with 68 Na(+) and 60 Cl(-) ions (an initial net charge of z = +8), and (2) a 1000 water molecule nanodrop with 65 Na(+) and 60 Cl(-) ions (an initial net charge of z = +5). Specifically, we used MD simulations to examine the validity of a model for the neutral evaporation rate incorporating both the Kelvin (surface curvature) and Thomson (electrostatic) influences, while both MD simulations and experimental measurements were compared to predictions of the ion evaporation rate equation of Labowsky et al. [Anal. Chim. Acta, 2000, 406, 105-118]. Within a single fit parameter, we find excellent agreement between simulated and modeled neutral evaporation rates for nanodrops with solute volume fractions below 0.30. Similarly, MD simulation inferred ion evaporation rates are in excellent agreement with predictions based on the Labowsky et al. equation. Measurements of the sizes and charge states of ESI generated NaCl clusters suggest that the charge states of these clusters are governed by ion evaporation, however, ion evaporation appears to have occurred with lower activation energies in experiments than was anticipated based on analytical calculations as well as MD simulations. Several possible reasons for this discrepancy are discussed.

Magnetic materials at finite temperatures: thermodynamics and combined spin and molecular dynamics derived from first principles calculations

International Nuclear Information System (INIS)

Eisenbach, Markus; Perera, Meewanage Dilina N.; Landau, David P; Nicholson, Don M.; Yin, Junqi; Brown, Greg

2015-01-01

We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.

Dynamical calculations of nuclear fission and heavy-ion reactions

International Nuclear Information System (INIS)

Nix, J.R.; Sierk, A.J.

1984-01-01

With the goal of determining the magnitude and mechanism of nuclear dissipation from comparisons of predictions with experimental data, we describe recent calculations in a unified macroscopic-microscopic approach to large-amplitude collective nuclear motion such as occurs in fission and heavy-ion reactions. We describe the time dependence of the distribution function in phase space of collective coordinates and momenta by a generalized Fokker-Planck equation. The nuclear potential energy of deformation is calculated as the sum of repulsive Coulomb and centrifugal energies and an attractive Yukawa-plus-exponential potential, the inertia tensor is calculated for a superposition of rigid-body rotation and incompressible, nearly irrotational flow by use of the Werner-Wheeler method, and the dissipation ensor that describes the conversion of collective energy into single-particle excitation energy is calculated for two prototype mechanisms that represent opposite extremes of large and small dissipation. We solve the generalized Hamilton equations of motion for the first moments of the distribution function to obtain the mean translational fission-fragment kinetic energy and mass of a third fragment that sometimes forms between the two end fragments, as well as dynamical thresholds, capture cross sections, and ternary events in heavy-ion reactions. 33 references

3MdB: the Mexican Million Models database

Science.gov (United States)

Morisset, C.; Delgado-Inglada, G.

2014-10-01

The 3MdB is an original effort to construct a large multipurpose database of photoionization models. This is a more modern version of a previous attempt based on Cloudy3D and IDL tools. It is accessed by MySQL requests. The models are obtained using the well known and widely used Cloudy photoionization code (Ferland et al, 2013). The database is aimed to host grids of models with different references to identify each project and to facilitate the extraction of the desired data. We present here a description of the way the database is managed and some of the projects that use 3MdB. Anybody can ask for a grid to be run and stored in 3MdB, to increase the visibility of the grid and the potential side applications of it.

Generalized monitor unit calculation for the Varian enhanced dynamic wedge field

International Nuclear Information System (INIS)

Liu Chihray; Kim, Siyong; Kahler, Darren L.; Palta, Jatinder R.

2003-01-01

The generalized monitor unit (MU) calculation equation for the Varian enhanced dynamic wedge (EDW) is derived. The assumption of this MU calculation method is that the wedge factor of the EDW at the center of the field is a function of field size, the position of the center of the field in the wedge direction, and the final position of the moving jaw. The wedge factors at the center of the field in both symmetric and asymmetric fields are examined. The difference between calculated and measured wedge factors is within 1.0%. The method developed here is easy to implement. The only datum required in addition to the standard set of conventional physical wedge implementation data is the off-axis output factor for the open field in the reference condition. The off-center point calculation is also examined. For the off-center point calculation, the dose profile in the wedge direction for the largest EDW field is used to obtain the relative off-center ratio in any smaller wedge field. The accuracy of the off-center point calculation decreases when the point of calculation is too close to the field edge

Determination of thermo-physical properties of (Th,Ce)O2 MOX using classical molecular dynamics simulations

International Nuclear Information System (INIS)

Ghosh, P.S.; Arya, A.; Dey, G.K.; Somayajulu, P.S.

2015-01-01

This paper calculates lattice thermal expansion (LTE) and thermal conductivity (TC) of Th 1-x Ce x O 2 (x=0.0, 0.0625 and 0.125) MOX using classical molecular dynamic simulations. The potential parameters of Coulomb-Buckingham function for Th-O, Ce-O and O-O were determined by fitting experimentally available LTE data for pure ThO 2 and CeO 2 . The calculated linear thermal expansion coefficients in the temperature range 300-1500K for ThO 2 , CeO 2 , Th 93.75 Ce 6.25 O 2 and Th 87.5 Ce 12.5 O 2 are 10.61, 13.08, 10.78 and 10.93x10 -6 K -1 , respectively. The MD calculated LTE values of ThO 2 and (Th,Ce)O 2 MOX are slightly higher than the experimentally determined values. The MD calculated TC values of ThO 2 and (Th,Ce)O 2 MOX in the high temperature range (600 to 1200 K) our results accords very well with the experimental measurements and at the low temperature range (300-500 K) our results are slightly different from some experimental results as the difference comes from our presumption that the dominant mechanism for phonon scattering is the Umklapp process. (author)

Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

Science.gov (United States)

Hoheisel, C.

1989-01-01

For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.

Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

International Nuclear Information System (INIS)

Hoheisel, C.

1989-01-01

For several liquid states of CF 4 and SF 6 , the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints were chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3 x 10 5 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF 4 , while for SF 6 the transport coefficients fall below the experimental ones by about 30%

Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

KAUST Repository

Buin, Andrei; Comin, Riccardo; Ip, Alexander H.; Sargent, Edward H.

2015-01-01

© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

KAUST Repository

Buin, Andrei

2015-06-18

© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

Multi-Device to Multi-Device (MD2MD Content-Centric Networking Based on Multi-RAT Device

Directory of Open Access Journals (Sweden)

Cheolhoon Kim

2017-11-01

Full Text Available This paper proposes a method whereby a device can transmit and receive information using a beacon, and also describes application scenarios for the proposed method. In a multi-device to multi-device (MD2MD content-centric networking (CCN environment, the main issue involves searching for and connecting to nearby devices. However, if a device can’t find another device that satisfies its requirements, the connection is delayed due to the repetition of processes. It is possible to rapidly connect to a device without repetition through the selection of the optimal device using the proposed method. Consequently, the proposed method and scenarios are advantageous in that they enable efficient content identification and delivery in a content-centric Internet of Things (IoT environment, in which multiple mobile devices coexist.

An efficient implementation of parallel molecular dynamics method on SMP cluster architecture

International Nuclear Information System (INIS)

Suzuki, Masaaki; Okuda, Hiroshi; Yagawa, Genki

2003-01-01

The authors have applied MPI/OpenMP hybrid parallel programming model to parallelize a molecular dynamics (MD) method on a symmetric multiprocessor (SMP) cluster architecture. In that architecture, it can be expected that the hybrid parallel programming model, which uses the message passing library such as MPI for inter-SMP node communication and the loop directive such as OpenMP for intra-SNP node parallelization, is the most effective one. In this study, the parallel performance of the hybrid style has been compared with that of conventional flat parallel programming style, which uses only MPI, both in cases the fast multipole method (FMM) is employed for computing long-distance interactions and that is not employed. The computer environments used here are Hitachi SR8000/MPP placed at the University of Tokyo. The results of calculation are as follows. Without FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 90% with the hybrid style, 75% with the flat-MPI style for MD simulation with 33,402 atoms. With FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 60% with the hybrid style, 48% with the flat-MPI style for MD simulation with 117,649 atoms. (author)

Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Erpenbeck, J.J.; Kincaid, J.M.

1985-01-01

A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo time correlation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau

Apple F-box Protein MdMAX2 Regulates Plant Photomorphogenesis and Stress Response

Directory of Open Access Journals (Sweden)

Jian-Ping An

2016-11-01

Full Text Available MAX2 (MORE AXILLARY GROWTH2 is involved in diverse physiological processes, including photomorphogenesis, the abiotic stress response, as well as karrikin and strigolactone signaling-mediated shoot branching. In this study, MdMAX2, an F-box protein that is a homolog of Arabidopsis MAX2, was identified and characterized. Overexpression of MdMAX2 in apple calli enhanced the accumulation of anthocyanin. Ectopic expression of MdMAX2 in Arabidopsis exhibited photomorphogenesis phenotypes, including increased anthocyanin content and decreased hypocotyl length. Further study indicated that MdMAX2 might promote plant photomorphogenesis by affecting the auxin signaling as well as other plant hormones. Transcripts of MdMAX2 were noticeably up-regulated in response to NaCl and Mannitol treatments. Moreover, compared with the wild type, the MdMAX2-overexpressing apple calli and Arabidopsis exhibited increased tolerance to salt and drought stresses. Taken together, these results suggest that MdMAX2 plays a positive regulatory role in plant photomorphogenesis and stress response.

Three-dimensional static and dynamic reactor calculations by the nodal expansion method

International Nuclear Information System (INIS)

Christensen, B.

1985-05-01

This report reviews various method for the calculation of the neutron-flux- and power distribution in an nuclear reactor. The nodal expansion method (NEM) is especially described in much detail. The nodal expansion method solves the diffusion equation. In this method the reactor core is divided into nodes, typically 10 to 20 cm in each direction, and the average flux in each node is calculated. To obtain the coupling between the nodes the local flux inside each node is expressed by use of a polynomial expansion. The expansion is one-dimensional, so inside each node such three expansions occur. To calculate the expansion coefficients it is necessary that the polynomial expansion is a solution to the one-dimensional diffusion equation. When the one-dimensional diffusion equation is established a term with the transversal leakage occur, and this term is expanded after the same polynomials. The resulting equation system with the expansion coefficients as the unknowns is solved with weigthed residual technique. The nodal expansion method is built into a computer program (also called NEM), which is divided into two parts, one part for steady-state calculations and one part for dynamic calculations. It is possible to take advantage of symmetry properties of the reactor core. The program is very flexible with regard to the number of energy groups, the node size, the flux expansion order and the transverse leakage expansion order. The boundary of the core is described by albedos. The program and input to it are described. The program is tested on a number of examples extending from small theoretical one up to realistic reactor cores. Many calculations are done on the wellknown IAEA benchmark case. The calculations have tested the accuracy and the computing time for various node sizes and polynomial expansions. In the dynamic examples various strategies for variation of the time step-length have been tested. (author)

Waiting time distribution in M/D/1 queueing systems

DEFF Research Database (Denmark)

Iversen, Villy Bæk; Staalhagen, Lars

1999-01-01

The well-known formula for the waiting time distribution of M/D/1 queueing systems is numerically unsuitable when the load is close to 1.0 and/or the results for a large waiting time are required. An algorithm for any load and waiting time is presented, based on the state probabilities of M/D/1...

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

Error Propagation dynamics: from PIV-based pressure reconstruction to vorticity field calculation

Science.gov (United States)

Pan, Zhao; Whitehead, Jared; Richards, Geordie; Truscott, Tadd; USU Team; BYU Team

2017-11-01

Noninvasive data from velocimetry experiments (e.g., PIV) have been used to calculate vorticity and pressure fields. However, the noise, error, or uncertainties in the PIV measurements would eventually propagate to the calculated pressure or vorticity field through reconstruction schemes. Despite the vast applications of pressure and/or vorticity field calculated from PIV measurements, studies on the error propagation from the velocity field to the reconstructed fields (PIV-pressure and PIV-vorticity are few. In the current study, we break down the inherent connections between PIV-based pressure reconstruction and PIV-based vorticity calculation. The similar error propagation dynamics, which involve competition between physical properties of the flow and numerical errors from reconstruction schemes, are found in both PIV-pressure and PIV-vorticity reconstructions.

Non-affine deformation in microstructure selection in solids II: Elastoplastic theory for the dynamics of solid state transformations

Energy Technology Data Exchange (ETDEWEB)

Paul, Arya; Bhattacharya, Jayee; Sengupta, Surajit [S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Calcutta 700 098 (India); Rao, Madan [Raman Research Institute, C V Raman Avenue, Bangalore 560 080 (India)

2008-09-10

We study the nucleation dynamics of a model solid state transformation and the criterion for microstructure selection. Using a molecular dynamics (MD) simulation, we had shown that the dynamics of the solid is accompanied by the creation of transient non-affine zones (NAZ), which evolve with the rapidly moving transformation front. Guided by our MD results, we formulate a dynamical continuum theory of solid state transformation, which couples the elastic strain to the non-affine deformation. We demonstrate that our elastoplastic description recovers all qualitative features of the MD simulation. We construct a dynamical phase diagram for microstructure selection, including regimes where martensite or ferrite obtains, in addition to making several testable predictions.

Dosimetric comparison of interactive planned and dynamic dose calculated prostate seed brachytherapy

International Nuclear Information System (INIS)

Meijer, Gert J.; Berg, Hetty A. van den; Hurkmans, Coen W.; Stijns, Pascal E.; Weterings, Jan H.

2006-01-01

Purpose: To compare the dosimetrical results of an interactive planning procedure and a procedure based on dynamic dose calculation for permanent prostate brachytherapy. Materials and methods: Between 6/2000 and 11/2005, 510 patients underwent 125 I implants for T1-T2 prostate cancer. Before 4/2003, 187 patients were treated using an interactive technique that included needle updating. After that period, 323 patients were treated with a more refined dynamic technique that included constant updating of the deposited seed position. The comparison is based on postimplant dose-volume parameters such as the V 100 and d 90 for the target, V 100 r for the rectum and d 10 u for the urethra. Furthermore, the target volume ratios (TVR=V 100 body /V 100 ), and the homogeneity indices (HI=[V 100 -V 150 ]/V 100 ) were calculated as additional quality parameters. Results: The dose outside the target volume was significantly reduced, the V 100 r decreased from 1.4cm 3 for the interactive technique to 0.6cm 3 for the dynamic technique. Similarly the mean TVR reduced from 1.66 to 1.44. In addition, the mean V 100 increased from 92% for the interactive procedure to 95% for the dynamic procedure. More importantly, the percentage of patients with a V 100 10 u (136% vs. 140%) and the HI (0.58 vs. 0.51). Conclusion: The dynamic implant procedure resulted in improved implants. Almost ideal dose coverage was achieved, while minimizing the dose outside the prostate

75 FR 49992 - Peter W.S. Grigg, M.D.; Revocation of Registration

Science.gov (United States)

2010-08-16

... DEPARTMENT OF JUSTICE Drug Enforcement Administration Peter W.S. Grigg, M.D.; Revocation of... Order to Show Cause and Immediate Suspension of Registration to Peter W.S. Grigg, M.D. (Respondent), of... Registration, BG2107856, issued to Peter W.S. Grigg, M.D., be, and it hereby is, revoked. This Order is...

Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

Energy Technology Data Exchange (ETDEWEB)

Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

2015-01-15

There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Qifeng Bai

Full Text Available We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551. The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.

A eural etwork Model for Dynamics Simulation

African Journals Online (AJOL)

Nafiisah

Results 5 - 18 ... situations, such as a dynamic environment (e.g., a molecular dynamics (MD) simulation whereby an atom constantly changes its local environment and number ..... of systems including both small clusters and bulk structures. 7.

One-loop calculation in time-dependent non-equilibrium thermo field dynamics

International Nuclear Information System (INIS)

Umezawa, H.; Yamanaka, Y.

1989-01-01

This paper is a review on the structure of thermo field dynamics (TFD) in which the basic concepts such as the thermal doublets, the quasi-particles and the self-consistent renormalization are presented in detail. A strong emphasis is put on the computational scheme. A detailed structure of this scheme is illustrated by the one-loop calculation in a non-equilibrium time-dependent process. A detailed account of the one-loop calculation has never been reported anywhere. The role of the self-consistent renormalization is explained. The equilibrium TFD is obtained as the long-time limit of non-equilibrium TFD. (author)

Polymer and Water Dynamics in Poly(vinyl alcohol/Poly(methacrylate Networks. A Molecular Dynamics Simulation and Incoherent Neutron Scattering Investigation

Directory of Open Access Journals (Sweden)

Ester Chiessi

2011-10-01

Full Text Available Chemically cross-linked polymer networks of poly(vinyl alcohol/poly(methacrylate form monolitic hydrogels and microgels suitable for biomedical applications, such as in situ tissue replacement and drug delivery. In this work, molecular dynamics (MD simulation and incoherent neutron scattering methods are used to study the local polymer dynamics and the polymer induced modification of water properties in poly(vinyl alcohol/poly(methacrylate hydrogels. This information is particularly relevant when the diffusion of metabolites and drugs is a requirement for the polymer microgel functionality. MD simulations of an atomic detailed model of the junction domain at the experimental hydration degree were carried out at 283, 293 and 313 K. The polymer-water interaction, the polymer connectivity and the water dynamics were investigated as a function of temperature. Simulation results are compared with findings of elastic and quasi-elastic incoherent neutron scattering measurements, experimental approaches which sample the same space-time window of MD simulations. This combined analysis shows a supercooled water component and an increase of hydrophilicity and mobility with temperature of these amphiphilic polymer networks.

Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations

Science.gov (United States)

Liang, Zhi; Hu, Ming

2018-05-01

Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.

Developing the MD Explorer

Science.gov (United States)

Howie, Philip V.

1993-04-01

The MD Explorer is an eight-seat twin-turbine engine helicopter which is being developed using integrated product definition (IPD) team methodology. New techniques include NOTAR antitorque system for directional control, a composite fuselage, an all-composite bearingless main rotor, and digital cockpit displays. Three-dimensional CAD models are the basis of the entire Explorer design. Solid models provide vendor with design clarification, removing much of the normal drawing interpretation errors.

MD Anderson's Population Health Approaches to Cancer Prevention.

Science.gov (United States)

Foxhall, Lewis; Moreno, Mark; Hawk, Ernest

2018-02-01

Texas's size and unique population demographics present challenges to addressing the state's cancer burden. The University of Texas MD Anderson Cancer Center is one of 69 National Cancer Institute-designated cancer centers across the United States. While these centers traditionally have focused on research, education and training, and providing research-driven patient care, they are in a unique position to collaboratively advance population health through cancer control. Unlike the traditional academic model of a three-legged stool representing research, education, and patient care, MD Anderson's mission includes a fourth leg that incorporates population health approaches. MD Anderson has leveraged state- and national-level data and freely available resources to develop population-health priorities and a set of evidence-based actions across policy, public and professional education, and community-based clinical service domains to address these priorities. Population health approaches complement dissemination and implementation research and treatment, and will be increasingly needed to address the growing cancer burden in Texas and the nation.

76 FR 17673 - Bienvenido Tan, M.D.; Denial of Application

Science.gov (United States)

2011-03-30

... (alprazolam) to help him sleep. Id. at 64. R.E. opted to buy the drugs from Respondent's dispensary and... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 09-12] Bienvenido Tan, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Bienvenido Tan, M.D...

Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

KAUST Repository

Wang, Peng; Cui, Yue; Ge, Qingchun; Fern Tew, Tjin; Chung, Neal Tai-Shung

2015-01-01

The incorporation of membrane distillation (MD) into forward osmosis (FO) provides process sustainability to regenerate the draw solution and to produce clean water simultaneously. However, the reverse salt flux is the major hurdle in the FO-MD system because it not only reduces the effective osmotic driving force across the membrane but also increases the replenishment cost and scaling issue. For the first time, a hydroacid complex with abundant hydrophilic groups and ionic species is evaluated as the draw solutes in the hybrid FO-MD system consisting of multi-bore PVDF MD membranes for seawater/brackish desalination. In order to evaluate the practicality of the hydroacid complex in the FO-MD system, FO and MD experiments were conducted at elevated temperatures and concentrations. The hydroacid complex has displayed desired properties such as high solubility, low viscosity, excellent thermal stability and minimal reverse salt flux suitable for FO and MD operations. FO-MD desalination process was demonstrated with a highest seawater desalination flux of 6/32 LMH (FO/MD). This study may open up the prospective of employing the hydroacid complex as the draw solute in FO-MD hybrid systems for seawater /brackish desalination. © 2015 Elsevier B.V.

Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

KAUST Repository

Wang, Peng

2015-11-01

The incorporation of membrane distillation (MD) into forward osmosis (FO) provides process sustainability to regenerate the draw solution and to produce clean water simultaneously. However, the reverse salt flux is the major hurdle in the FO-MD system because it not only reduces the effective osmotic driving force across the membrane but also increases the replenishment cost and scaling issue. For the first time, a hydroacid complex with abundant hydrophilic groups and ionic species is evaluated as the draw solutes in the hybrid FO-MD system consisting of multi-bore PVDF MD membranes for seawater/brackish desalination. In order to evaluate the practicality of the hydroacid complex in the FO-MD system, FO and MD experiments were conducted at elevated temperatures and concentrations. The hydroacid complex has displayed desired properties such as high solubility, low viscosity, excellent thermal stability and minimal reverse salt flux suitable for FO and MD operations. FO-MD desalination process was demonstrated with a highest seawater desalination flux of 6/32 LMH (FO/MD). This study may open up the prospective of employing the hydroacid complex as the draw solute in FO-MD hybrid systems for seawater /brackish desalination. © 2015 Elsevier B.V.

Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.

Science.gov (United States)

Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying

2017-06-01

Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.

Structure and Ionic Conductivity of Li2S-P2S5 Glass Electrolytes Simulated with First-Principles Molecular Dynamics

Directory of Open Access Journals (Sweden)

Takeshi eBaba

2016-06-01

Full Text Available Lithium thiophosphate-based materials are attractive as solid electrolytes in all-solid-state lithium batteries because glass or glass-ceramic structures of these materials are associated with very high conductivity. In this work, we modeled lithium thiophosphates with amorphous structures and investigated Li+ mobilities by using molecular dynamics calculations based on density functional theory (DFT-MD. The structures of xLi2S-(100 - xP2S5 (x = 67, 70, 75, and 80 were created by randomly identifying appropriate compositions of Li+, PS43-, P2S74-, and S2- and then annealing them with DFT-MD calculations. Calculated relative stabilities of the amorphous structures with x = 67, 70, and 75 relative to crystals with the same compositions were 0.04, 0.12, and 0.16 kJ/g, respectively. The implication is that these amorphous structures are metastable. There was good agreement between calculated and experimental structure factors determined from X-ray scattering. The differences between the structure factors of amorphous structures were small, except for the first sharp diffraction peak, which was affected by the environment between Li and S atoms. Li+ diffusion coefficients obtained from DFT-MD calculations at various temperatures for picosecond simulation times were on the order of 10-3 - 10-5 Angstrom2/ps. Ionic conductivities evaluated by the Nernst-Einstein relationship at 298.15 K were on the order of 10-5 S/cm. The ionic conductivity of the amorphous structure with x = 75 was the highest among the amorphous structures because there was a balance between the number density and diffusibility of Li+. The simulations also suggested that isolated S atoms suppress Li+ migration.

Calculation of dynamic and electronic properties of perfect and defect crystals by semiempirical quantum mechanical methods

International Nuclear Information System (INIS)

Zunger, A.

1975-07-01

Semiempirical all-valence-electron LCAO methods, that were previously used to study the electronic structure of molecules are applied to three problems in solid state physics: the electronic band structure of covalent crystals, point defect problems in solids and lattice dynamical study of molecular crystals. Calculation methods for the electronic band structure of regular solids are introduced and problems regarding the computation of the density matrix in solids are discussed. Three models for treating the electronic eigenvalue problem in the solid, within the proposed calculation schemes, are discussed and the proposed models and calculation schemes are applied to the calculation of the electronic structure of several solids belonging to different crystal types. The calculation models also describe electronic properties of deep defects in covalent insulating crystals. The possible usefulness of the semieipirical LCAO methods in determining the first order intermolecular interaction potential in solids and an improved model for treating the lattice dynamics and related thermodynamical properties of molecular solids are presented. The improved lattice dynamical is used to compute phonon dispersion curves, phonon density of states, stable unit cell structure, lattice heat capacity and thermal crystal parameters, in α and γ-N 2 crystals, using the N 2 -N 2 intermolecular interaction potential that has been computed from the semiempirical LCAO methods. (B.G.)

Dosimetric comparison of interactive planned and dynamic dose calculated prostate seed brachytherapy.

Science.gov (United States)

Meijer, Gert J; van den Berg, Hetty A; Hurkmans, Coen W; Stijns, Pascal E; Weterings, Jan H

2006-09-01

To compare the dosimetrical results of an interactive planning procedure and a procedure based on dynamic dose calculation for permanent prostate brachytherapy. Between 6/2000 and 11/2005, 510 patients underwent (125)I implants for T1-T2 prostate cancer. Before 4/2003, 187 patients were treated using an interactive technique that included needle updating. After that period, 323 patients were treated with a more refined dynamic technique that included constant updating of the deposited seed position. The comparison is based on postimplant dose - volume parameters such as the V(100) and d(90) for the target, V(100)(r) for the rectum and d(10)(u) for the urethra. Furthermore, the target volume ratios (TVR identical with V(100)(body)/V(100)), and the homogeneity indices (HI identical with [V(100)-V(150)]/V(100)) were calculated as additional quality parameters. The dose outside the target volume was significantly reduced, the V(100)(r) decreased from 1.4 cm(3) for the interactive technique to 0.6 cm(3) for the dynamic technique. Similarly the mean TVR reduced from 1.66 to 1.44. In addition, the mean V(100) increased from 92% for the interactive procedure to 95% for the dynamic procedure. More importantly, the percentage of patients with a V(100) < 80% reduced from 5% to 1%. A slight decline was observed with regard to the d(10)(u) (136% vs. 140%) and the HI (0.58 vs. 0.51). The dynamic implant procedure resulted in improved implants. Almost ideal dose coverage was achieved, while minimizing the dose outside the prostate.

A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit

Science.gov (United States)

Smith, Edward

2016-11-01

What happens to turbulent motions below the Kolmogorov length scale? In order to explore this question, a 300 million molecule Molecular Dynamics (MD) simulation is presented for the minimal Couette channel in which turbulence can be sustained. The regeneration cycle and turbulent statistics show excellent agreement to continuum based computational fluid dynamics (CFD) at Re=400. As MD requires only Newton's laws and a form of inter-molecular potential, it captures a much greater range of phenomena without requiring the assumptions of Newton's law of viscosity, thermodynamic equilibrium, fluid isotropy or the limitation of grid resolution. The fundamental nature of MD means it is uniquely placed to explore the nature of turbulent transport. A number of unique insights from MD are presented, including energy budgets, sub-grid turbulent energy spectra, probability density functions, Lagrangian statistics and fluid wall interactions. EPSRC Post Doctoral Prize Fellowship.

Sorption and permeation of gaseous molecules in amorphous and crystalline PPX C membranes: molecular dynamics and grand canonical Monte Carlo simulation studies

International Nuclear Information System (INIS)

Bian Liang; Shu Yuan-Jie; Wang Xin-Feng

2012-01-01

Amorphous and crystalline poly (chloro-p-xylylene) (PPX C) membranes are constructed by using a novel computational technique, that is, a combined method of NVT+NPT-molecular dynamics (MD) and gradually reducing the size (GRS) methods. The related free volumes are defined as homology clusters. Then the sorption and the permeation of gases in PPX C polymers are studied using grand canonical Monte Carlo (GCMC) and NVT-MD methods. The results show that the crystalline PPX C membranes provide smaller free volumes for absorbing or transferring gases relative to the amorphous PPX C area. The gas sorption in PPX C membranes mainly belongs to the physical one, and H bonds can appear obviously in the amorphous area. By cluster analyzing on the mean square displacement of gases, we find that gases walk along the x axis in the crystalline area and walk randomly in the amorphous area. The calculated permeability coefficients are close to the experimental data. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

77 FR 5201 - Drawbridge Operation Regulation; Bear Creek, Dundalk, MD

Science.gov (United States)

2012-02-02

...-AA09 Drawbridge Operation Regulation; Bear Creek, Dundalk, MD AGENCY: Coast Guard, DHS. ACTION: Notice... operation of the Baltimore County highway bridge at Wise Avenue across Bear Creek, mile 3.4, between Dundalk... Avenue across Bear Creek, mile 3.4 between Dundalk and Sparrows Point, MD. This change would require the...

Analysis of MD5 authentication in various routing protocols using simulation tools

Science.gov (United States)

Dinakaran, M.; Darshan, K. N.; Patel, Harsh

2017-11-01

Authentication being an important paradigm of security and Computer Networks require secure paths to make the flow of the data even more secure through some security protocols. So MD-5(Message Digest 5) helps in providing data integrity to the data being sent through it and authentication to the network devices. This paper gives a brief introduction to the MD-5, simulation of the networks by including MD-5 authentication using various routing protocols like OSPF, EIGRP and RIPv2. GNS3 is being used to simulate the scenarios. Analysis of the MD-5 authentication is done in the later sections of the paper.

High performance computer code for molecular dynamics simulations

International Nuclear Information System (INIS)

Levay, I.; Toekesi, K.

2007-01-01

Complete text of publication follows. Molecular Dynamics (MD) simulation is a widely used technique for modeling complicated physical phenomena. Since 2005 we are developing a MD simulations code for PC computers. The computer code is written in C++ object oriented programming language. The aim of our work is twofold: a) to develop a fast computer code for the study of random walk of guest atoms in Be crystal, b) 3 dimensional (3D) visualization of the particles motion. In this case we mimic the motion of the guest atoms in the crystal (diffusion-type motion), and the motion of atoms in the crystallattice (crystal deformation). Nowadays, it is common to use Graphics Devices in intensive computational problems. There are several ways to use this extreme processing performance, but never before was so easy to programming these devices as now. The CUDA (Compute Unified Device) Architecture introduced by nVidia Corporation in 2007 is a very useful for every processor hungry application. A Unified-architecture GPU include 96-128, or more stream processors, so the raw calculation performance is 576(!) GFLOPS. It is ten times faster, than the fastest dual Core CPU [Fig.1]. Our improved MD simulation software uses this new technology, which speed up our software and the code run 10 times faster in the critical calculation code segment. Although the GPU is a very powerful tool, it has a strongly paralleled structure. It means, that we have to create an algorithm, which works on several processors without deadlock. Our code currently uses 256 threads, shared and constant on-chip memory, instead of global memory, which is 100 times slower than others. It is possible to implement the total algorithm on GPU, therefore we do not need to download and upload the data in every iteration. On behalf of maximal throughput, every thread run with the same instructions

AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble.

Science.gov (United States)

Abdul-Wahid, Badi'; Feng, Haoyun; Rajan, Dinesh; Costaouec, Ronan; Darve, Eric; Thain, Douglas; Izaguirre, Jesús A

2014-10-27

A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to compute. This is due to the rarity of observing transitions between metastable states since high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and allow calculation of unbiased rates. However, while WE can sample correctly and efficiently, a scalable implementation applicable to interesting biomolecular systems is not available. We provide here a GPLv2 implementation called AWE-WQ of a WE algorithm using the master/worker distributed computing WorkQueue (WQ) framework. AWE-WQ is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage (such as central processing units (CPU) and graphical processing units (GPUs) concurrently), seamless heterogeneous cluster usage (i.e., campus grids and cloud providers), and support for arbitrary MD codes such as GROMACS, while ensuring that all statistics are unbiased. We applied AWE-WQ to a 34 residue protein which simulated 1.5 ms over 8 months with peak aggregate performance of 1000 ns/h. Comparison was done with a 200 μs simulation collected on a GPU over a similar timespan. The folding and unfolded rates were of comparable accuracy.

Improving the accuracy of dynamic mass calculation

Directory of Open Access Journals (Sweden)

Oleksandr F. Dashchenko

2015-06-01

Full Text Available With the acceleration of goods transporting, cargo accounting plays an important role in today's global and complex environment. Weight is the most reliable indicator of the materials control. Unlike many other variables that can be measured indirectly, the weight can be measured directly and accurately. Using strain-gauge transducers, weight value can be obtained within a few milliseconds; such values correspond to the momentary load, which acts on the sensor. Determination of the weight of moving transport is only possible by appropriate processing of the sensor signal. The aim of the research is to develop a methodology for weighing freight rolling stock, which increases the accuracy of the measurement of dynamic mass, in particular wagon that moves. Apart from time-series methods, preliminary filtration for improving the accuracy of calculation is used. The results of the simulation are presented.

Osmotically and thermally isolated forward osmosis-membrane distillation (fo-md) integrated module for water treatment applications

KAUST Repository

Ghaffour, Noreddine

2016-09-01

An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.

Osmotically and thermally isolated forward osmosis-membrane distillation (fo-md) integrated module for water treatment applications

KAUST Repository

Ghaffour, NorEddine; Francis, Lijo; Li, Zhenyu; Valladares, Rodrigo; Alsaadi, Ahmad S.; Ghdaib, Muhannad Abu; Amy, Gary L.

2016-01-01

An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.

Structure and dynamics of hydrated Fe(II) and Fe(III) ions. Quantum mechanical and molecular mechanical simulations

International Nuclear Information System (INIS)

Remsungnen, T.

2002-11-01

Classical molecular dynamics (MD) and combined em ab initio quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations have been performed to investigate structural, dynamical and energetical properties of Fe(II), and Fe(III) transition metal ions in aqueous solution. In the QM/MM-MD simulations the ion and its first hydration sphere were treated at the Hartree-Fock ab initio quantum mechanical level, while ab initio generated pair plus three-body potentials were employed for the remaining system. For the classical MD simulation the pair plus three-body potential were employed for all ion-water interactions. The coordination number of the first hydration shell is 100 % of 6 in both cases. The number of waters in the second hydration shell obtained from classical simulations are 13.4 and 15.1 for Fe(II) and Fe(III), respectively, while QM/MM-MD gives the values of 12.4 and 13.4 for Fe(II) and Fe(III). The energies of hydration obtained from MD and QM/MM-MD for Fe(II) are 520 and 500 kcal/mol, and for Fe(III) 1160 and 1100 kcal/mol respectively. The mean residence times of water in the second shell obtained from QM/MM-MD are 24 and 48 ps for Fe(II) and Fe(III), respectively. In contrast to the data obtained from classical MD simulation, the QM/MM-MD values are all in good agreement with the experimental data available. These investigations and results clearly indicate that many-body effects are essential for the proper description of all properties of the aqueous solution of both Fe(II) and Fe(III) ions. (author)

33 CFR 110.70a - Northeast River, North East, Md.

Science.gov (United States)

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Northeast River, North East, Md. 110.70a Section 110.70a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.70a Northeast River, North East, Md. The water...

Dynamic calculation of structures in seismic zones. 2. ed.

International Nuclear Information System (INIS)

Capra, Alain; Davidovici, Victor

1982-01-01

The aims of this book are both didactic and practical. It is therefore addressed to both experienced engineers and students. Some general information about earthquakes and their occurrence is first given. The problem of a simple oscillator is presented. In this way, the reader is provided with an insight into undestanding the dynamic phenomena taking place and is introduced to the concept of response spectra and to an intuitive comprehension of the behavior of structures during earthquakes. The next chapter is devoted to the cases most frequently encountered with multiple oscillator structures. Theoretical studies are based on the usual modal decomposition method. The various practical methods of calculation employed are then examined, emphasis being given to the various different stages involved and to which of them is the best suited for a particular type of structure. Advise is given on how to select the model whose behavior best describes the real structure, both manual and computer methods of calculation being envisaged [fr

Summary of calculations of dynamic response characteristics and design stress of the 1/5 scale PSE torus

International Nuclear Information System (INIS)

Arthur, D.

1977-01-01

The Lawrence Livermore Laboratory is currently involved in a 1/5 scale testing program on the Mark I BWR pressure suppression system. A key element of the test setup is a pressure vessel that is a 90 0 sector of a torus. Proper performance of the 90 0 torus depends on its structural integrity and structural dynamic characteristics. It must sustain the internal pressurization of the planned tests, and its dynamic response to the transient test loads should be minimal. If the structural vibrations are too great, interpretation of important load cell and pressure transducer data will be difficult. The purpose of the report is to bring together under one cover calculations pertaining to the structural dynamic characteristics and structural integrity of 90 0 torus. The report is divided into the following sections: (1) system description in which the torus and associated hardware are briefly described; (2) structural dynamics in which calculations of natural frequency and dynamic response are presented; and (3) structural integrity in which stress calculations for design purposes are presented; and an appendix which contains an LLL internal report comparing the expected load cell response for a three and four-point supported torus

77 FR 29692 - Segun M. Rasaki, M.D.; Decision and Order

Science.gov (United States)

2012-05-18

... CFR 1316.67. Dated: May 4, 2012. Michele M. Leonhart, Administrator. Paul E. Soeffing, Esq., for the... reinstatement.'' Stuart A. Bergman, M.D., 70 Fed. Reg. 33,193 (DEA 2005); Roger A. Rodriguez, M.D., 70 Fed. Reg...

77 FR 35021 - Kwan Bo Jin, M.D.; Decision and Order

Science.gov (United States)

2012-06-12

...] DEA registration is not appropriate.'' Anibal P. Herrera, M.D., 61 FR 65,075, 65,078 (DEA 1996); see... ``there were serious questions as to the integrity of the registrant.'' Anibal P. Herrera, M.D., 61 FR 65...

Molecular Cloning and Expression Analysis of a Hexokinase Gene, MdHXK1 in Apple

Directory of Open Access Journals (Sweden)

Jin Zhao

2016-03-01

Full Text Available A hexokinase gene named MdHXK1 (MDP0000309677 was cloned from ‘Gala’ apple (Malus × domestica Borkh.. Sequence analysis showed that the MdHXK1 gene was 1 497 bp long and encoded 499 amino acids. The predicted molecular mass of this protein was 54.05 kD, and the pI was 5.76. A phylogenetic tree indicated apple MdHXK1 exhibited the highest sequence similarity to Pyrus bretschneideri PbHXK1. Analysis of the functional domain showed that the MdHXK1 protein included two conserved kinase domains. The prediction of subcellular localization suggested that the MdHXK1 protein was mainly localized in the cytoplasm. There was an indication that MdHXK1 existed as one copy in the apple genome by Southern blotting. Silico analysis suggested that the promoter sequence contained several typical cis-acting elements, including defense, sugar signaling and phytohormone responsive elements. Quantitative real-time PCR analysis demonstrated that the MdHXK1 gene was mainly expressed in stem and flower tissues. During the development of apple fruits, the expression of the MdHXK1 gene initially increased and then decreased. The changes on Glc phosphorylation relative activity and glucose concentration showed the same trend. In addition, the expression of this gene was induced by salt stress, low temperature, and abscisic acid (ABA. Finally, we obtained and purified the fused MdHXK1 protein by recombinant prokaryotic expression. Studies have demonstrated that MdHXK1 may participate in sugar metabolism in apple fruits. Enzyme encoded by MdHXK1 is a key factor in the mediation of sugar accumulation. Recently, researchers on hexokinase at home and abroad mainly focused on model plants, such as Arabidopsis, tobacco and rice, but orchard fruit like apple were underresearched. Our research established the foundation for the further study of the functions of MdHXK1.

Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

Science.gov (United States)

Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

2017-08-30

A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

Stability of molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren

2012-01-01

The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

A pilot study of MD (psychiatry) theses-based research.

Science.gov (United States)

Srivastava, Shrikant; Agarwal, Vivek; Subramanyam, Alka; Srivastava, Mona; Sathyanarayana Rao, T S; Rao, G Prasad; Khurana, Hitesh; Singh, Archana

2018-01-01

Undertaking a research project is mandatory for MD Psychiatry trainees. The present study was undertaken to assess the type of research activity being undertaken as part of MD Psychiatry dissertation, and its contribution to national and international literature. Three medical colleges supplied the data about the topic, names of the supervisor and the candidate, collaboration, funding accrued, and publication details of MD-based research carried out between years 2000 and 2010 inclusive; 95 records were collected for the final analysis. The details of the publications provided were cross-checked on the internet, which would have taken care of missed publications as well. Most studies were single-point assessment clinical studies. Only 2 studies had been funded, 11 had collaboration with other departments within the same institute, and 5 had inter-institute collaborations. Majority of the studies were not published. Only 30 were published as full paper and 9 as abstracts. Of these 30 full publications, only 3 were published in journals having JCI impact factor values (1.4, 1.3, and 1.4, respectively). The main finding of this pilot study was that MD-based research has low contribution to the national and international literature, and those articles which are published are in low impact journals. Suggestions for modifying this state of affairs are discussed.

Theoretical Studies of the Structure and the Dynamics on Clean and Chemisorbed Metal Surfaces

Science.gov (United States)

Yang, Liqiu

Molecular dynamics (MD) and lattice dynamics (LD) techniques are employed to investigate several phenomena related to the structure and vibrations at metal surfaces. The MD simulations are performed with the many-body interaction potentials obtained using the Embedded-Atom Method (EAM). As specific examples, we present the results for Ag(100) at 300 K and Cu(100) at 150 K, 300 K, and 600 K. The calculated frequencies and polarizations of all surface modes and resonances at the high-symmetry points in the two-dimensional Brillouin zone are in good agreement with available data, as well as, existing lattice dynamics results with force constants obtained from first-principles calculations. Our calculated surface relaxation is also in reasonable agreement with the data. We also test a much simpler lattice dynamics model with nearest neighbor central force interactions, and conclude that it can reproduce the main features of the phonon modes, but only when adjustable surface parameters are used. Additionally, the temperature dependent studies of the phonon line-widths and the mean-square displacement (MSD) of surface atoms are indicative of enhanced surface anharmonicity. On several chemisorbed metal surfaces, for which force constants are not available from first-principles calculations or the EAM, we perform lattice dynamics studies of phonon dispersion curves using simple force-constant models. These studies provide reliable mean-square displacement of surface atoms and can distinguish between possible reconstruction patterns, the results being insensitive to the exact values of the surface parameters. On c(2 times 2)S-Ni(100), it is found that the parallel component of the mean-square displacement for sulfur is around 50% larger than the vertical component, but for the mean-square displacement of oxygen atoms in the system c(2 times 2)O-Ni(100), the opposite is the case. As regards surface reconstruction, for both p(2 times 1)O-Ag(110) and p(2 times 1)O-Ni(110

MD 2485: Active halo control using narrowband and colored noise excitations

CERN Document Server

Garcia Morales, Hector; Kotzian, Gerd; Maclean, Ewen Hamish; Redaelli, Stefano; Valuch, Daniel; Wagner, Joschka; CERN. Geneva. ATS Department

2018-01-01

This MD note summarizes the actions carried out during the MD 2485 on Active halo control using narrowband and colored noise excitations. The goal of the MD was to repeat some promising cases already tested in the past and introduce a new excitation type based on applying a colored noise. Although we were able to repeat some cases using a narrowband excitation, due to a problem with the waveform generator, the colored noise excitation could not be accomplished as expected. In any case, we provide some results that may be useful for future MDs.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

Science.gov (United States)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169

Science.gov (United States)

Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

2018-01-01

Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3–6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0–4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications. PMID:29293588

Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169.

Science.gov (United States)

Lyman, Mathew; Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

2018-01-01

Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3-6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0-4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications.

Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?

Science.gov (United States)

Moustafa, Ibrahim M; Gohara, David W; Uchida, Akira; Yennawar, Neela; Cameron, Craig E

2015-11-23

The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.

78 FR 47412 - Tyson D. Quy, M.D.; Decision and Order

Science.gov (United States)

2013-08-05

... Green, Jr., M.D., 59 FR 51,453 (DEA 1994); David E. Trawick, D.D.S., 53 FR 5,326 (DEA 1988). Here, the...) (ten years); Norman Alpert, M.D., 58 FR 67,420, 67,421 (DEA 1993) (seven years). Here, the conditions...

Dynamical calculation of nuclear temperature

International Nuclear Information System (INIS)

Zheng Yuming

1998-01-01

A new dynamical approach for measuring the temperature of a Hamiltonian dynamical system in the microcanonical ensemble of thermodynamics is presented. It shows that under the hypothesis of ergodicity the temperature can be computed as a time average of a function on the energy surface. This method not only yields an efficient computational approach for determining the temperature, but also provides an intrinsic link between dynamical system theory and the statistical mechanics of Hamiltonian system

Directly calculated electrical conductivity of hot dense hydrogen from molecular dynamics simulation beyond Kubo-Greenwood formula

Science.gov (United States)

Ma, Qian; Kang, Dongdong; Zhao, Zengxiu; Dai, Jiayu

2018-01-01

Electrical conductivity of hot dense hydrogen is directly calculated by molecular dynamics simulation with a reduced electron force field method, in which the electrons are represented as Gaussian wave packets with fixed sizes. Here, the temperature is higher than electron Fermi temperature ( T > 300 eV , ρ = 40 g / cc ). The present method can avoid the Coulomb catastrophe and give the limit of electrical conductivity based on the Coulomb interaction. We investigate the effect of ion-electron coupled movements, which is lost in the static method such as density functional theory based Kubo-Greenwood framework. It is found that the ionic dynamics, which contributes to the dynamical electrical microfield and electron-ion collisions, will reduce the conductivity significantly compared with the fixed ion configuration calculations.

Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

Directory of Open Access Journals (Sweden)

Jianping AN

2017-03-01

Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

Science.gov (United States)

Gaspari, Roberto; Rapallo, Arnaldo

2008-06-28

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum

Structural, elastic, electronic and dynamical properties of OsB and ReB: Density functional calculations

Science.gov (United States)

Li, Yanling; Zeng, Zhi; Lin, Haiqing

2010-06-01

The structural, elastic, electronic and dynamical properties of ReB and OsB are investigated by first-principles calculations based on density functional theory. It turns out that ReB and OsB are metallic ultra-incompressible solids with small elastic anisotropy and high hardness. The change of c/ a ratio in OsB indicates that there is a structural phase transition at about 31 GPa. Phonon spectra calculations show that both OsB and ReB are stable dynamically and there are abnormal phonon dispersions along special directions in Brillouin zone. OsB and ReB do not show superconductivity due to very weak electron-phonon interactions in them.

BayesMD: flexible biological modeling for motif discovery

DEFF Research Database (Denmark)

Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

2008-01-01

We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane

Science.gov (United States)

Das, Arya; Ali, Sk. Musharaf

2018-02-01

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane.

Science.gov (United States)

Das, Arya; Ali, Sk Musharaf

2018-02-21

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by

Non equilibrium effects in nuclear dynamics

Energy Technology Data Exchange (ETDEWEB)

Papa, M.; Arena, N.; Cardella, G.; Lanzano, G.; Filippo, E. de; Lanzalone, G.; Pagano, A.; Pirrone, S.; Politi, G. [Catania Univ., INFN Catania and Dipartimento di Fisica e Astronomia (Italy); Amorini, F.; Anzalone, A.; Bonasera, A.; Cavallaro, S.; Di Pietro, A.; Figuera, P.; Giustolisi, F.; Iacono Manno, M.; La Guidara, E.; Maiolino, C.; Porto, F.; Rizzo, F.; Sperduto, M.L. [Catania Univ., INFN-LNS and Dipartimento di Fisica e Astronomia (Italy); Auditore, L.; Trifiro, A.; Trimarchi, M. [Messina Univ., INFN and Dipartimento di Fisica (Italy)

2003-07-01

A Constraint Molecular Dynamics (CoMD) approach is used to study dynamical effects related to both the average dynamics and the fluctuations around it. Data obtained in the REVERSE and in TRASMARAD experiments were compared with the theoretical simulations. The concept of temperature, as derived from a fully dynamical description of the GDR (giant dipole resonance) mode, is also discussed. In this contribution we have discussed the comparison between the CoMD model and two classes of phenomena, induced by heavy ion collisions. The first one is related to the IMF (intermediate mass fragment) production in semi-peripheral collisions for the {sup 124}Sn + {sup 64}Ni system at 35 MeV/nucleon. The comparison put in evidence clear preequilibrium effects in the fragment production mechanism which are essentially related to the behavior of the average dynamics. The second one concerns the high {gamma}-ray productions, due to dipolar resonant mechanisms, in the {sup 40}Ca + {sup 48}Ca system at 25 MeV/nucleon. In this case the comparisons with the model allows to put in evidence preequilibrium effects related both to the average dynamics and to the fluctuating one.

Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide

International Nuclear Information System (INIS)

Ohto, Umeharu; Satow, Yoshinori

2008-01-01

Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization. Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The c A axis of domain A coincides with the c B axis of domain B with a smaller lattice, and the a A axis corresponds to the (a B + b B ) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P4 1 2 1 2 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method

Dynamical Orientation of Large Molecules on Oxide Surfaces and its Implications for Dye-Sensitized Solar Cells

KAUST Repository

Brennan, Thomas P.

2013-11-12

A dual experimental-computational approach utilizing near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory-molecular dynamics (DFT-MD) is presented for determining the orientation of a large adsorbate on an oxide substrate. A system of interest in the field of dye-sensitized solar cells is studied: an organic cyanoacrylic acid-based donor-π-acceptor dye (WN1) bound to anatase TiO2. Assessment of nitrogen K-edge NEXAFS spectra is supported by calculations of the electronic structure that indicate energetically discrete transitions associated with the two π systems of the C-N triple bond in the cyanoacrylic acid portion of the dye. Angle-resolved NEXAFS spectra are fitted to determine the orientation of these two orbital systems, and the results indicate an upright orientation of the adsorbed dye, 63 from the TiO2 surface plane. These experimental results are then compared to computational studies of the WN1 dye on an anatase (101) TiO2 slab. The ground state structure obtained from standard DFT optimization is less upright (45 from the surface) than the NEXAFS results. However, DFT-MD simulations, which provide a more realistic depiction of the dye at room temperature, exhibit excellent agreement - within 2 on average - with the angles determined via NEXAFS, demonstrating the importance of accounting for the dynamic nature of adsorbate-substrate interactions and DFT-MD\\'s powerful predictive abilities. © 2013 American Chemical Society.

Dynamical Orientation of Large Molecules on Oxide Surfaces and its Implications for Dye-Sensitized Solar Cells

KAUST Repository

Brennan, Thomas P.; Tanskanen, Jukka T.; Bakke, Jonathan R.; Nguyen, William H.; Nordlund, Dennis; Toney, Michael F.; McGehee, Michael D.; Sellinger, Alan; Bent, Stacey F.

2013-01-01

A dual experimental-computational approach utilizing near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory-molecular dynamics (DFT-MD) is presented for determining the orientation of a large adsorbate on an oxide substrate. A system of interest in the field of dye-sensitized solar cells is studied: an organic cyanoacrylic acid-based donor-π-acceptor dye (WN1) bound to anatase TiO2. Assessment of nitrogen K-edge NEXAFS spectra is supported by calculations of the electronic structure that indicate energetically discrete transitions associated with the two π systems of the C-N triple bond in the cyanoacrylic acid portion of the dye. Angle-resolved NEXAFS spectra are fitted to determine the orientation of these two orbital systems, and the results indicate an upright orientation of the adsorbed dye, 63 from the TiO2 surface plane. These experimental results are then compared to computational studies of the WN1 dye on an anatase (101) TiO2 slab. The ground state structure obtained from standard DFT optimization is less upright (45 from the surface) than the NEXAFS results. However, DFT-MD simulations, which provide a more realistic depiction of the dye at room temperature, exhibit excellent agreement - within 2 on average - with the angles determined via NEXAFS, demonstrating the importance of accounting for the dynamic nature of adsorbate-substrate interactions and DFT-MD's powerful predictive abilities. © 2013 American Chemical Society.

Sustainable water recovery from oily wastewater via forward osmosis-membrane distillation (FO-MD).

Science.gov (United States)

Zhang, Sui; Wang, Peng; Fu, Xiuzhu; Chung, Tai-Shung

2014-04-01

This study proposed and investigated a hybrid forward osmosis - membrane distillation (FO-MD) system for sustainable water recovery from oily wastewater by employing lab-fabricated FO and MD hollow fiber membranes. Stable oil-in-water emulsions of different concentrations with small droplet sizes (oil droplets and partial permeation of acetic acid could be achieved. Finally, an integrated FO-MD system was developed to treat the oily wastewater containing petroleum, surfactant, NaCl and acetic acid at 60 °C in the batch mode. The water flux in FO undergoes three-stage decline due to fouling and reduction in osmotic driving force, but is quite stable in MD regardless of salt concentration. Oily wastewater with relatively high salinity could be effectively recovered by the FO-MD hybrid system while maintaining large water flux, at least 90% feed water recovery could be readily attained with only trace amounts of oil and salts, and the draw solution was re-generated for the next rounds of FO-MD run. Interestingly, significant amount of acetic acid was also retained in the permeate for further reuse as a chemical additive during the production of crude oil. The work has demonstrated that not only water but also organic additives in the wastewater could be effectively recovered by FO-MD systems for reuse or other utilizations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Center of excellence for mobile sensor data-to-knowledge (MD2K).

Science.gov (United States)

Kumar, Santosh; Abowd, Gregory D; Abraham, William T; al'Absi, Mustafa; Beck, J Gayle; Chau, Duen Horng; Condie, Tyson; Conroy, David E; Ertin, Emre; Estrin, Deborah; Ganesan, Deepak; Lam, Cho; Marlin, Benjamin; Marsh, Clay B; Murphy, Susan A; Nahum-Shani, Inbal; Patrick, Kevin; Rehg, James M; Sharmin, Moushumi; Shetty, Vivek; Sim, Ida; Spring, Bonnie; Srivastava, Mani; Wetter, David W

2015-11-01

Mobile sensor data-to-knowledge (MD2K) was chosen as one of 11 Big Data Centers of Excellence by the National Institutes of Health, as part of its Big Data-to-Knowledge initiative. MD2K is developing innovative tools to streamline the collection, integration, management, visualization, analysis, and interpretation of health data generated by mobile and wearable sensors. The goal of the big data solutions being developed by MD2K is to reliably quantify physical, biological, behavioral, social, and environmental factors that contribute to health and disease risk. The research conducted by MD2K is targeted at improving health through early detection of adverse health events and by facilitating prevention. MD2K will make its tools, software, and training materials widely available and will also organize workshops and seminars to encourage their use by researchers and clinicians. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

Directory of Open Access Journals (Sweden)

Jenny Farmer

2017-11-01

Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

Hydration Control of the Mechanical and Dynamical Properties of Cellulose

Energy Technology Data Exchange (ETDEWEB)

Petridis, Loukas; O’Neill, Hugh M.; Johnsen, Mariah [Ripon College, Ripon, Wisconsin 54971, United States; Fan, Bingxin [Department; Schulz, Roland [Department; Mamontov, Eugene; Maranas, Janna [Department; Langan, Paul [Department; Smith, Jeremy C. [Department

2014-10-13

The mechanical and dynamical properties of cellulose, the most abundant biomolecule on earth, are essential for its function in plant cell walls and advanced biomaterials. Cellulose is almost always found in a hydrated state, and it is therefore important to understand how hydration influences its dynamics and mechanics. Here, the nanosecond-time scale dynamics of cellulose is characterized using dynamic neutron scattering experiments and molecular dynamics (MD) simulation. The experiments reveal that hydrated samples exhibit a higher average mean-square displacement above ~240 K. The MD simulation reveals that the fluctuations of the surface hydroxymethyl atoms determine the experimental temperature and hydration dependence. The increase in the conformational disorder of the surface hydroxymethyl groups with temperature follows the cellulose persistence length, suggesting a coupling between structural and mechanical properties of the biopolymer. In the MD simulation, 20% hydrated cellulose is more rigid than the dry form, due to more closely packed cellulose chains and water molecules bridging cellulose monomers with hydrogen bonds. This finding may have implications for understanding the origin of strength and rigidity of secondary plant cell walls. The detailed characterization obtained here describes how hydration-dependent increased fluctuations and hydroxymethyl disorder at the cellulose surface lead to enhancement of the rigidity of this important biomolecule.

MdHB1 down-regulation activates anthocyanin biosynthesis in the white-fleshed apple cultivar 'Granny Smith'.

Science.gov (United States)

Jiang, Yonghua; Liu, Cuihua; Yan, Dan; Wen, Xiaohong; Liu, Yanli; Wang, Haojie; Dai, Jieyu; Zhang, Yujie; Liu, Yanfei; Zhou, Bin; Ren, Xiaolin

2017-02-01

Coloration in apple (Malus×domestica) flesh is mainly caused by the accumulation of anthocyanin. Anthocyanin is biosynthesized through the flavonoid pathway and regulated by MYB, bHLH, and WD40 transcription factors (TFs). Here, we report that the HD-Zip I TF MdHB1 was also involved in the regulation of anthocyanin accumulation. MdHB1 silencing caused the accumulation of anthocyanin in 'Granny Smith' flesh, whereas its overexpression reduced the flesh content of anthocyanin in 'Ballerina' (red-fleshed apple). Moreover, flowers of transgenic tobacco (Nicotiana tabacum 'NC89') overexpressing MdHB1 showed a remarkable reduction in pigmentation. Transient promoter activation assays and yeast one-hybrid results indicated that MdHB1 indirectly inhibited expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and UDP-glucose:flavonoid 3-O-glycosyltransferase (UFGT). Yeast two-hybrid and bimolecular fluorescence complementation determined that MdHB1 acted as a homodimer and could interact with MYB, bHLH, and WD40 in the cytoplasm, consistent with its cytoplasmic localization by green fluorescent protein fluorescence observations. Together, these results suggest that MdHB1 constrains MdMYB10, MdbHLH3, and MdTTG1 to the cytoplasm, and then represses the transcription of MdDFR and MdUFGT indirectly. When MdHB1 is silenced, these TFs are released to activate the expression of MdDFR and MdUFGT and also anthocyanin biosynthesis, resulting in red flesh in 'Granny Smith'. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.

Science.gov (United States)

Meyer, Tim; Knapp, Ernst-Walter

2015-06-09

For a benchmark set of 194 measured pKa values in 13 proteins, electrostatic energy computations are performed in which pKa values are computed by solving the Poisson-Boltzmann equation. In contrast to the previous approach of Karlsberg(+) (KB(+)) that essentially used protein crystal structures with variations in their side chain conformations, the present approach (KB2(+)MD) uses protein conformations from four molecular dynamics (MD) simulations of 10 ns each. These MD simulations are performed with different specific but fixed protonation patterns, selected to sample the conformational space for the different protonation patterns faithfully. The root-mean-square deviation between computed and measured pKa values (pKa RMSD) is shown to be reduced from 1.17 pH units using KB(+) to 0.96 pH units using KB2(+)MD. The pKa RMSD can be further reduced to 0.79 pH units, if each conformation is energy-minimized with a dielectric constant of εmin = 4 prior to calculating the electrostatic energy. The electrostatic energy expressions upon which the computations are based have been reformulated such that they do not involve terms that mix protein and solvent environment contributions and no thermodynamic cycle is needed. As a consequence, conformations of the titratable residues can be treated independently in the protein and solvent environments. In addition, the energy terms used here avoid the so-called intrinsic pKa and can therefore be interpreted without reference to arbitrary protonation states and conformations.

MD simulation of cluster formation during sputtering

International Nuclear Information System (INIS)

Muramoto, T.; Okai, M.; Yamashita, Y.; Yorizane, K.; Yamamura, Y.

2001-01-01

The cluster ejection due to cluster impact on a solid surface is studied through molecular dynamics (MD) simulations. Simulations are performed for Cu cluster impacts on the Cu(1 1 1) surface for cluster energy 100 eV/atom, and for clusters of 6, 13, 28 and 55 atoms. Interatomic interactions are described by the AMLJ-EAM potential. The vibration energy spectrum is independent of the incident cluster size and energy. This comes from the fact that sputtered clusters become stable through the successive fragmentation of nascent large sputtered clusters. The vibration energy spectra for large sputtered clusters have a peak, whose energy corresponds to the melting temperature of Cu. The exponent of the power-law fit of the abundance distribution and the total sputtering yield for the cluster impacts are higher than that for the monatomic ion impacts with the same total energy, where the exponent δ is given by Y n ∝n δ and Y n is the yield of sputtered n-atom cluster. The exponent δ follows a unified function of the total sputtering yield, which is a monotonic increase function, and it is nearly equal to δ ∼ -3 for larger yield

Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

Science.gov (United States)

Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

2017-05-05

Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design. Copyright © 2017. Published by Elsevier Masson SAS.

A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution

Directory of Open Access Journals (Sweden)

Roghayeh Abedi Karjiban

2013-01-01

Full Text Available The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC, dilauroylphosphatidylcholine (DLPC, dimyristoylphosphatidylcholine (DMPC, and distearoylphosphatidylcholine (DSPC in water were investigated using a coarse-grained molecular dynamics (CG-MD simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.

Structure and Ionic Conductivity of Li2S–P2S5 Glass Electrolytes Simulated with First-Principles Molecular Dynamics

International Nuclear Information System (INIS)

Baba, Takeshi; Kawamura, Yoshiumi

2016-01-01

Lithium thiophosphate-based materials are attractive as solid electrolytes in all-solid-state lithium batteries because glass or glass-ceramic structures of these materials are associated with very high conductivity. In this work, we modeled lithium thiophosphates with amorphous structures and investigated Li + mobilities by using molecular dynamics calculations based on density functional theory (DFT-MD). The structures of xLi 2 S–(100 − x)P 2 S 5 (x = 67, 70, 75, and 80) were created by randomly identifying appropriate compositions of Li + , PS 4 3− ,P 2 S 7 4− , and S 2− and then annealing them with DFT-MD calculations. Calculated relative stabilities of the amorphous structures with x = 67, 70, and 75 to crystals with the same compositions were 0.04, 0.12, and 0.16 kJ/g, respectively. The implication is that these amorphous structures are metastable. There was good agreement between calculated and experimental structure factors determined from X-ray scattering. The differences between the structure factors of amorphous structures were small, except for the first sharp diffraction peak, which was affected by the environment between Li and S atoms. Li + diffusion coefficients obtained from DFT-MD calculations at various temperatures for picosecond simulation times were on the order of 10 −3 –10 −5 Å 2 /ps. Ionic conductivities evaluated by the Nernst–Einstein relationship at 298.15 K were on the order of 10 −5 S/cm. The ionic conductivity of the amorphous structure with x = 75 was the highest among the amorphous structures because there was a balance between the number density and diffusibility of Li + . The simulations also suggested that isolated S atoms suppress Li + migration.

Automatic generation of active coordinates for quantum dynamics calculations: Application to the dynamics of benzene photochemistry

International Nuclear Information System (INIS)

Lasorne, Benjamin; Sicilia, Fabrizio; Bearpark, Michael J.; Robb, Michael A.; Worth, Graham A.; Blancafort, Lluis

2008-01-01

A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments

Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

Science.gov (United States)

Zheng, Mo; Li, Xiaoxia; Guo, Li

2013-04-01

Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.

Study of lanthanide tri-cations in aqueous solution by molecular dynamic

International Nuclear Information System (INIS)

Duvail, M.

2007-11-01

This is essentially a lanthanide tri-cation hydration study by means of classical molecular dynamics (CLMD) simulations using explicit polarization. Explicit polarization is calculated with a Car-Parrinello type of dynamics on induced dipoles, which decreases the CPU time as compared to the self-consistent resolution. Several pair interaction potentials are parametrized from ab initio calculations (MP2) and tested for the La 3+ -OH 2 interaction. The best results are obtained with an exponential-6 Buckingham potential. Next, the La 3+ -OH 2 interaction potential parameters are extrapolated to the other Ln 3+ -OH 2 interactions, only by using the ionic radii. The CLMD results reproduce the reliable experimental data (EXAFS distances), and the sigmoidal variation of the coordination number (with S shape), from 9 for La 3+ to 8 for Lu 3+ . This variation is explained by the linear variation of DrG0 (9,298) vs. atomic number. Insights are also given on the Co 2+ hydration, CPMD simulations, reconstruction of EXAFS signal from MD simulations, and OH - complexation of La 3+ in aqueous solution. (author)

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

NARCIS (Netherlands)

Marrink, SJ; Mark, AE

2003-01-01

Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

Approximate dynamic fault tree calculations for modelling water supply risks

International Nuclear Information System (INIS)

Lindhe, Andreas; Norberg, Tommy; Rosén, Lars

2012-01-01

Traditional fault tree analysis is not always sufficient when analysing complex systems. To overcome the limitations dynamic fault tree (DFT) analysis is suggested in the literature as well as different approaches for how to solve DFTs. For added value in fault tree analysis, approximate DFT calculations based on a Markovian approach are presented and evaluated here. The approximate DFT calculations are performed using standard Monte Carlo simulations and do not require simulations of the full Markov models, which simplifies model building and in particular calculations. It is shown how to extend the calculations of the traditional OR- and AND-gates, so that information is available on the failure probability, the failure rate and the mean downtime at all levels in the fault tree. Two additional logic gates are presented that make it possible to model a system's ability to compensate for failures. This work was initiated to enable correct analyses of water supply risks. Drinking water systems are typically complex with an inherent ability to compensate for failures that is not easily modelled using traditional logic gates. The approximate DFT calculations are compared to results from simulations of the corresponding Markov models for three water supply examples. For the traditional OR- and AND-gates, and one gate modelling compensation, the errors in the results are small. For the other gate modelling compensation, the error increases with the number of compensating components. The errors are, however, in most cases acceptable with respect to uncertainties in input data. The approximate DFT calculations improve the capabilities of fault tree analysis of drinking water systems since they provide additional and important information and are simple and practically applicable.

MD study of pyrimidine base damage on DNA and its recognition by repair enzyme

International Nuclear Information System (INIS)

Pinak, M.

2000-01-01

The molecular dynamics (MD) simulation was used on the study of two specific damages of pyrimidine bases of DNA. Pyrimidine bases are major targets either of free radicals induced by ionizing radiation in DNA surrounding environment or UV radiation. Thymine dimer (TD) is UV induced damage, in which two neighboring thymines in one strand are joined by covalent bonds of C(5)-C(5) and C(6)-C(6) atoms of thymines. Thymine glycol (TG) is ionizing radiation induced damage in which the free water radical adds to unsaturated bond C(5)-C(6) of thymine. Both damages are experimentally suggested to be mutagenetic and carcinogenic unless properly repaired by repair enzymes. In the case of MD of TD, there is detected strong kink around the TD site that is not observed in native DNA. In addition there is observed the different value of electrostatic energy at the TD site - negative '-10 kcal/mol', in contrary to nearly neutral value of native thymine site. Structural changes and specific electrostatic energy - seems to be important for proper recognition of TD damaged site, formation of DNA-enzyme complex and thus for subsequent repair of DNA. In the case of TG damaged DNA there is major structural distortion at the TG site, mainly the increased distance between TG and the C5' of adjacent nucleotide. This enlarged gap between the neighboring nucleotides may prevent the insertion of complementary base during replication causing the replication process to stop. In which extend this structural feature together with energy properties of TG contributes to the proper recognition of TG by repair enzyme Endonuclease III is subject of further computational MD study. (author)

76 FR 81826 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

Science.gov (United States)

2011-12-29

... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to... five hours advance notice is given. The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke...

Model of fracture of metal melts and the strength of melts under dynamic conditions

International Nuclear Information System (INIS)

Mayer, P. N.; Mayer, A. E.

2015-01-01

The development of a continuum model of deformation and fracture of melts is needed for the description of the behavior of metals in extreme states, in particular, under high-current electron and ultrashort laser irradiation. The model proposed includes the equations of mechanics of a two-phase continuum and the equations of the kinetics of phase transitions. The change (exchange) of the volumes of dispersed and carrier phases and of the number of dispersed particles is described, and the energy and mass exchange between the phases due to phase transitions is taken into account. Molecular dynamic (MD) calculations are carried out with the use of the LAMMPS program. The continuum model is verified by MD, computational, and experimental data. The strength of aluminum, copper, and nickel is determined at various temperatures and strain rates. It is shown that an increase in the strain rate leads to an increase in the strength of a liquid metal, while an increase in temperature leads to a decrease in its strength

Model of fracture of metal melts and the strength of melts under dynamic conditions

Energy Technology Data Exchange (ETDEWEB)

Mayer, P. N., E-mail: polina.nik@mail.ru; Mayer, A. E., E-mail: mayer@csu.ru [Chelyabinsk State University (Russian Federation)

2015-07-15

The development of a continuum model of deformation and fracture of melts is needed for the description of the behavior of metals in extreme states, in particular, under high-current electron and ultrashort laser irradiation. The model proposed includes the equations of mechanics of a two-phase continuum and the equations of the kinetics of phase transitions. The change (exchange) of the volumes of dispersed and carrier phases and of the number of dispersed particles is described, and the energy and mass exchange between the phases due to phase transitions is taken into account. Molecular dynamic (MD) calculations are carried out with the use of the LAMMPS program. The continuum model is verified by MD, computational, and experimental data. The strength of aluminum, copper, and nickel is determined at various temperatures and strain rates. It is shown that an increase in the strain rate leads to an increase in the strength of a liquid metal, while an increase in temperature leads to a decrease in its strength.

The effect of interatomic potential in molecular dynamics simulation of low energy ion implantation

International Nuclear Information System (INIS)

Chan, H.Y.; Nordlund, K.; Peltola, J.; Gossmann, H.-J.L.; Ma, N.L.; Srinivasan, M.P.; Benistant, F.; Chan, Lap

2005-01-01

Being able to accurately predict dopant profiles at sub-keV implant energies is critical for the microelectronic industry. Molecular Dynamics (MD), with its capability to account for multiple interactions as energy lowers, is an increasingly popular simulation method. We report our work on sub-keV implantation using MD and investigate the effect of different interatomic potentials on the range profiles. As an approximation, only pair potentials are considered in this work. Density Functional Theory (DFT) is used to calculate the pair potentials for a wide range of dopants (B, C, N, F, Si, P, Ga, Ge, As, In and Sb) in single crystalline silicon. A commonly used repulsive potential is also included in the study. Importance of the repulsive and attractive regions of the potential has been investigated with different elements and we show that a potential depicting the right attractive forces is especially important for heavy elements at low energies

The molecular mechanism underlying anthocyanin metabolism in apple using the MdMYB16 and MdbHLH33 genes.

Science.gov (United States)

Xu, Haifeng; Wang, Nan; Liu, Jingxuan; Qu, Changzhi; Wang, Yicheng; Jiang, Shenghui; Lu, Ninglin; Wang, Deyun; Zhang, Zongying; Chen, Xuesen

2017-05-01

MdMYB16 forms homodimers and directly inhibits anthocyanin synthesis via its C-terminal EAR repressor. It weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis when overexpressing MdbHLH33 in callus overexpressing MdMYB16. MdMYB16 could interact with MdbHLH33. Anthocyanins are strong antioxidants that play a key role in the prevention of cardiovascular disease, cancer, and diabetes. The germplasm of Malus sieversii f. neidzwetzkyana is important for the study of anthocyanin metabolism. To date, only limited studies have examined the negative regulatory mechanisms underlying anthocyanin synthesis in apple. Here, we analyzed the relationship between anthocyanin levels and MdMYB16 expression in mature Red Crisp 1-5 apple (M. domestica) fruit, generated an evolutionary tree, and identified an EAR suppression sequence and a bHLH binding motif of the MdMYB16 protein using protein sequence analyses. Overexpression of MdMYB16 or MdMYB16 without bHLH binding sequence (LBSMdMYB16) in red-fleshed callus inhibited MdUFGT and MdANS expression and anthocyanin synthesis. However, overexpression of MdMYB16 without the EAR sequence (LESMdMYB16) in red-fleshed callus had no inhibitory effect on anthocyanin. The yeast one-hybrid assay showed that MdMYB16 and LESMdMYB16 interacted the promoters of MdANS and MdUFGT, respectively. Yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays showed that MdMYB16 formed homodimers and interacted with MdbHLH33, however, the LBSMdMYB16 could not interact with MdbHLH33. We overexpressed MdbHLH33 in callus overexpressing MdMYB16 and found that it weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis. Together, these results suggested that MdMYB16 and MdbHLH33 may be important part of the regulatory network controlling the anthocyanin biosynthetic pathway.

Validating clustering of molecular dynamics simulations using polymer models

Directory of Open Access Journals (Sweden)

Phillips Joshua L

2011-11-01

Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

Identification of potent inhibitors against snake venom metalloproteinase (SVMP) using molecular docking and molecular dynamics studies.

Science.gov (United States)

Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan

2015-01-01

Snake venom metalloproteinase (SVMP) (Echis coloratus (Carpet viper) is a multifunctional enzyme that is involved in producing several symptoms that follow a snakebite, such as severe local hemorrhage, nervous system effects and tissue necrosis. Because the three-dimensional (3D) structure of SVMP is not known, models were constructed, and the best model was selected based on its stereo-chemical quality. The stability of the modeled protein was analyzed through molecular dynamics (MD) simulation studies. Structure-based virtual screening was performed, and 15 potential molecules with the highest binding energies were selected. Further analysis was carried out with induced fit docking, Prime/MM-GBSA (ΔGBind calculations), quantum-polarized ligand docking, and density functional theory calculations. Further, the stability of the lead molecules in the SVMP-active site was examined using MD simulation. The results showed that the selected lead molecules were highly stable in the active site of SVMP. Hence, these molecules could potentially be selective inhibitors of SVMP. These lead molecules can be experimentally validated, and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for snake antivenom.

Comparison of inverse dynamics calculated by two- and three-dimensional models during walking

DEFF Research Database (Denmark)

Alkjaer, T; Simonsen, E B; Dyhre-Poulsen, P

2001-01-01

recorded the subjects as they walked across two force plates. The subjects were invited to approach a walking speed of 4.5 km/h. The ankle, knee and hip joint moments in the sagittal plane were calculated by 2D and 3D inverse dynamics analysis and compared. Despite the uniform walking speed (4.53 km....../h) and similar footwear, relatively large inter-individual variations were found in the joint moment patterns during the stance phase. The differences between individuals were present in both the 2D and 3D analysis. For the entire sample of subjects the overall time course pattern of the ankle, knee and hip...... the magnitude of the joint moments calculated by 2D and 3D inverse dynamics but the inter-individual variation was not affected by the different models. The simpler 2D model seems therefore appropriate for human gait analysis. However, comparisons of gait data from different studies are problematic...

Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex.

Science.gov (United States)

Keinan, Shahar; Nocek, Judith M; Hoffman, Brian M; Beratan, David N

2012-10-28

Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface

Large scale exact quantum dynamics calculations: Ten thousand quantum states of acetonitrile

Science.gov (United States)

Halverson, Thomas; Poirier, Bill

2015-03-01

'Exact' quantum dynamics (EQD) calculations of the vibrational spectrum of acetonitrile (CH3CN) are performed, using two different methods: (1) phase-space-truncated momentum-symmetrized Gaussian basis and (2) correlated truncated harmonic oscillator basis. In both cases, a simple classical phase space picture is used to optimize the selection of individual basis functions-leading to drastic reductions in basis size, in comparison with existing methods. Massive parallelization is also employed. Together, these tools-implemented into a single, easy-to-use computer code-enable a calculation of tens of thousands of vibrational states of CH3CN to an accuracy of 0.001-10 cm-1.

Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5

Directory of Open Access Journals (Sweden)

Inger Lindin

2014-03-01

Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.

Science.gov (United States)

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD

Conformational analysis of the Sda determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations

International Nuclear Information System (INIS)

Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.

2000-01-01

The conformational behaviour of the spacer-linked synthetic Sd a tetrasaccharide β-d-GalpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (1) and the two mimics β-d-Galp-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O)(CH 2 ) 5 NH 2 (2) and β-d-GlcpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (3) were investigated by 1 H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1 H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the β-d-Hex(NAc)-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp fragments. The α- Neu5-Ac-(2 → 3)-β-d-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated......Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known to form amyloids is Transthyretine (TTR), the secondary transporter of thyroxine and transporter of retinol-binding-protein. Several...

Multiscale Modeling using Molecular Dynamics and Dual Domain Material Point Method

Energy Technology Data Exchange (ETDEWEB)

Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division. Fluid Dynamics and Solid Mechanics Group, T-3; Rice Univ., Houston, TX (United States)

2016-07-07

For problems involving large material deformation rate, the material deformation time scale can be shorter than the material takes to reach a thermodynamical equilibrium. For such problems, it is difficult to obtain a constitutive relation. History dependency become important because of thermodynamic non-equilibrium. Our goal is to build a multi-scale numerical method which can bypass the need for a constitutive relation. In conclusion, multi-scale simulation method is developed based on the dual domain material point (DDMP). Molecular dynamics (MD) simulation is performed to calculate stress. Since the communication among material points is not necessary, the computation can be done embarrassingly parallel in CPU-GPU platform.

TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid

Science.gov (United States)

Kononova, Olga; Maksudov, Farkhad; Marx, Kenneth A.; Barsegov, Valeri

2018-01-01

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and C_α -based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.

The effect of dynamical quark mass on the calculation of a strange quark star's structure

Institute of Scientific and Technical Information of China (English)

Gholam Hossein Bordbar; Babak Ziaei

2012-01-01

We discuss the dynamical behavior of strange quark matter components,in particular the effects of density dependent quark mass on the equation of state of strange quark matter.The dynamical masses of quarks are computed within the Nambu-Jona-Lasinio model,then we perform strange quark matter calculations employing the MIT bag model with these dynamical masses.For the sake of comparing dynamical mass interaction with QCD quark-quark interaction,we consider the one-gluon-exchange term as the effective interaction between quarks for the MIT bag model.Our dynamical approach illustrates an improvement in the obtained equation of state values.We also investigate the structure of the strange quark star using TolmanOppenheimer-Volkoff equations for all applied models.Our results show that dynamical mass interaction leads to lower values for gravitational mass.

Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei.

Directory of Open Access Journals (Sweden)

Rommie E Amaro

2007-11-01

Full Text Available RNA editing ligase 1 (TbREL1 is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei, the parasite responsible for the devastating tropical disease African sleeping sickness. The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes, and no close human homolog is known to exist. In addition, the high-resolution crystal structure revealed several unique features of the active site, making this enzyme a promising target for structure-based drug design. In this work, two 20 ns atomistic molecular dynamics (MD simulations are employed to investigate the dynamics of TbREL1, both with and without the ATP substrate present. The flexibility of the active site, dynamics of conserved residues and crystallized water molecules, and the interactions between TbREL1 and the ATP substrate are investigated and discussed in the context of TbREL1's function. Differences in local and global motion upon ATP binding suggest that two peripheral loops, unique to the trypanosomes, may be involved in interdomain signaling events. Notably, a significant structural rearrangement of the enzyme's active site occurs during the apo simulations, opening an additional cavity adjacent to the ATP binding site that could be exploited in the development of effective inhibitors directed against this protozoan parasite. Finally, ensemble averaged electrostatics calculations over the MD simulations reveal a novel putative RNA binding site, a discovery that has previously eluded scientists. Ultimately, we use the insights gained through the MD simulations to make several predictions and recommendations, which we anticipate will help direct future experimental studies and structure-based drug discovery efforts against this vital enzyme.

Dynamics of ions in the selectivity filter of the KcsA channel: Towards a coupled Brownian particle description

OpenAIRE

Cosseddu, Salvatore M.; Khovanov, Igor A.; Allen, Michael P.; Rodger, P. M.; Luchinsky, Dmitry G.; McClintock, Peter V. E.

2013-01-01

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by u...

Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels

NARCIS (Netherlands)

Nedea, S.V.; Frijns, A.J.H.; Steenhoven, van A.A.; Markvoort, Albert. J.; Hilbers, P.A.J.

2005-01-01

We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk

ESSENTIAL DYNAMICS OF PROTEINS

NARCIS (Netherlands)

AMADEI, A; LINSSEN, ABM; BERENDSEN, HJC

1993-01-01

Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ''essential'' subspace containing only a few degrees of freedom in which anharmonic motion occurs that

Molecular dynamics for near melting temperatures simulations of metals using modified embedded-atom method

Science.gov (United States)

Etesami, S. Alireza; Asadi, Ebrahim

2018-01-01

Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.

Molecular dynamics simulations and structural descriptors of radioisotope glass vectors for in situ radiotherapy.

Science.gov (United States)

Christie, Jamieson K; Tilocca, Antonio

2012-10-18

The low solubility (high durability) of yttrium aluminosilicate (YAS) glass is one of its most important properties for use in in situ radiotherapy. Simple parameters, such as silica or yttria content or network connectivity, are not sufficient to rationalize the dependence of the solubility on the glass composition observed experimentally. We performed classical molecular dynamics (MD) simulations of eight different YAS glasses of known solubility and analyzed the MD trajectories to identify specific structural features that are correlated and can be used to predict the solubility. We show that the (Si-)O-Si coordination number CN(SiOSi), the yttrium-yttrium clustering ratio R(YY), and the number of intratetrahedral O-Si-O bonds per yttrium atom N(intra) can be combined into a single structural descriptor s = f(CN(SiOSi),R(YY),N(intra)) with a high correlation with the solubility. The parameter s can thus be calculated from MD simulations and used to predict the solubility of YAS compositions, allowing one to adjust them to the range required by radiotherapy applications. For instance, its trend shows that high-silica- and low-yttria-content YAS glasses should be sufficiently durable for the radiotherapy application, although additional clinical considerations may set a lower limit to the yttria content.

Spin-diffusions and diffusive molecular dynamics

Science.gov (United States)

Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

2017-12-01

Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching.

Science.gov (United States)

Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko

2014-02-01

Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively

The dynamic capacity calculation method and the flood control ability of the Three Gorges Reservoir

Science.gov (United States)

Zhang, Shanghong; Jing, Zhu; Yi, Yujun; Wu, Yu; Zhao, Yong

2017-12-01

To evaluate the flood control ability of a river-type reservoir, an accurate simulation method for the flood storage, discharge process, and dynamic capacity of the reservoir is important. As the world's largest reservoir, the storage capacity and flood control capacity of the Three Gorges Reservoir (TGR) has attracted widespread interest and academic debate for nearly 20 years. In this study, a model for calculating the dynamic capacity of a river-type reservoir is established based on data from 394 river cross sections and 2.5-m resolution digital elevation model (DEM) data of the TGR area. The storage capacity and flood control capacity of the TGR were analysed based on the scheduling procedures of a normal impoundment period. The results show that the static capacity of the TGR is 43.43 billion m3, the dynamic flood control capacity is 22.45 billion m3, and the maximum floodwater flow regulated by the dynamic capacity at Zhicheng is no more than 67,700 m3/s. This study supply new simulation method and up-to-date high-precision data to discuss the 20 years debate, and the results reveal the TGR design is conservative for flood control according to the Preliminary Design Report of the Three Gorges Project. The dynamic capacity calculation method used here can provide a reference for flood regulation of large river-type reservoirs.

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

Science.gov (United States)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Study of radiation damage in BaTiO3, using Molecular-dynamics simulations

International Nuclear Information System (INIS)

Gonzalez, E.; Abreu, Y.; Cruz, C. M.; Pinnera, I.; Leyva, A.

2015-01-01

Molecular-dynamics (MD) simulations were used to calculate atomic displacement probability curves along main crystallographic directions in BaTiO 3 perovskite. A primary knock-on atom (PKA) with a energy range between 10 to 300 eV in principal crystallographic directions at 300 K was introduced. For each sublattice, the simulation was repeated from different initial conditions to estimate the variation in the defect formation process. The formation of Frenkel pairs vary considerably with crystallographic direction and sublattice. Major quantity oxygen defects were found for all the simulated crystallographic directions. Threshold displacement energies are calculated for each atomic specie in the BaTiO 3 material. Also simulations with SRIM code, modeling + Mn implantation in a BaTiO 3 target, at 250 keV were made. (Author)

The dynamic multisite interactions between two intrinsically disordered proteins

KAUST Repository

Wu, Shaowen

2017-05-11

Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a structured protein, while the Interaction between two IDPs is poorly understood. In this study, we combined NMR, smFRET, and molecular dynamics (MD) simulation to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by MD and mutagenesis studies. Our study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.

High-pressure lattice dynamics and thermodynamic properties of zinc-blende BN from first-principles calculation

International Nuclear Information System (INIS)

Wang Huanyou; Xu Hui; Wang Xianchun; Jiang Chunzhi

2009-01-01

The density function perturbation theory (DFPT) is employed to study the lattice dynamics and thermodynamic properties (with quasiharmonic approximation) of zinc-blende BN. First we discuss the structural properties and compare the phonon spectrum with available Raman scattering experiments. Thereafter using the calculated phonon dispersions we obtain the PTV equation of state from the free energy. Our results for the above properties are generally speaking in good agreement with experiments and with similar theoretical calculations. Owing to the anharmonic effect at high temperature, the calculated linear thermal expansion coefficients (CTE) are low to experimental data.

Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

International Nuclear Information System (INIS)

Sanz-Navarro, Carlos F.

2002-01-01

The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

MdATG18a overexpression improves tolerance to nitrogen deficiency and regulates anthocyanin accumulation through increased autophagy in transgenic apple.

Science.gov (United States)

Sun, Xun; Jia, Xin; Huo, Liuqing; Che, Runmin; Gong, Xiaoqing; Wang, Ping; Ma, Fengwang

2018-02-01

Nitrogen (N) availability is an essential factor for plant growth. Recycling and remobilization of N have strong impacts on crop yield and quality under N deficiency. Autophagy is a critical nutrient-recycling process that facilitates remobilization under starvation. We previously showed that an important AuTophaGy (ATG) protein from apple, MdATG18a, has a positive role in drought tolerance. In this study, we explored its biological role in response to low-N. Overexpression of MdATG18a in both Arabidopsis and apple improved tolerance to N-depletion and caused a greater accumulation of anthocyanin. The increased anthocyanin concentration in transgenic apple was possibly due to up-regulating flavonoid biosynthetic and regulatory genes (MdCHI, MdCHS, MdANS, MdPAL, MdUFGT, and MdMYB1) and higher soluble sugars concentration. MdATG18a overexpression enhanced starch degradation with up-regulating amylase gene (MdAM1) and up-regulated sugar metabolism related genes (MdSS1, MdHXKs, MdFK1, and MdNINVs). Furthermore, MdATG18a functioned in nitrate uptake and assimilation by up-regulating nitrate reductase MdNIA2 and 3 high-affinity nitrate transporters MdNRT2.1/2.4/2.5. MdATG18a overexpression also elevated other important MdATG genes expression and autophagosomes formation under N-depletion, which play key contributions to above changes. Together, these results demonstrate that overexpression of MdATG18a enhances tolerance to N-deficiencies and plays positive roles in anthocyanin biosynthesis through greater autophagic activity. © 2017 John Wiley & Sons Ltd.

Fluid and structural dynamics calculations to determine core barrel loads during blowdown (EV 3,000)

International Nuclear Information System (INIS)

Krieg, R.; Schlechtendahl, E.G.

1977-01-01

To begin with, the main physical phenomena in connection with blowdown loads on the care barrel and the computer models used are briefly described. These models have also been used in the design of the HTR test care barrel. The fluid dynamics part of the calculations was carried out using the WHAMMOD and DAPSY codes; for the structural dynamics part, the STRUDL/Dynal code was employed. (orig./RW) [de

Molecular dynamics modeling and simulation of void growth in two dimensions

Science.gov (United States)

Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

2013-10-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Molecular dynamics modeling and simulation of void growth in two dimensions

International Nuclear Information System (INIS)

Chang, H-J; Segurado, J; LLorca, J; Rodríguez de la Fuente, O; Pabón, B M

2013-01-01

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids. (paper)

STRATEGI PEMASARAN PUBLIC RELATIONS MD ENTERTAINMENT PADA PEMASARAN FILM HABIBIE & AINUN

OpenAIRE

Trisna Adi Permana; Lilis Puspitasari

2015-01-01

Tujuan penelitian ini adalah untuk mengetahui perencanaan, implementasi serta evaluasi dari strategi Marketing Public Relations yang ditetapkan PR MD Entertainment pada film Habibie & Ainun pada tahun 2012-2013. Metode yang dilakukan adalah metode deskriptif yang bertujuan melukiskan secara sistematis fakta atau karakteristik populasi tertentu atau bidang tertentu secara faktual dan cermat. Hasil penelitian menunjukan PR MD Entertainment telah melakukan tahapan-tahapan atau Teknik...

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

Science.gov (United States)

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

A Molecular Dynamics Approach for Nucleation-Growth of Cryogenic Cavitation

KAUST Repository