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Sample records for dynamics simulation study

  1. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  2. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  3. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  4. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    Science.gov (United States)

    Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.

    2016-10-01

    SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.

  5. Simulation study of water and sugar dynamics in supercooled mixtures

    Science.gov (United States)

    Molinero, Valeria; Cagin, Tahir; Goddard, William A.

    2003-03-01

    Water dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology, where low water mobility is desirable to slow down chemical degradation and preserve biomolecules. We have studied the microscopic mechanism of water diffusion in binary and polydisperse malto-oligosaccharides and water mixtures by means of molecular dynamics simulations. The computations were performed with a coarse grain model (M3B), derived from atomistic simulations of water and malto-oligosaccharides. The use of the M3B model permits simulations of the order of 0.1 microsecond, thus allowing us to explore water dynamics from the liquid to the deep supercooled regime. The dynamics of water confined in the sugar matrix is slowed down with respect to bulk water. We found that at low moisture content and low temperature, ranslational diffusion of water and glucose rotation proceed through a hopping-diffusion mechanism. Moreover, we found water mobility to be heterogeneous: there is a broad distribution of time scales for different water molecules in the mixtures. We discuss whether there is a relationship between the heterogeneous structure of these mixtures in the sub-nanometer scale and the heterogeneous dynamics of water molecules.

  6. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    Science.gov (United States)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  7. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  8. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    Science.gov (United States)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  9. Hypervelocity Impact on Interfaces: A Molecular-Dynamics Simulations Study

    Science.gov (United States)

    Bachlechner, Martina E.; Owens, Eli T.; Leonard, Robert H.; Cockburn, Bronwyn C.

    2008-03-01

    Silicon/silicon nitride interfaces are found in micro electronics and solar cells. In either application the mechanical integrity of the interface is of great importance. Molecular-dynamics simulations are performed to study the failure of interface materials under the influence of hypervelocity impact. Silicon nitride plates impacting on silicon/silicon nitride interface targets of different thicknesses result in structural phase transformation and delamination at the interface. Detailed analyses of atomic velocities, bond lengths, and bond angles are used to qualitatively examine the respective failure mechanisms.

  10. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the pos......In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  11. Simulation studies of high-latitude magnetospheric boundary dynamics

    Institute of Scientific and Technical Information of China (English)

    PU; Zuyin; SHI; Quanqi; XIAO; Chijie; FU; Suiyan; ZHANG; Hu

    2004-01-01

    Magnetic reconnection at the high-latitude magnetopause is studied using 2.5-dimensional Hail-MHD simulation. Concentric flow vortices and magnetic islands appear when both Hall effect and sheared flow are considered. Plasma mixing across the magnetopause occurs in the presence of the flow vortices. Reconnected structure generated in the vicinity of the subsolar point changes its geometry with increasing flow shear while moving to high latitudes. In the presence of flow shear, with the Hail-MHD reconnection a higher reconnection rate than with the traditional MHD is obtained. The out-of-plane components of flow and magnetic field produced by the Hall current are redistributed under the action of the flow shear, which makes the plasma transport across the boundaries more complicated. The simulation results provide some help in understanding the dynamic processes at the high latitude magnetopause.

  12. Hydrotropic Solubilization by Urea Derivatives: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Yong Cui

    2013-01-01

    Full Text Available Hydrotropy is a phenomenon where the presence of a large quantity of one solute enhances the solubility of another solute. The mechanism of this phenomenon remains a topic of debate. This study employed molecular dynamics simulation to investigate the hydrotropic mechanism of a series of urea derivatives, that is, urea (UR, methylurea (MU, ethylurea (EU, and butylurea (BU. A poorly water-soluble compound, nifedipine (NF, was used as the model solute that was solubilized. Structural, dynamic, and energetic changes upon equilibration were analyzed to supply insights to the solubilization mechanism. The study demonstrated that NF and urea derivatives underwent significant nonstoichiometric molecular aggregation in the aqueous solution, a result consistent with the self-aggregation of urea derivatives under the same conditions. The analysis of hydrogen bonding and energy changes revealed that the aggregation was driven by the partial restoration of normal water structure. The energetic data also suggested that the promoted solubilization of NF is favored in the presence of urea derivatives. While the solutes aggregated to a varying degree, the systems were still in single-phase liquid state as attested by their active dynamics.

  13. Studies of climate dynamics with innovative global-model simulations

    Science.gov (United States)

    Shi, Xiaoming

    Climate simulations with different degrees of idealization are essential for the development of our understanding of the climate system. Studies in this dissertation employ carefully designed global-model simulations for the goal of gaining theoretical and conceptual insights into some problems of climate dynamics. Firstly, global warming-induced changes in extreme precipitation are investigated using a global climate model with idealized geography. The precipitation changes over an idealized north-south mid-latitude mountain barrier at the western margin of an otherwise flat continent are studied. The intensity of the 40 most intense events on the western slopes increases by about ~4°C of surface warming. In contrast, the intensity of the top 40 events on the eastern mountain slopes increases at about ~6°C. This higher sensitivity is due to enhanced ascent during the eastern-slope events, which can be explained in terms of linear mountain-wave theory relating to global warming-induced changes in the upper-tropospheric static stability and the tropopause level. Dominated by different dynamical factors, changes in the intensity of extreme precipitation events over plains and oceans might differ from changes over mountains. So the response of extreme precipitation over mountains and flat areas are further compared using larger data sets of simulated extreme events over the two types of surfaces. It is found that the sensitivity of extreme precipitation to increases in global mean surface temperature is 3% per °C lower over mountains than over the oceans or the plains. The difference in sensitivity among these regions is not due to thermodynamic effects, but rather to differences between the gravity-wave dynamics governing vertical velocities over the mountains and the cyclone dynamics governing vertical motions over the oceans and plains. The strengthening of latent heating in the storms over oceans and plains leads to stronger ascent in the warming climate

  14. Neutron Scattering and Computer Simulation Studies of Ice Dynamics

    Institute of Scientific and Technical Information of China (English)

    DONG Shunle; YU Xinsheng

    2002-01-01

    In this article we describe a range of simulations (lattice dynamics and molecular dynamics) of the inelastic inco-herent neutron scattering spectra of ices (normal ice, ice Ⅱ and ice Ⅷ ). These simulations use a variety of different inter-molecular potentials from simple classic pair-wise (rigid and non-rigid molecule) potentials to sophisticated polarisable poten-tials. It was found that MCY makes stretching and bending interactions too weak while others do them well. We demon-strate that in order to reproduce the measured neutron spectrum, greater anisotropy (or orientational variation) is requiredthan these potentials presently provide.

  15. Simulation study and function analysis of the dynamic aortic valve

    Institute of Scientific and Technical Information of China (English)

    XIA Dongdong; BAI Jing

    2006-01-01

    The dynamic aortic valve (DAV) is a new left ventricular assist device, a micro-axial blood pump implemented at the position of the aortic valve, pumping blood from the left ventricle into the aortic artery. The present dynamic aortic valve operates at 7 different rotation speeds, ranging from 3000 r/min (speed 1) to 9000 r/min (speed 7). Because in vivo experiments need a lot of live animals and take a long period of time, modeling and simulation have been widely used to simulate and analyze hydra-dynamic property of the DAV and its assisting effects. With the measurements from the mock circulatory loop, a mathematic model of the DAV is established and embedded into the previously developed canine circulatory system. Using this model, the effect of the DAV on the failing heart at each rotation speed level is investigated. The vital cardiac variables are computed and compared with in vivo experimental results, which are in good agreement with an acceptable difference mostly 15 %. The establishment of the DAV model and its simulation are useful for further improvement of the DAV device.

  16. Thermophoresis in liquids: a molecular dynamics simulation study.

    Science.gov (United States)

    Han, Minsub

    2005-04-01

    Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.

  17. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study.

    Science.gov (United States)

    Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two

  18. 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

    We present a method to calculate 31P solid-state NMR spectra based on the dynamic input from extended molecular dynamics (MD) simulations. The dynamic information confered by MD simulations is much more comprehensive than the information provided by traditional NMR dynamics models based on......, 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...

  19. Dynamic rod worth simulation study for a sodium-cooled TRU burner

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Ji; Ha, Pham Nhu Viet, E-mail: phamha@kaeri.re.kr; Lee, Min Jae; Kang, Chang Mu

    2015-12-15

    Highlights: • Dynamic rod worth calculation methodology for a sodium-cooled TRU burner was developed. • The spatial weighting functions were relatively insensitive to control rods position. • The simulated pseudo detector response agreed well with the calculated core power. • The simulated dynamic rod worths compared well against the simulated static values. • Impact of individual detector on the simulated dynamic worth was evaluated. - Abstract: This paper presents a preliminary dynamic rod worth simulation study for a TRU burner core mockup of the PGSFR (Korean Prototype Gen-IV Sodium-cooled Fast Reactor) named BFS-76-1A so as to establish a calculation methodology for evaluating the rod worth of the PGSFR. The simulation method was mainly based on a three-dimensional multi-group nodal diffusion transient code for fast reactors in which the rod drop simulation for the BFS-76-1A was performed and all the fuel assemblies were taken into account for the detector response calculation. Then the dynamic rod worths were inferred from the simulated detector responses using an inverse point kinetics model and compared against the simulated static worths. The results show good agreement between the simulated pseudo detector response and the calculated core power as well as between the simulated dynamic and static rod worths, and thus indicate that the dynamic rod worth simulation method developed in this work can be applied to the rod worth estimation and validation for the PGSFR.

  20. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...... methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme...

  1. Virus capsid dissolution studied by microsecond molecular dynamics simulations.

    Science.gov (United States)

    Larsson, Daniel S D; Liljas, Lars; van der Spoel, David

    2012-01-01

    Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

  2. Interactions in charged colloidal suspensions: A molecular dynamics simulation study

    Science.gov (United States)

    Padidela, Uday Kumar; Behera, Raghu Nath

    2017-07-01

    Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

  3. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  4. A molecular dynamics simulation study of dynamic process and mesoscopic structure in liquid mixture systems

    Science.gov (United States)

    Yang, Peng

    The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results

  5. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  6. Virus capsid dissolution studied by microsecond molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Daniel S D Larsson

    Full Text Available Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

  7. The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations.

    Science.gov (United States)

    Grouleff, Julie; Irudayam, Sheeba Jem; Skeby, Katrine K; Schiøtt, Birgit

    2015-09-01

    The plasma membrane, which encapsulates human cells, is composed of a complex mixture of lipids and embedded proteins. Emerging knowledge points towards the lipids as having a regulating role in protein function. Furthermore, insight from protein crystallography has revealed several different types of lipids intimately bound to membrane proteins and peptides, hereby possibly pointing to a site of action for the observed regulation. Cholesterol is among the lipid membrane constituents most often observed to be co-crystallized with membrane proteins, and the cholesterol levels in cell membranes have been found to play an essential role in health and disease. Remarkably little is known about the mechanism of lipid regulation of membrane protein function in health as well as in disease. Herein, we review molecular dynamics simulation studies aimed at investigating the effect of cholesterol on membrane protein and peptide properties. This article is part of a Special Issue entitled: Lipid-protein interactions. Copyright © 2015. Published by Elsevier B.V.

  8. Optorsim: A Grid Simulator for Studying Dynamic Data Replication Strategies

    CERN Document Server

    Bell, William H; Millar, A Paul; Capozza, Luigi; Stockinger, Kurt; Zini, Floriano

    2003-01-01

    Computational grids process large, computationally intensive problems on small data sets. In contrast, data grids process large computational problems that in turn require evaluating, mining and producing large amounts of data. Replication, creating geographically disparate identical copies of data, is regarded as one of the major optimization techniques for reducing data access costs. In this paper, several replication algorithms are discussed. These algorithms were studied using the Grid simulator: OptorSim. OptorSim provides a modular framework within which optimization strategies can be studied under different Grid configurations. The goal is to explore the stability and transient behaviour of selected optimization techniques. We detail the design and implementation of OptorSim and analyze various replication algorithms based on different Grid workloads.

  9. Data Systems Dynamic Simulation - A total system for data system design assessments and trade studies

    Science.gov (United States)

    Hooper, J. W.; Rowe, D. W.

    1978-01-01

    Data Systems Dynamic Simulation is a simulation system designed to reduce cost and time and increase the confidence and comprehensiveness of Data Systems Simulation. It is designed to simulate large data processing and communications systems from end-to-end or by subsystem. Those features relevant to system timing, control, sizing, personnel support activities, cost and external influences are modeled. Emphasis is placed on ease of use, comprehensive system performance measures, and extensive post simulation analysis capability. The system has been used to support trade studies of the NASA data system needs in the 1985 to 1990 time frame.

  10. Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations

    Science.gov (United States)

    Zhu, Hong; Xiao, Shiyan; Liang, Haojun

    2013-01-01

    Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies. PMID:23951152

  11. Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Hong Zhu

    Full Text Available Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel G-quadruplex. A series of molecular dynamics (MD simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1 the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2 The TA base pair makes the adjacent G-quartet more stable than others. (3 For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4 The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5 For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0, as it has multiple conformations with similar free energies.

  12. Structure and Dynamics in Amphiphilic Bilayers: NMR and MD simulation Studies

    OpenAIRE

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations were employed to study molecular structure and dynamics in amphiphilic bilayers. This thesis reports on method development and practical applications to two types of bilayer systems: simple cell membrane models composed of phosphatidylcholine lipids and cholesterol; and liquid crystals composed of ethyleneoxide-based surfactants often used in technological applications and in fundamental studies ...

  13. Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies

    Science.gov (United States)

    Roccatano, Danilo

    2015-07-01

    The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.

  14. Dynamic characteristics of nanoindentation in Ni:A molecular dynamics simulation study

    Institute of Scientific and Technical Information of China (English)

    Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; S.A.Ahmad

    2012-01-01

    In this work,three-dimensional molecular dynamics simulation is carried out to elucidate the nanoindentation behaviour of single crystal Ni.The substrate indenter system is modelled using hybrid interatomic potentials including the manybody potential (embedded atom method) and two-body Morse potential.The spherical indenter is chosen,and the simulation is performed for different loading rates from 10 m/s to 200 m/s.Results show that the maximum indentation load and hardness of the system increase with the increase of velocity.The effect of indenter size on the nanoindentation response is also analysed.It is found that the maximum indentation load is higher for the large indenter whereas the hardness is higher for the smaller indenter.Dynamic nanoindentation is carried out to investigate the behaviour of Ni substrate to multiple loading-unloading cycles.It is observed from the results that the increase in the number of loading unloading cycles reduces the maximum load and hardness of the Ni substrate.This is attributed to the decrease in recovery force due to defects and dislocations produced after each indentation cycle.

  15. Study on Simulation Method of Pipeline Networks' Dynamic Characteristic in Hydraulic Manifold Block

    Institute of Scientific and Technical Information of China (English)

    CAO Yu-ning; TIAN Shu-jun; WANG Yong-an; GAO Yan-ming

    2008-01-01

    In the design of Hydraulic Manifold Blocks (HMB), dynamic performance of inner pipeline networks usually should be evaluated.To meet the design requirements, dynamic characteristic simulation is often needed.Based on comprehensive study on the existing simulation methods, a new method combined of Power Bond Graph(PBG) and Computational Fluid Dynamic (CFD) is proposed.In this method, flow field of typical channels inside HMB is analyzed with CFD to obtain the local resistance coefficients.Then, with these coefficients, a new sectional lumped-parameter model including kinetic friction factor is developed using PBG.A typical HMB design example is given and the comparison between the simulation and the experimental results demonstrates the feasibility and effectiveness of the proposed method.

  16. Dynamic Simulation in the Processing Industries: Case Studies from Mobil Experience

    Directory of Open Access Journals (Sweden)

    J.W. Womack

    1985-10-01

    Full Text Available This paper provides an overview of Mobil's recent use of dynamic simulation. It provides examples of applications to capital projects, to operator training, and to existing facilities. Techniques and methodology of dynamic simulation are considered. Desirable future developments for dynamic simulation software are discussed.

  17. Structure and dynamics of surfactant and hydrocarbon aggregates on graphite: a molecular dynamics simulation study.

    Science.gov (United States)

    Sammalkorpi, Maria; Panagiotopoulos, Athanassios Z; Haataja, Mikko

    2008-03-13

    We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.

  18. Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

    Science.gov (United States)

    Dhindsa, Gurpreet K.

    Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

  19. Clinical study and numerical simulation of brain cancer dynamics under radiotherapy

    Science.gov (United States)

    Nawrocki, S.; Zubik-Kowal, B.

    2015-05-01

    We perform a clinical and numerical study of the progression of brain cancer tumor growth dynamics coupled with the effects of radiotherapy. We obtained clinical data from a sample of brain cancer patients undergoing radiotherapy and compare it to our numerical simulations to a mathematical model of brain tumor cell population growth influenced by radiation treatment. We model how the body biologically receives a physically delivered dose of radiation to the affected tumorous area in the form of a generalized LQ model, modified to account for the conversion process of sublethal lesions into lethal lesions at high radiation doses. We obtain good agreement between our clinical data and our numerical simulations of brain cancer progression given by the mathematical model, which couples tumor growth dynamics and the effect of irradiation. The correlation, spanning a wide dataset, demonstrates the potential of the mathematical model to describe the dynamics of brain tumor growth influenced by radiotherapy.

  20. Dynamic simulation and experimental study of inspection robot for high-voltage transmission-line

    Institute of Scientific and Technical Information of China (English)

    XIAO Xiao-hui; WU Gong-ping; DU E; SHI Tie-lin

    2005-01-01

    A mobile robot developed by Wuhan University for full-path hotline inspection on 220 kV transmission lines was presented. With 4 rotating joints and 2 translational ones, such robot is capable of traveling along non-obstacle straight-line segment and surmounting straight-line segment obstacles as well as transferring between two spans automatically. Lagrange's equations were utilized to derive dynamic equations of all the links, including items of inertia, coupling inertia, Coriolis acceleration, centripetal acceleration and gravity. And a dynamic response experiment on elemental motions of robot prototype's travelling along non-obstacle straight-line segment and surmounting obstacles was performed on 220 kV 1∶1 simulative overhanging transmission-line in laboratory. In addition, dynamic numerical simulation was conducted in the corresponding condition. Comparison and analysis on results of experiment and numerical simulation have validated theoretical model and simulation resolution. Therefore, the dynamic model formed hereunder can be used for the study of robot control.

  1. Simulation study of coal mine safety investment based on system dynamics

    Institute of Scientific and Technical Information of China (English)

    Tong Lei; Dou Yuanyuan

    2014-01-01

    To generate dynamic planning for coal mine safety investment, this study applies system dynamics to decision-making, classifying safety investments by accident type. It validates the relationship between safety investments and accident cost, by structurally analyzing the causality between safety investments and their influence factors. Our simulation model, based on Vensim software, conducts simulation anal-ysis on a series of actual data from a coalmine in Shanxi Province. Our results indicate a lag phase in safety investments, and that increasing pre-phase safety investment reduces accident costs. We found that a 24%increase in initial safety investment could help reach the target accident costs level 14 months earlier. Our simulation test included nine kinds of variation trends of accident costs brought by different investment ratios on accident prevention. We found an optimized ratio of accident prevention invest-ments allowing a mine to reach accident cost goals 4 months earlier, without changing its total investment.

  2. Conformation of Randomly Sulfonated Pentablock Ionomers in Dilute Solution: Molecular Dynamic Simulation Study

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

    2011-03-01

    As part of our efforts to define the factors that control the structure and dynamics of structures ionic polymers, the conformation of a pentablock copolymer that consists of randomly sulfonated polystyrene, an ionomeric block, bound to poly-ethylene-r-propylene end caped by poly-t-butylstyrene has been studied in dilute solutions using molecular dynamic simulations. Multi-block copolymers offer a means to tailor several properties into one molecule, taking advantage of their rich phase diagram together with unique properties of specific blocks. We varied the solvent quality for the different blocks and followed the changes in conformation. The spatial configuration of the pentablock as well as the dynamics of the polymer was studied. We find that, independent on the solvent, the higher the sulfonation level, the lower Rg . The static and dynamic structure factors were calculated and compared in an implicit poor solvent, water and a common solvent. These data are compared with results obtained from neutron scattering.

  3. NUMERICAL SIMULATION BY COMPUTATIONAL FLUID DYNAMICS AND EXPERIMENTAL STUDY ON STIRRED BIOREACTOR WITH PUNCHED IMPELLER

    Institute of Scientific and Technical Information of China (English)

    WANG Yu; HE Pingting; YE Hong; XIN Zhihong

    2007-01-01

    Instantaneous flow field and temperature field of the two-phase fluid are measured by particle image velocimetry (PIV) and steady state method during the state of onflow. A turbulent two-phase fluid model of stirred bioreactor with punched impeller is established by the computational fluid dynamics (CFD), using a rotating coordinate system and sliding mesh to describe the relative motion between impeller and baffles. The simulation and experiment results of flow and temperature field prove their warps are less than 10% and the mathematic model can well simulate the fields, which will also provide the study on optimized-design and scale-up of bioreactors with reference value.

  4. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  5. Molecular Dynamics Simulation Study on the Carbon Nanotube Interacting with a Polymer

    Energy Technology Data Exchange (ETDEWEB)

    Saha, Leton C.; Mian, Shabeer A.; Jang, Joon Kyung [Pusan National University, Busan (Korea, Republic of)

    2012-03-15

    Using molecular dynamics simulation method, we studied the carbon nanotube (CNT) non-covalently interacting with a polymer. As the polymer coiled around the CNT, the diameter of CNT deformed by more than 40% of its original value within 50 ps. By considering three different polymers, we conclude that the interaction between the CNT and polymer is governed by the number of repeating units in the polymer, not by the molecular weight of polymer

  6. Laser Induced C60 Cage Opening Studied by Semiclassical Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Yusheng Dou

    2011-01-01

    Full Text Available Laser induced opening of the C60 cage is studied by a semiclassical electron-radiation-ion dynamics technique. The simulation results indicate that the C60 cage is abruptly opened immediately after laser excitation. The opening of the C60 cage induces a quick increase in kinetic energy and a sharp decrease in electronic energy, suggesting that the breaking of the C60 cage efficiently heats up the cluster and enhances the thermal fragmentation of C60 fullerene.

  7. Interactive Dynamic-System Simulation

    CERN Document Server

    Korn, Granino A

    2010-01-01

    Showing you how to use personal computers for modeling and simulation, Interactive Dynamic-System Simulation, Second Edition provides a practical tutorial on interactive dynamic-system modeling and simulation. It discusses how to effectively simulate dynamical systems, such as aerospace vehicles, power plants, chemical processes, control systems, and physiological systems. Written by a pioneer in simulation, the book introduces dynamic-system models and explains how software for solving differential equations works. After demonstrating real simulation programs with simple examples, the author

  8. Molecular dynamics simulation study on behaviors of liquid 1,2-dichioroethane under external electric fields

    Institute of Scientific and Technical Information of China (English)

    杜志强; 陈正隆

    2003-01-01

    Molecular dynamics simulation was carried out to study the behavior of liquid 1,2-dichloroethane molecules under external electric fields including direct current field, alternating current field and positive-half-period cosin field. The maximum applied field strength was 108 V/m , the maximum frequency of the alternating current field and that of the positive-half-period cosine field was 1012 Hz . The simulation revealed that the field type and field strength act on the population of the molecular configuration. In the strong direct current field, all trans forms converted completely into gauche forms. Order parameter and the correlation of the system torsion angle were also investigated. The results suggested that these two dynamical parameters depended also on the field type and the field strength. The maximum of order parameter was found to be at 0.6in the strong direct current field.

  9. Molecular dynamics simulation study on behaviors of liquid 1,2-dichloroethane under external electric fields

    Institute of Scientific and Technical Information of China (English)

    杜志强; 陈正隆

    2003-01-01

    Molecular dynamics simulation was carried out to study the behavior of liquid 1,2-dichloroethane molecules under external electric fields including direct current field, alternating current field and positive-half-period cosin field. The maximum applied field strength was 108 V/m , the maximum frequency of the alternating current field and that of the positive-half-period cosine field was 1012 Hz .The simulation revealed that the field type and field strength act on the population of the molecular configuration. In the strong direct current field, all trans forms converted completely into gauche forms. Order parameter and the correlation of the system torsion angle were also investigated. The results suggested that these two dynamical parameters depended also on the field type and the field strength. The maximum of order parameter was found to be at 0.6 in the strong direct current field.

  10. Thermal expansion coefficient of graphene using molecular dynamics simulation: A comparative study on potential functions

    Science.gov (United States)

    Ghasemi, Hamid; Rajabpour, Ali

    2017-01-01

    In this paper, we studied the thermal expansion coefficient (TEC) of pristine graphene sheets (GSs) using molecular dynamics (MD) simulation. We validated our model with previous studies employing AIREBO potential function and repeated the same simulation with the optimized Tersoff potential function. We also discussed the differences of the results and the corresponding reasons: evaluating the negative TEC of graphene by measuring the C-C bond length and out-of-plane vibrations of the GS. We finally showed that the ripples and wrinkles are more represented over the GS during the simulation with the AIREBO potential function rather than the optimized Tersoff. Comparing the results of both potential functions; it is seen that the results obtained by AIREBO potential function are in better agreement with those reported by previous scholars.

  11. Dynamical Simulation of Probabilities

    Science.gov (United States)

    Zak, Michail

    1996-01-01

    It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices(such as random number generators). Self-orgainizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed. Special attention was focused upon coupled stochastic processes, defined in terms of conditional probabilities, for which joint probability does not exist. Simulations of quantum probabilities are also discussed.

  12. Application of molecular dynamic simulation to study food proteins: A review.

    Science.gov (United States)

    Singh, Ashutosh; Vanga, Sai Kranthi; Orsat, Valerie; Raghavan, Vijaya

    2017-07-19

    This review presents an overview of the application of molecular dynamic simulation to study food proteins. Processing of food using thermal, chemical, radiation, electromagnetic, and mechanical techniques is subject to its macromolecular bio-components such as carbohydrates and proteins to extreme heat, ionic strength, pH, and mechanical deformation. These processing factors affect protein's functional properties such as emulsification, dough formation, gelation, etc., which are associated with changes in their structure. It is difficult to study the structural changes of protein during processing using standard methods like Circular dichroism, Nuclear Magnetic Resonance (NMR), and X-ray diffraction. Hence, in this manuscript application of molecular dynamic simulation to visualize and analyze the protein dynamics during processing has been evaluated. Effect of external stresses such as hydration, temperature, and electric field on protein structure have been analyzed and related mechanisms are explained. The response of food proteins to these stresses demonstrated that it is necessary to gain insight into protein dynamics to be able to develop novel and/or modify existing food processing techniques to improve the overall nutritional and organoleptic qualities of processed food products.

  13. Molecular dynamics simulation study of the melting of Pd-Pt nanoclusters

    Science.gov (United States)

    Sankaranarayanan, Subramanian K. R. S.; Bhethanabotla, Venkat R.; Joseph, Babu

    2005-05-01

    Bimetallic nanoclusters are of interest because of their utility in catalysis and sensors. The thermal characteristics of bimetallic Pt-Pd nanoclusters of different sizes and compositions were investigated through molecular dynamics simulations using quantum Sutton-Chen (QSC) many-body potentials. Monte Carlo simulations employing the bond order simulation model were used to generate minimum energy configurations, which were utilized as the starting point for molecular dynamics simulations. The calculated initial configurations of the Pt-Pd system consisted of surface segregated Pd atoms and a Pt-rich core. Melting characteristics were studied by following the changes in potential energy and heat capacity as functions of temperature. Structural changes accompanying the thermal evolution were studied by the bond order parameter method. The Pt-Pd clusters exhibited a two-stage melting: surface melting of the external Pd atoms followed by homogeneous melting of the Pt core. These transitions were found to depend on the composition and size of the nanocluster. Melting temperatures of the nanoclusters were found to be much lower than those of bulk Pt and Pd. Bulk melting temperatures of Pd and Pt simulated using periodic boundary conditions compare well with experimental values, thus providing justification for the use of QSC potentials in these simulations. Deformation parameters were calculated to characterize the structural evolution resulting from diffusion of Pd and Pt atoms. The results indicate that in Pd-Pt clusters, Pd atoms prefer to remain at the surface even after melting. In addition, Pt also tends to diffuse to the surface after melting due to reduction of its surface energy with temperature. This mixing pattern is different from those reported in some of the earlier studies on melting of bimetallics.

  14. Dynamic stochastic simulation as a tool for studying bovine virus diarrhoea virus infections at the herd level

    DEFF Research Database (Denmark)

    Sørensen, J.T.; Enevoldsen, Carsten

    1994-01-01

    Infectious diseases, such as bovine virus diarrhoea (BVD) virus infections in cattle, are often studied by Markov chain models. However, it is difficult to simulate dynamic interactions between production of a reproductive herd and the disease by this type of model. As an alternative, a dynamic...... stochastic model simulating the herd production was suggested. A dynamic stochastic model simulating the effect of BVD virus infection in a dairy cattle herd was used to exemplify how this type of model could be applied in research. The simulation example demonstrated that the effect of a BVD virus infection...

  15. Insights into pharmaceutical nanocrystal dissolution: a molecular dynamics simulation study on aspirin.

    Science.gov (United States)

    Greiner, Maximilian; Elts, Ekaterina; Briesen, Heiko

    2014-09-02

    The presented molecular dynamics simulations are the first simulations to reveal dynamic dissolution of a pharmaceutical crystal in its experimentally determined shape. Continuous dissolution at constant undersaturation of the surrounding medium is ensured by introducing a plane of sticky dummy atoms into the water slab. These atoms have a strong interaction potential with dissolved aspirin molecules, but interactions with water are excluded from the calculations. Thus, the number of aspirin molecules diffusing freely in solution is kept at a low value and continuous dissolution of the aspirin crystal is monitored. Further insight into face-specific dissolution is drawn. The dissolution mechanism of receding edges is found for the (001) plane. These findings are in good agreement with experimental results. While the proposed dissolution mechanism for the (100) plane is terrace sinking on a rough surface, no pronounced dissolution of the perfectly flat face is seen in the present work. Molecular simulations of pharmaceuticals in their experimentally obtained structure therefore have shown to be especially suited for the investigation of dissolving faces, where the edges have a pronounced effect. In contrast to previous studies a propagation of the dissolution front into the crystal face is reported, and the crystal bulk is stable over the whole simulation time of 150 ns.

  16. 27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

    Science.gov (United States)

    DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

  17. Dynamic simulation of color blindness for studying color vision requirements in practice

    NARCIS (Netherlands)

    Lucassen, M.P.; Alferdinck, J.W.A.M.

    2006-01-01

    We report on a dynamic simulation of defective color vision. Using an RGB video camera connected to a PC or laptop, the captured and displayed RGB colors are translated by our software into modified RGB values that simulate the color appearance of a person with a color deficiency. Usually, the simul

  18. Dynamic simulation of color blindness for studying color vision requirements in practice

    NARCIS (Netherlands)

    Lucassen, M.P.; Alferdinck, J.W.A.M.

    2006-01-01

    We report on a dynamic simulation of defective color vision. Using an RGB video camera connected to a PC or laptop, the captured and displayed RGB colors are translated by our software into modified RGB values that simulate the color appearance of a person with a color deficiency. Usually, the simul

  19. Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    S. Tolosa

    2013-01-01

    Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

  20. Simulation Study of AC Contactor Dynamic Contacts Contact Pressure Based on ADAMS

    Directory of Open Access Journals (Sweden)

    Gu Yungao

    2015-01-01

    Full Text Available A multi-body dynamics simulation model of CJ20-25 AC contactor was established with Pro/E(Pro/Engineerin this paper. A coupling simulation with machine, electric, magnetic on the contactor has been achieved in this model. Dynamic parameters which were called use the secondary development technology of ADAMS. The dynamic contact pressure signal of an AC contactor was obtained with ADAMS’s own simultaneous solution such as electromagnetic suction, kinematics and dynamics equations. The simulation results and actual measurement of contactor contact pressure signals are very similar. However, the complexity of the measured contacts vibration is greater than the simulation results because the actual working condition is more complex. This result provides a theoretical foundation to the dynamic contacts contact pressure test.

  1. A two-dimensional global simulation study of inductive-dynamic magnetosphere-ionosphere coupling

    Science.gov (United States)

    Tu, Jiannan; Song, Paul

    2016-12-01

    We present the numerical methods and results of a global two-dimensional multifluid-collisional-Hall magnetohydrodynamic (MHD) simulation model of the ionosphere-thermosphere system, an extension of our one-dimensional three-fluid MHD model. The model solves, self-consistently, Maxwell's equations, continuity, momentum, and energy equations for multiple ion and neutral species incorporating photochemistry, collisions among the electron, ion and neutral species, and various heating sources in the energy equations. The inductive-dynamic approach (solving self-consistently Faraday's law and retaining inertia terms in the plasma momentum equations) used in the model retains all possible MHD waves, thus providing faithful physical explanation (not merely description) of the magnetosphere-ionosphere/thermosphere (M-IT) coupling. In the present study, we simulate the dawn-dusk cross-polar cap dynamic responses of the ionosphere to imposed magnetospheric convection. It is shown that the convection velocity at the top boundary launches velocity, magnetic, and electric perturbations propagating with the Alfvén speed toward the bottom of the ionosphere. Within the system, the waves experience reflection, penetration, and rereflection because of the inhomogeneity of the plasma conditions. The reflection of the Alfvén waves may cause overshoot (stronger than the imposed magnetospheric convection) of the plasma velocity in some regions. The simulation demonstrates dynamic propagation of the field-aligned currents and ionospheric electric field carried by the Alfvén waves, as well as formation of closure horizontal currents (Pedersen currents in the E region), indicating that in the dynamic stage the M-I coupling is via the Alfvén waves instead of field-aligned currents or electric field mapping as described in convectional M-I coupling models.

  2. Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

    Directory of Open Access Journals (Sweden)

    Vijayan ManickamAchari

    Full Text Available The rational design of a glycolipid application (e.g. drug delivery with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20% in the hydrophobic region of the lamellar crystal (LC phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

  3. Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation.

    Science.gov (United States)

    Busselez, Rémi; Cerclier, Carole V; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

    2014-10-07

    A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.

  4. Stability of the beta-sheet of the WW domain: A molecular dynamics simulation study.

    Science.gov (United States)

    Ibragimova, G T; Wade, R C

    1999-10-01

    The WW domain consists of approximately 40 residues, has no disulfide bridges, and forms a three-stranded antiparallel beta-sheet that is monomeric in solution. It thus provides a model system for studying beta-sheet stability in native proteins. We performed molecular dynamics simulations of two WW domains, YAP65 and FBP28, with very different stability characteristics, in order to explore the initial unfolding of the beta-sheet. The less stable YAP domain is much more sensitive to simulation conditions than the FBP domain. Under standard simulation conditions in water (with or without charge-balancing counterions) at 300 K, the beta-sheet of the YAP WW domain disintegrated at early stages of the simulations. Disintegration commenced with the breakage of a hydrogen bond between the second and third strands of the beta-sheet due to an anticorrelated transition of the Tyr-28 psi and Phe-29 phi angles. Electrostatic interactions play a role in this event, and the YAP WW domain structure is more stable when simulated with a complete explicit model of the surrounding ionic strength. Other factors affecting stability of the beta-sheet are side-chain packing, the conformational entropy of the flexible chain termini, and the binding of cognate peptide.

  5. Effect of cadence regulation on muscle activation patterns during robot assisted gait: a dynamic simulation study.

    Science.gov (United States)

    Hussain, Shahid; Xie, Sheng Q; Jamwal, Prashant K

    2013-03-01

    Cadence or stride frequency is an important parameter being controlled in gait training of neurologically impaired subjects. The aim of this study was to examine the effects of cadence variation on muscle activation patterns during robot assisted unimpaired gait using dynamic simulations. A twodimensional (2-D) musculoskeletal model of human gait was developed considering eight major muscle groups along with existing ground contact force (GCF) model. A 2-D model of a robotic orthosis was also developed which provides actuation to the hip, knee and ankle joints in the sagittal plane to guide subjects limbs on reference trajectories. A custom inverse dynamics algorithm was used along with a quadratic minimization algorithm to obtain a feasible set of muscle activation patterns. Predicted patterns of muscle activations during slow, natural and fast cadence were compared and the mean muscle activations were found to be increasing with an increase in cadence. The proposed dynamic simulation provide important insight into the muscle activation variations with change in cadence during robot assisted gait and provide the basis for investigating the influence of cadence regulation on neuromuscular parameters of interest during robot assisted gait.

  6. Study of procaine and tetracaine in the lipid bilayer using molecular dynamics simulation.

    Science.gov (United States)

    Jalili, Seifollah; Saeedi, Marzieh

    2017-04-01

    Despite available experimental results, the molecular mechanism of action of local anesthetics upon the nervous system and contribution of the cell membrane to the process are still controversial. In this work, molecular dynamics simulations were performed to investigate the effect of two clinically used local anesthetics, procaine and tetracaine, on the structure and dynamics of a fully hydrated dimyristoylphosphatidylcholine lipid bilayer. We focused on comparing the main effects of uncharged and charged drugs on various properties of the lipid membrane: mass density distribution, diffusion coefficient, order parameter, radial distribution function, hydrogen bonding, electrostatic potential, headgroup angle, and water dipole orientation. To compare the diffusive nature of anesthetic through the lipid membrane quantitatively, we investigated the hexadecane/water partition coefficient using expanded ensemble simulation. We predicted the permeability coefficient of anesthetics in the following order: uncharged tetracaine > uncharged procaine > charged tetracaine > charged procaine. We also shown that the charged forms of drugs are more potent in hydrogen bonding, disturbing the lipid headgroups, changing the orientation of water dipoles, and increasing the headgroup electrostatic potential more than uncharged drugs, while the uncharged drugs make the lipid diffusion faster and increase the tail order parameter. The results of these simulation studies suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which provides new insights into their molecular mechanism.

  7. Molecular dynamics simulation study of meso-confined propane in TiO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Gautam, Siddharth, E-mail: gautam.25@osu.edu; Cole, David

    2015-09-08

    Highlights: • Structure and dynamics of propane in a TiO{sub 2} is studied at different loadings. • Propane molecules show a tendency to form sequential layers near pore walls. • Three different regimes of translational motion can be identified. • Layering of propane has important consequences on loading dependence of dynamics. • Propane molecules exhibit very fast free rotation followed by rotational diffusion. - Abstract: We report the structural and dynamical properties of propane confined in mesoporous TiO{sub 2}, studied using MD simulations. Results indicate that the propane molecules have a tendency to be adsorbed at the pore walls forming sequential layers. Three different regimes of translational motion can be identified which correspond to motion at different time scales accessible to different experimental probes. The variation of the dynamical behavior with loading differs for different regimes and the trend for one of these is consistent with that obtained in recent neutron scattering experiments on propane in mesoporous TiO{sub 2} and silica aerogel. The rotational motion of propane molecules confined in the pore exhibits a very fast free rotation at short times which is followed by isotropic rotational diffusion. This work provides an explanation to the counterintuitive observations of an enhancement in the diffusivity with an increased loading of confined propane in recent neutron scattering experiments.

  8. Guest-Host Interaction Study in Clathrate Hydrates Using Lattice Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    Maofeng Jing; Shunle Dong

    2005-01-01

    Lattice dynamics simulation of several gas hydrates (helium, argon, and methane) with different occupancy rates has been performed using TIP3P potential model. Results show that the coupling between the guest and host is not simple as depicted by the conventional viewpoints. For clathrate hydrate enclosing small guest, the small cages are dominantly responsible for the thermodynamic stability of clathrate hydrates. And the spectrum of methane hydrate is studied compared with argon hydrate,then as a result, shrink effect from positive hydrogen shell is proposed.

  9. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Science.gov (United States)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  10. Stability of the beta-sheet of the WW domain: A molecular dynamics simulation study.

    OpenAIRE

    Ibragimova, G T; Wade, R C

    1999-01-01

    The WW domain consists of approximately 40 residues, has no disulfide bridges, and forms a three-stranded antiparallel beta-sheet that is monomeric in solution. It thus provides a model system for studying beta-sheet stability in native proteins. We performed molecular dynamics simulations of two WW domains, YAP65 and FBP28, with very different stability characteristics, in order to explore the initial unfolding of the beta-sheet. The less stable YAP domain is much more sensitive to simulatio...

  11. Molecular Dynamics Simulation Studies on the Cooling Process of Polyvinyl Chloride

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    By means of molecular dynamics simulation, the transition of the conformations of polyvinyl chloride during a cooling process from 600 to 300 K was studied. The results show that the amorphous polyvinyl chloride chain experiences the melting state, elastic state and glass state and the conformations can be characterized by the increases of the trans-state of C-C-C-C and the near gauche-state of C-C-C-Cl with the decrease of temperature. It is found that the transition of the conformations is driven mainly by the Coulomb interaction between chain segments.

  12. The simulation of occasional road disturbances for studying mobile vehicles dynamics

    Directory of Open Access Journals (Sweden)

    T.A. Alexeeva

    2015-06-01

    Full Text Available This paper presents a procedure for simulating random road disturbances based on the method of non-canonically decomposing random functions in the form of deterministic functions depending on just three random quantities under any probability distribution law. The mathematical methods developed for modeling random road disturbances give an accurate representation of the random function perturbations in the framework of the correlation theory using just three random variables. The proposed approach allows to obtain more reliable data on the spectral composition of the microrelief, to simplify the study of the dynamics of mobile vehicles and reduce the amount of computation in comparison with other methods.

  13. Structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry and molecular dynamics simulations.

    Science.gov (United States)

    Borysik, Antoni J

    2015-09-01

    The structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry (IMS) and vacuum molecular dynamics (MD) simulations is reported. Direct evidence is provided for the ability of the surfactant dodecyl-β-D-maltoside (DDM) to prevent charge-induced unfolding of the membrane protein (PagP) in the gas-phase. Restraints obtained by IMS are used to map the surfactant positions onto the protein surface. Surfactants occupying more exposed positions at the apexes of the β-barrel structure are most in-line with the experimental observations. MD simulations provide additional evidence for this assembly organization through surfactant inversion and migration on the protein structure in the absence of solvent. Surfactant migration entails a net shift from apolar membrane spanning regions to more polar regions of the protein structure with the DDM molecule remaining attached to the protein via headgroup interactions. These data provide evidence for the role of protein-DDM headgroup interactions in stabilizing membrane protein structure from gas-phase unfolding.

  14. Ab initio simulations and neutron scattering studies of structure and dynamics in PdH

    CERN Document Server

    Totolici, I E

    2001-01-01

    The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...

  15. Structural and Dynamic Characterization of Mutated Keap1 for Varied Affinity toward Nrf2: A Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Cheng, I-Chung; Chen, Ya-Jyun; Ku, Chia-Wei; Huang, Yu-Wen; Yang, Chia-Ning

    2015-10-26

    Keap1 is an adaptor protein that regulates Nrf2 in response to oxidative stress. Under basal conditions, Nrf2 is negatively regulated through ubiquitination by Keap1. However, upon exposure to oxidative stress, the ubiquitination of Nrf2 is inhibited, resulting in an increased steady-state level of Nrf2 in the nucleus and increased transcription of cytoprotective genes. A gene variant G364C and somatic mutation G430C on Keap1 have recently been reported to substantially impair the Keap1-Nrf2 interaction and to be associated with lung cancer. By contrast, alanine scanning experiments have shown that the mutations S363A, S508A, S555A, and S602A do not affect the ability of Keap1 to bind to Nrf2, regardless of the fact that G364 and G430 are not in contact with Nrf2 whereas the four serine residues are involved in the accommodation of Nrf2 with their hydroxy groups. In this study, molecular dynamics simulations were performed to investigate the structural and dynamic variances among wild-type (WT) Keap1 and the six mutants in unbound form. Principal component analysis of the collected MD trajectories was performed to provide dynamic diversity. Our dynamic and structural observations suggest that the G364C and G430C mutants possess a mobile D385 that moves toward R380, an anchor residue to accommodate an acidic residue in Nrf2, thereby hampering the Keap1-Nrf2 recognition of an electrostatic nature. By contrast, none of the four serine-to-alanine mutants alters the H-bond network formed by the serine backbone to its partner; accordingly, these mutants are almost as intact as the WT structurally and dynamically.

  16. GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

    Science.gov (United States)

    Sunarso, Alfeus; Tsuji, Tomohiro; Chono, Shigeomi

    2010-08-01

    We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.

  17. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

  18. Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

    Science.gov (United States)

    Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.

    2016-12-01

    Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

  19. High density gas state at water/graphite interface studied by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Chun-Lei; Li Zhao-Xia; Li Jing-Yuan; Xiu Peng; Hu Jun; Fang Hai-Ping

    2008-01-01

    In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results: gas films (pancake-like) for a larger ratio and nanobubbles for a Smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film (pancake-like) and nanobubbles.

  20. Carbonization in polyacrylonitrile (PAN) based carbon fibers studied by ReaxFF molecular dynamics simulations.

    Science.gov (United States)

    Saha, Biswajit; Schatz, George C

    2012-04-19

    The carbonization mechanism in polyacrylonitrile (PAN) based carbon nanofibers is studied using ReaxFF molecular dynamics simulations. Simulations are performed at two carbonization temperatures, 2500 and 2800 K, and also at two densities, 1.6 and 2.1 g/cm(3), that are relevant to the experimental carbonization conditions. The results are analyzed by examining the evolution of species with time, including carbon-only ring structures and gaseous species. Formation mechanisms are proposed for species like N(2), H(2), NH(3), and HCN and five-, six-, and seven-membered carbon-only rings, along with polycyclic structures. Interestingly, the formation of five-membered rings follows N(2) formation and usually occurs as a precursor to six-membered rings. Elimination mechanisms for the gaseous molecules are found that are in agreement with previously proposed mechanisms; however, alternative mechanisms are also proposed.

  1. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    Directory of Open Access Journals (Sweden)

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  2. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    CERN Document Server

    Bhuiyan, G M; González, D J; 10.5488/CMP.15.33604

    2012-01-01

    Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  3. Computer simulation studies on passive recruitment dynamics of lipids induced by the adsorption of charged nanoparticles.

    Science.gov (United States)

    Li, Yang

    2014-07-07

    The recruitment dynamics of lipids in the biomembrane is believed to play an important role in a variety of cellular processes. In this work, we investigate the nanoparticle-induced recruitment dynamics of lipids in the heterogeneous phospholipid bilayers of distearoyl-phosphatidylcholine (DSPC) and dioleoyl-phosphatidylglycerol (DOPG) via coarse-grained molecular dynamics simulations. Three dynamic modes of individual charged DOPG lipid molecules have been taken into account in the recruitment process: lateral diffusion, protrusions, and flip-flops. Based on analysis of the mobility pattern of lipids, structural variations in the membrane as well as activation energy of the structure of lipid eyelids characterized by the potential of mean force, we have concluded that the electrostatic attraction of nanoparticles plays a crucial role in the recruitment process of lipids in phospholipid bilayers. These studies are consistent with experimental observations and to some extent give insight into the origin of some cellular processes such as signaling, formation of lipid rafts, and endocytosis.

  4. Dynamical properties of alcohol + 1-hexyl-3-methylimidazolium ionic liquid mixtures: a computer simulation study.

    Science.gov (United States)

    Méndez-Morales, Trinidad; Carrete, Jesús; García, Manuel; Cabeza, Oscar; Gallego, Luis J; Varela, Luis M

    2011-12-29

    In this work, extensive molecular dynamics simulations of the dynamics of mixtures of ionic liquids (ILs) composed of the cation 1-hexyl-3-methylimidazolium and several anions of different hydrophobicity degrees (Cl(-), BF(4)(-), PF(6)(-)) with alcohols of different chain lengths (methanol and ethanol) are reported. We evaluated the influence of the nature of the anion, the length of the molecular chain of the alcohol, and the alcohol concentration on some dynamical properties of the mixtures, such as self-diffusion coefficients of all the species, mean square displacements (with an analysis of both ballistic and diffusive regimes), and velocity autocorrelation functions of alcohol molecules. The diffusivity of the mixtures was found to be highly dependent on the nature of the anion since the interaction between chloride and alcohols is greater than that with fluorinated anions and leads to slower dynamics. Additionally, our results show that self-diffusion coefficients increase with alcohol concentration. On the other hand, a subdiffusive regime over thousands of picoseconds was detected at intermediate times through analysis of the center-of-mass mean square displacements of alcohol molecules, a region that becomes narrower as alcohol concentration increases. Finally, the study of the role of the anion and of solvent concentration on velocity autocorrelation functions reflects an increase in mean collision times as the amount of alcohol increases until the value of pure alcohols is reached. These collision times are smaller in mixtures with halogenated ILs. © 2011 American Chemical Society

  5. Molecular dynamics simulation study of friction force and torque on a rough spherical particle.

    Science.gov (United States)

    Kohale, Swapnil C; Khare, Rajesh

    2010-06-21

    Recent developments in techniques of micro- and nanofluidics have led to an increased interest in nanoscale hydrodynamics in confined geometries. In our previous study [S. C. Kohale and R. Khare, J. Chem. Phys. 129, 164706 (2008)], we analyzed the friction force experienced by a smooth spherical particle that is translating in a fluid confined between parallel plates. The magnitude of three effects--velocity slip at particle surface, the presence of confining surfaces, and the cooperative hydrodynamic interactions between periodic images of the moving particle--that determine the friction force was quantified in that work using molecular dynamics simulations. In this work, we have studied the motion of a rough spherical particle in a confined geometry. Specifically, the friction force experienced by a translating particle and the torque experienced by a rotating particle are studied using molecular dynamics simulations. Our results demonstrate that the surface roughness of the particle significantly reduces the slip at the particle surface, thus leading to higher values of the friction force and hence a better agreement with the continuum predictions. The particle size dependence of the friction force and the torque values is shown to be consistent with the expectations from the continuum theory. As was observed for the smooth sphere, the cooperative hydrodynamic interactions between the images of the sphere have a significant effect on the value of the friction force experienced by the translating sphere. On the other hand, the torque experienced by a spherical particle that is rotating at the channel center is insensitive to this effect.

  6. Vacancy profile in reverse osmosis membranes studied by positron annihilation lifetime measurements and molecular dynamics simulations

    Science.gov (United States)

    Shimazu, A.; Goto, H.; Shintani, T.; Hirose, M.; Suzuki, R.; Kobayashi, Y.

    2013-06-01

    The positron annihilation technique using a slow positron beam can be used for the study of the vacancy profiles in typical reverse osmosis (RO) membranes. In this study, the vacancy profile in the polyamide membrane that exhibits a high permselectivity between ions and water was studied using the positron annihilation technique and molecular dynamics simulations. Ortho-positronium (o-Ps) lifetimes in the surface region of the membranes were evaluated by using a slow positron beam. The diffusion behavior of Na+ and water in the polyamides was simulated by molecular dynamics (MD) methods using the TSUBAME2 supercomputer at the Tokyo Institute of Technology and discussed with the vacancy profile probed by the o-Ps. The results suggested that the large hydration size of Na+ compared to the vacancy size in the polyamides contributes to the increased diffusivity selectivity of water/Na+ that is related to the NaCl desalination performance of the membrane. Both the hydration size of the ions and the vacancy size appeared to be significant parameters to discuss the diffusivity selectivity of water/ions in typical polyamide membranes.

  7. Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides.

    Science.gov (United States)

    Chin, Stacy L; Lu, Qing; Dane, Eric L; Dominguez, Laura; McKnight, Christopher J; Straub, John E; Grinstaff, Mark W

    2016-05-25

    Poly-amido-saccharides (PAS) are carbohydrate-based, enantiopure synthetic polymers in which sugar repeat units are joined by amide linkages. This unique and relatively rigid pyranose backbone contributes to their defined helical secondary structure and remarkable chemical properties. Glucose- (glc-) and galactose- (gal-) PAS 10-mer structures are synthesized and investigated with molecular dynamics (MD) simulations and experimental measurements. Quantum mechanical DFT energy minimization calculations, as well as experimental observables including circular dichroism, (1)H,(13)C-HSQC, and (1)H,(1)H-NOESY 2D-NMR studies, validated the all-atom simulation models produced using a modified CHARMM force field. Water radial distribution functions show distinct differences in the glc- and gal-PAS systems that correlate well with observed differences in solubility between gal-PASs and glc-PASs. The computational analysis and MD simulations are in good agreement with experimental results, validating the proposed models as reliable representations of novel glc- and gal-PASs.

  8. Growth of single-walled gold nanotubes confined in carbon nanotubes, studied by molecular dynamics simulations

    Science.gov (United States)

    Han, Yang; Hu, Ting; Dong, Jinming

    2013-01-01

    Growth of the single-walled gold nanotube (SWGNT), confined in the single-walled carbon nanotube (SWCNT) has been studied by using the classical molecular dynamics (MD) simulations, in which two different empirical potentials (the glue and EAM potentials) are used for the interaction between gold atoms. It is found that under the glue potential, three new SWGNTs, (3, 2), (4, 2) and (6, 3) gold tubes can be formed, in addition to the previously found (3, 3), (4, 3) and (5, 3) ones, among which two achiral ones, (4, 2) and (6, 3) gold tubes are particularly interesting because they were thought to be not the tube-like structures, or to have large enough diameter, permitting an extra gold atom chain in it. However, when the EAM potential is used, only four SWGNTs, i.e., (3, 2), (4, 2), (4, 3) and (5, 3) gold tubes could be formed in our MD simulations. After comparing all the MD simulation results with those of the first principles calculations, it is found that the EAM potential is better to describe the interaction between gold atoms than the glue potential for the MD simulation on the growth of gold tubular structure in confined CNT.

  9. Planarization process of single crystalline silicon asperity under abrasive rolling effect studied by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Si, Lina [Tsinghua University, State Key Laboratory of Tribology, Beijing (China); Beijing Institute of Technology, School of Mechanical Engineering, Beijing (China); Guo, Dan; Luo, Jianbin; Xie, Guoxin [Tsinghua University, State Key Laboratory of Tribology, Beijing (China)

    2012-10-15

    In the chemical mechanical polishing (CMP) process, the complex behaviors of abrasive particles play important roles in the planarization of wafer surface. Particles embedded in the pad remove materials by ploughing, while particles immersed in the slurry by rolling across the wafer surface. In this paper, processes of the particle rolling across a silicon surface with an asperity under various down forces and external driving forces were studied using molecular dynamics (MD) simulation method. The simulations clarified the asperity shape evolution during the rolling process and analyzed the energy changes of the simulation system and the interaction forces acted on the silica particle. It was shown that both the down force and the driving force had important influences on the amount of the material removed. With relatively small down forces and driving forces applied on the particle, the material removal occurred mainly in the front end of the asperity; when the down forces and driving forces were large enough, e.g., 100 nN, the material removal could take place at the whole top part of the asperity. The analysis of energy changes and interaction forces provided favorable explanations to the simulation results. (orig.)

  10. A two-dimensional global simulation study of inductive-dynamic magnetosphere-ionosphere/thermosphere coupling

    Science.gov (United States)

    Tu, J.; Song, P.

    2016-12-01

    We have developed a new numerical simulation model of the ionosphere/thermosphere by using an inductive-dynamic approach (including self-consistent solutions of Faraday's law and retaining inertia terms in ion momentum equations), that is, based on magnetic field B and plasma velocity v (B, v paradigm), which is distinctive from the conventional modeling based on electric field E and current j. The model solves self-consistently time-dependent continuity, momentum, and energy equations for multiple species of ions and neutrals including photochemistry, and Maxwell's equations. The governing equations solved in the model are a set of multifluid-collisional-Hall MHD equations which are one of unique features of our ionosphere/thermosphere model. With such an inductive-dynamic approach, not only sound wave mode but also all possible MHD wave modes are retained in the solutions of the governing equations so that the dynamic coupling between the magnetosphere and ionosphere and among different regions of the ionosphere can be self-consistently investigated. In the present study, we demonstrate dynamic propagation of field-aligned currents and ionospheric electric field carried by Alfven waves, as well as formation of closure horizontal currents (Pedersen currents in the E-region), indicating that the M-I coupling is via the Alfven waves instead of the field-aligned currents or electric field mapping. The simulation results also show that the Poynting flux and strongest energy dissipation in the ionosphere/thermosphere is in the regions of the largest ion velocities and not necessarily in the auroral oval where the field-aligned currents reside. The frictional heating increases plasma temperature and thus drives ion upflows. The frictional heating also increase neutral temperature and produces neutral upflows but in a much longer time scale. Furthermore, the coupling of high-to-low latitude ionosphere is investigated in terms of propagation of fast MHD waves.

  11. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Shea, Joan-Emma; Levine, Zachary A

    2016-01-01

    The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.

  12. Dynamic simulation of color blindness for studying color vision requirements in practice

    NARCIS (Netherlands)

    Lucassen, M.P.; Alferdinck, J.W.A.M.

    2006-01-01

    We report on a dynamic simulation of defective color vision. Using an RGB video camera connected to a PC or laptop, the captured and displayed RGB colors are translated by our software into modified RGB values that simulate the color appearance of a person with a color deficiency. Usually, the

  13. The effect of salt on the melting of ice: A molecular dynamics simulation study

    Science.gov (United States)

    Kim, Jun Soo; Yethiraj, Arun

    2008-09-01

    The effect of added salt (NaCl) on the melting of ice is studied using molecular dynamics simulations. The equilibrium freezing point depression observed in the simulations is in good agreement with experimental data. The kinetic aspects of melting are investigated in terms of the exchange of water molecules between ice and the liquid phase. The ice/liquid equilibrium is a highly dynamic process with frequent exchange of water molecules between ice and the liquid phase. The balance is disturbed when ice melts and the melting proceeds in two stages; the inhibition of the association of water molecules to the ice surface at short times, followed by the increased dissociation of water molecules from the ice surface at longer times. We also find that Cl- ions penetrate more deeply into the interfacial region than Na+ ions during melting. This study provides an understanding of the kinetic aspects of melting that could be useful in other processes such as the inhibition of ice growth by antifreeze proteins.

  14. Molecular Dynamics Simulation Study of the Selectivity of a Silica Polymer for Ibuprofen

    Directory of Open Access Journals (Sweden)

    Riccardo Concu

    2016-07-01

    Full Text Available In the past few years, the sol-gel polycondensation technique has been increasingly employed with great success as an alternative approach to the preparation of molecularly imprinted materials (MIMs. The main aim of this study was to study, through a series of molecular dynamics (MD simulations, the selectivity of an imprinted silica xerogel towards a new template—the (±-2-(P-Isobutylphenyl propionic acid (Ibuprofen, IBU. We have previously demonstrated the affinity of this silica xerogel toward a similar molecule. In the present study, we simulated the imprinting process occurring in a sol-gel mixture using the Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA force field, in order to evaluate the selectivity of this xerogel for a template molecule. In addition, for the first time, we have developed and verified a new parameterisation for the Ibuprofen® based on the OPLS-AA framework. To evaluate the selectivity of the polymer, we have employed both the radial distribution functions, interaction energies and cluster analyses.

  15. Studies on sensitivity to tension and gating pathway of MscL by molecular dynamic simulation

    Institute of Scientific and Technical Information of China (English)

    Jun-Yu Xie; Guang-Hong Ding

    2013-01-01

    Mechanosensitive (MS) ion channels play an important role in various physiological processes.Although the determination of the structure of mechanosensitive channel of large conductance (MscL) makes the simulation study possible,it has not so far been possible to directly simulate the gating mechanism of MscL in atomic detail.In this article,MscL has been studied via molecular dynamic (MD)simulations to gain a detailed description of the sensitivity to lateral tension and the gating pathway.MscL undergoes conformational rearrangement in sustaining lateral tension,and the open state is obtained when 2.0 MPa lateral tension is directly applied on the pure protein.During the opening process,Loop region responds to tension first,and the mechanical sensitivity is followed by S1 domain.Transmembrane (TM) bundle is the key position for channel opening,and the motion of TM1 helices finally realizes the significant expansion of the constricted gating pore.C-terminus domain presents expansion later during the TM opening.In our study,return of the whole protein to the initial closed state is achieved only in the early opening stage.During the relaxation from the open state,the TM helices are the most mobile domain,which is different from the opening process.

  16. Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Liqun

    2017-04-01

    Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665-681. © 2016 Wiley Periodicals, Inc.

  17. Molecular dynamics simulation studies of ionic liquid electrolytes for electric double layer capacitors

    Science.gov (United States)

    Hu, Zongzhi

    Molecular Dynamics (MD) simulation has been performed on various Electric Double Layer Capacitors (EDLCs) systems with different Room Temperature Ionic Liquids (RTILs) as well as different structures and materials of electrodes using a computationally efficient, low cost, united atom (UA)/explicit atom (EA) force filed. MD simulation studies on two 1-butyl-3-methylimidazolium (BMIM) based RTILs, i.e., [BMIM][BF4] and [BMIM][PF6], have been conducted on both atomic flat and corrugated graphite as well as (001) and (011) gold electrode surfaces to understand the correlations between the Electric Double Layer (EDL) structure and their corresponding differential capacitance (DC). Our MD simulations have strong agreement with some experimental data. The structures of electrodes also have a strong effect on the capacitance of EDLCs. MD simulations have been conducted on RTILs of N-methyl-N- propylpyrrolidinium [pyr13] and bis(fluorosulfonyl)imide (FSI) as well as [BMIM][PF6] on both curvature electrodes (fullerenes, nanotube, nanowire) and atomic flat electrode surfaces. It turns out that the nanowire electrode systems have the largest capacitance, following by fullerene systems. Nanotube electrode systems have the smallest capacitance, but they are still larger than that of atomically flat electrode system. Also, RTILs with slightly different chemical structure such as [Cnmim], n = 2, 4, 6, and 8, FSI and bis(trifluoromethylsulfonyl)imide (TFSI), have been examined by MD simulation on both flat and nonflat graphite electrode surfaces to study the effect of cation and anion's chemical structures on EDL structure and DC. With prismatic (nonflat) graphite electrodes, a transition from a bell-shape to a camel-shape DC dependence on electrode potential was observed with increase of the cation alkyl tail length for FSI systems. In contrast, the [Cnmim][TFSI] ionic liquids generated only a camel-shape DC on the rough surface regardless of the length of alkyl tail.

  18. Data Systems Dynamic Simulator

    Science.gov (United States)

    Rouff, Christopher; Clark, Melana; Davenport, Bill; Message, Philip

    1993-01-01

    The Data System Dynamic Simulator (DSDS) is a discrete event simulation tool. It was developed for NASA for the specific purpose of evaluating candidate architectures for data systems of the Space Station era. DSDS provides three methods for meeting this requirement. First, the user has access to a library of standard pre-programmed elements. These elements represent tailorable components of NASA data systems and can be connected in any logical manner. Secondly, DSDS supports the development of additional elements. This allows the more sophisticated DSDS user the option of extending the standard element set. Thirdly, DSDS supports the use of data streams simulation. Data streams is the name given to a technique that ignores packet boundaries, but is sensitive to rate changes. Because rate changes are rare compared to packet arrivals in a typical NASA data system, data stream simulations require a fraction of the CPU run time. Additionally, the data stream technique is considerably more accurate than another commonly-used optimization technique.

  19. Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

    Science.gov (United States)

    Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

    2017-10-01

    Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, Km and kcat, increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (kcat/Km). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

  20. Correlation spectroscopy and molecular dynamics simulations to study the structural features of proteins.

    Directory of Open Access Journals (Sweden)

    Antonio Varriale

    Full Text Available In this work, we used a combination of fluorescence correlation spectroscopy (FCS and molecular dynamics (MD simulation methodologies to acquire structural information on pH-induced unfolding of the maltotriose-binding protein from Thermus thermophilus (MalE2. FCS has emerged as a powerful technique for characterizing the dynamics of molecules and it is, in fact, used to study molecular diffusion on timescale of microsecond and longer. Our results showed that keeping temperature constant, the protein diffusion coefficient decreased from 84±4 µm(2/s to 44±3 µm(2/s when pH was changed from 7.0 to 4.0. An even more marked decrease of the MalE2 diffusion coefficient (31±3 µm(2/s was registered when pH was raised from 7.0 to 10.0. According to the size of MalE2 (a monomeric protein with a molecular weight of 43 kDa as well as of its globular native shape, the values of 44 µm(2/s and 31 µm(2/s could be ascribed to deformations of the protein structure, which enhances its propensity to form aggregates at extreme pH values. The obtained fluorescence correlation data, corroborated by circular dichroism, fluorescence emission and light-scattering experiments, are discussed together with the MD simulations results.

  1. A feasibility study on the design and walking operation of a biped locomotor via dynamic simulation

    Science.gov (United States)

    Wang, Mingfeng; Ceccarelli, Marco; Carbone, Giuseppe

    2016-06-01

    A feasibility study on the mechanical design and walking operation of a Cassino biped locomotor is presented in this paper. The biped locomotor consists of two identical 3 degrees-of-freedom tripod leg mechanisms with a parallel manipulator architecture. Planning of the biped walking gait is performed by coordinating the motions of the two leg mechanisms and waist. A threedimensional model is elaborated in SolidWorks® environment in order to characterize a feasible mechanical design. Dynamic simulation is carried out in MSC.ADAMS® environment with the aims of characterizing and evaluating the dynamic walking performance of the proposed design. Simulation results show that the proposed biped locomotor with proper input motions of linear actuators performs practical and feasible walking on flat surfaces with limited actuation and reaction forces between its feet and the ground. A preliminary prototype of the biped locomotor is built for the purpose of evaluating the operation performance of the biped walking gait of the proposed locomotor.

  2. Computer simulation study of surface wave dynamics at the crystal--melt interface

    CERN Document Server

    Benet, Jorge; Sanz, Eduardo

    2014-01-01

    We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (like e. g. Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is ar...

  3. The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.

    Science.gov (United States)

    Furukawa-Hagiya, Tomoka; Furuta, Tadaomi; Chiba, Shuntaro; Sohma, Yoshiro; Sakurai, Minoru

    2013-01-10

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a "closed-apo" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions.

  4. Nanoscale soldering of axially positioned single-walled carbon nanotubes: a molecular dynamics simulation study.

    Science.gov (United States)

    Cui, Jianlei; Yang, Lijun; Zhou, Liang; Wang, Yang

    2014-02-12

    The miniaturization of electronics devices into the nanometer scale is indispensable for next-generation semi-conductor technology. Carbon nanotubes (CNTs) are considered to be the promising candidates for future interconnection wires. To study the carbon nanotubes interconnection during nanosoldering, the melting process of nanosolder and nanosoldering process between single-walled carbon nanotubes are simulated with molecular dynamics method. As the simulation results, the melting point of 2 nm silver solder is about 605 K because of high surface energy, which is below the melting temperature of Ag bulk material. In the nanosoldering process simulations, Ag atoms may be dragged into the nanotubes to form different connection configuration, which has no apparent relationship with chirality of SWNTs. The length of core filling nanowires structure has the relationship with the diameter, and it does not become longer with the increasing diameter of SWNT. Subsequently, the dominant mechanism of was analyzed. In addition, as the heating temperature and time, respectively, increases, more Ag atoms can enter the SWNTs with longer length of Ag nanowires. And because of the strong metal bonds, less Ag atoms can remain with the tight atomic structures in the gap between SWNT and SWNT. The preferred interconnection configurations can be achieved between SWNT and SWNT in this paper.

  5. Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol, E-mail: krlee@kist.re.kr [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of); Department of Nanomaterial Science and Technology, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113 (Korea, Republic of); Srivastava, Pooja; Choi, Keunsu [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of)

    2016-03-28

    Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

  6. Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study

    Science.gov (United States)

    Haliloglu, Turkan; Bahar, Ivet; Erman, Burak

    1996-08-01

    The behavior of a single polyethylene chain grafted to an impenetrable surface, under shear flow, is investigated using Brownian dynamics simulations. Both short-range conformational energies and excluded volume effects are included in the model. Simulations are performed in good and poor solvent conditions in order to explore the effect of solvent quality. The shear flow is represented by the superposition of a force profile increasing linearly with the distance from the surface. Distribution of rotational angles, chain dimensions, components of the radius of gyration, segment density distribution, average layer thickness, and average orientation of bond vectors with respect to flow direction are determined and compared with other studies. Above a certain value of the shear rate, a significant increase in chain dimensions is observed for both good and poor solvents, the transition from coiled to stretched state being sharper in poor solvent. In good solvent, chain dimensions along the two perpendicular directions to the flow direction diminish with increasing shear rate. On the other hand, in poor solvent, there is an overall expansion in chain dimensions in all directions at low shear rates, which is subsequently followed by the orientation and alignment of the chain along the direction of flow. The experimentally observed increase in chain dimensions normal to the flow field at low shear rates is evidenced for the first time by simulations.

  7. Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study

    Science.gov (United States)

    Bertoša, Branimir; Kojić-Prodić, Biserka; Wade, Rebecca C.; Tomić, Sanja

    2008-01-01

    Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. To understand the proposed receptor function of ABP1 we carried out a detailed molecular modeling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilized by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site. PMID:17766341

  8. DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations

    Institute of Scientific and Technical Information of China (English)

    QI Wen-Peng; LEI Xiao-Ling

    2011-01-01

    @@ Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction.The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA.We study the conformational variations of a 22-mer DNA caused by stretching both 3'-and 5'-termini by molecular dynamics simulations.It requires 250kJ/mol to stretch the DNA molecule by 3'5'-termini for 3.5 run and the force plateau is at 123.8 pN.The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34°to 20°and the successive base pairs rolls to the side of the DNA major groove.The distances between successive base pairs increases from 3.2.(A) to 5.6(A).%Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction. The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA. We study the conformational variations of a 22-met DNA caused by stretching both 3'- and 5'-termini by molecular dynamics simulations. It requires 250k J/mol to stretch the DNA molecule by 3'5'-termini for 3.5nm and the force plateau is at 123.8pN. The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34° to 20° and the successive base pairs rolls to the side of the DNA major groove. The distances between successive base pairs increases from 3.2 (A) to 5.6 (A).

  9. Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces.

    Science.gov (United States)

    Picaud, Sylvain; Collignon, B; Hoang, Paul N M; Rayez, J C

    2006-04-27

    In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high.

  10. In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors.

    Science.gov (United States)

    Mahapatra, Manoj Kumar; Bera, Krishnendu; Singh, Durg Vijay; Kumar, Rajnish; Kumar, Manoj

    2017-04-21

    Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.

  11. Molecular Dynamics Simulation Study of PEO-Based Nanocomposite Polymer Electrolytes el

    Science.gov (United States)

    Borodin, Oleg; Bandyopadhyaya, Rajdip; Smith, Grant D.

    2002-03-01

    Solid polymer electrolytes exhibit good chemical, electrochemical and photochemical stability in combination with good mechanical properties, ease of processing and adequate conductivity at elevated temperatures. Addition of solid nanoparticle fillers such as TiO2 and SiO2 to lithium solid polymer electrolytes is known to improve mechanical properties, interfacial stability, conductivity and transfer numbers, particularly for poly(ethylene oxide) (PEO) based polymer electrolytes. We have performed molecular dynamics simulations of PEO/LiBF4 and PEO/LiBF4/TiO2 systems in order to study changes of the structure and mechanism of ion conduction in PEO/LiBF4 near TiO2 surfaces compared to the bulk PEO/LiBF4.

  12. EFFECT OF STRAIN FIELD ON THRESHOLD DISPLACEMENT ENERGY OF TUNGSTEN STUDIED BY MOLECULAR DYNAMICS SIMULATION

    Energy Technology Data Exchange (ETDEWEB)

    Wang, D.; Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.; Gao, X.; He, W. H.

    2016-03-31

    The influence of hydrostatic strain on point defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten was studied with molecular dynamics simulations. Two different tungsten potentials (Fikar and Juslin) were used. The minimum Ed direction calculated with the Fikar-potential was <100>, but with the Juslin-potential it was <111>. The most stable self-interstitial (SIA) configuration was a <111>-crowdion for both potentials. The stable SIA configuration did not change with applied strain. Varying the strain from compression to tension increased the vacancy formation energy but decreased the SIA formation energy. The SIA formation energy changed more significantly than for a vacancy such that Ed decreased with applied strain from compression to tension.

  13. Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study

    OpenAIRE

    Guàrdia Manuel, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-01-01

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the ...

  14. Simulation of material properties below the Debye temperature: A path-integral molecular dynamics case study of quartz

    Science.gov (United States)

    Müser, Martin H.

    2001-04-01

    Classical and path integral molecular dynamics (PIMD) simulations are used to study α and β quartz in a large range of temperatures at zero external stress. PIMD account for quantum fluctuations of atomic vibrations, which can modify material properties at temperatures below the Debye temperature. The difference between classical and quantum mechanical results for bond lengths, bond angles, elastic moduli, and some dynamical properties is calculated and comparison to experimental data is done. Only quantum mechanical simulations are able to reproduce the correct thermomechanical properties below room temperature. It is discussed in how far classical and PIMD simulations can be helpful in constructing improved potential energy surfaces for silica.

  15. Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

    Institute of Scientific and Technical Information of China (English)

    YAN; Han; ZHU; HaoMiao; SHEN; Jian

    2007-01-01

    Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The results showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".

  16. Theoretical studies of zirconium and carbon clusters with molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, B.

    1993-08-01

    In this dissertation, we will present a systematic study of structures of fullerenes ranging from C{sub 20} to C{sub 100} by introducing a novel scheme. Using our new scheme, we not only reproduce all known fullerene structures but also successfully predicted several other fullerene structures which were confirmed by experiments. By utilizing the tight-binding molecular-dynamic (TBMD) simulation, we also studied the dynamical behavior of fullerenes: Vibrations, thermal disintegration of individual clusters as well as collisions between fullerenes. If the beauty of carbon fullerene is not enough, people found that carbon can also form tubules and even speculated that they can form three-dimensional graphite-like networks. By extending our fullerene structure searching scheme, we performed a search for the ground-state structure of three dimensional carbon network. We found the most stable structure people ever proposed for simple cubic based networks. From the difference of this new form of carbon and graphite in the electronic and vibrational properties, we propose an experimental probe to identify these novel three-dimensional carbon networks.

  17. Molecular dynamics computer simulation studies of aqueous solutions in clusters, in bulk, and at interfaces

    Science.gov (United States)

    Yeh, In-Chul

    1999-10-01

    This dissertation investigates the structural and dynamical properties of aqueous solutions in clusters, in bulk, and at interfaces using molecular dynamics computer simulations. First, the photodetachment spectra of Cl- (H 2O)n (n = 2,3,...15) clusters have been calculated. The dependence of the spectra on the variations in the temperature of the clusters, the potential parameter for the postejected ion, and the type of the potential (pair-wise non-polarizable vs. many-body polarizable) has been investigated. Next, I have compared structural and dynamical properties of bulk water calculated by the simple point charge (SPC) and extended simple point charge (SPC/E) models. Tetrahedral network in SPC water is found to be weaker than those in SPC/E water due to smaller point charges, resulting in a larger self-diffusion coefficient. As a model interfacial system, I discuss the structure of water next to metal surfaces: Pt(100) and Pt(111). The two dimensional Ewald summation technique has been used for the calculation of long range Coulombic forces. Water next to an uncharged metallic surface is perturbed to a distance of 1 nm. Next to the charged surface water is reorienting and when the external field is strong, undergoes a layering transition. The dielectric constant of water as a function of electric fields has been also calculated. Simulations of water between walls and bulk water have been done to confirm the macroscopic nature of the dielectric constant. Calculated dielectric constants have been compared with those obtained by a theoretical prediction and a recent simulation study. Distance dependent density profiles of water near charged Ag(111) surfaces have been calculated and compared with experimental profiles. The effect of ionic screening is accounted for by an exponetially decaying electric field. Finally, I propose a modification in the three dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab

  18. Molecular dynamics simulation studies on ethane and acetylene mixture in CuBTC metal organic framework

    Science.gov (United States)

    Prabhudesai, S. A.; Sharma, V. K.; Mitra, S.; Mukhopadhyay, R.

    2014-04-01

    Molecular Dynamics (MD) simulation studies have been carried out on the mixture containing ethane and acetylene molecules in 1:1 ratio at various concentrations of each species in CuBTC metal organic framework (MOF). MOFs are important class of materials which are tremendously useful for applications such as gas storage and separation. They have complex structure consisting of pore and pockets connected by windows. Results obtained from MD simulation showed that the self diffusivity of the ethane increases with the concentration while it decreases in case of acetylene. Correlation effects are responsible for this kind of phenomena. Pair distribution function showed the strong peaks at higher correlation length indicating the complex crystalline structure of the host matrix. We have also obtained the velocity auto correlation function (VACF) and velocity cross correlation functions (VCCF) at each studied concentration and found that the contribution from VCCF is almost negligible at lower concentration. Since the transport properties of mixture also depend on the mutual diffusivity and distinct diffusivity besides the self diffusivity, attempt has been made to quantify both the diffusivities. In the present system, at lower concentration, contribution to the mutual diffusivity comes from self diffusivities of species alone and distinct diffusivity contributes only at higher concentration.

  19. A regional climate simulation study with land cover dynamics in Northern China

    Science.gov (United States)

    Wang, Hanjie; Ju, Yongmao; Li, Jianyun; Qiu, Guoyu

    2007-09-01

    A social-economic database based on the Governmental Statistical Annals, county-to-county investigation, literature verification, as well as the satellite identification was completed recently by the Remote Sensing and GIS Research Center, Beijing Normal University of China. The GIS Operational System handing this database not only provides details of the social, ecological, and economic information of the Northern China's 13 provinces since earlier 1950s, but also gives out predictions of these information by 2050 with different sceneries concerning the population increase, land use variation, governmental policy adjusting, administrating capability, science and technology development, National GDP increment, as well as world climate change. Aims at further regional climate simulation study, there is a special module nested in the GIS Operational System that interprets the county-level administrative data-units to a 60 × 60 km numerical mesh-grid suitable for climate model. By incorporating the land use dynamics provided by the above database, the new generation of the Regional Integrate Environment Modeling System (RIEMS2.0) was used for climate simulation study. The preliminary simulation studies show that: (1) the regional climate will be affected by the LULC variation because the equilibrium of water and heat transfer in the air-vegetation interface is changed; (2) the integrate impact of the LULC variation on climate (such as temperature, humidity and net long-wave radiation, precipitation) is not only limited to the Northern China where LULC varies, but also to the whole numerical domain where the LULC does not vary at all; (3) the ecological construction engineering implemented in Northern China including the Green-Great Wall construction engineering, the replace farming with forestry and grass movement, and the natural forest conservation etc has shown and will work positively on the eco-environment improvement, particularly shown as the increased

  20. Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation

    Science.gov (United States)

    Okuda, Masaki; Higashi, Masahiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2017-09-01

    The vibrational dynamics of SCN- in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong.

  1. From a single molecule to a membrane of structured ionic polymers: A molecular dynamic simulation study

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

    2012-02-01

    The association of an A-B-C-B-A co-polymer with an ionizable center and a bulky end block has been investigated using molecular dynamic simulations. The center block consists of a randomly sulfonated polystyrene connected to a flexible poly (ethylene-r-propylene) bridge and end caped with poly (t-butyl styrene). Tailoring the nature of individual segments within a block co-polymer is a potential design tool to form membranes with desired properties. The association mode and the dynamics of the segments control the overall characteristics. The membranes with three sulfonation level for the center block were made by evaporating a common solvent for all blocks. The local structure including size and distribution of the ionic blocks and the continuity of the styrene phase as well as long range correlations were identified at 300 and 500K. The initial membrane structure is affected by the structure in solution. Studies on changes that take place above the glass transition temperature for each of the blocks will also be presented.

  2. Dissipative particle dynamics simulation study of the bilayer-vesicle transition

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A bilayer structure is an important immediate for the vesicle formation. However,the mechanism for the bilayer-vesicle transition remains unclear. In this work,a dissipative particle dynamics(DPD) simulation method was employed to study the mechanism of the bilayer-vesicle transition. A coarse-grained model was built based on a lipid molecule termed dimyristoylphosphatidylcholine(DMPC). Simulations were performed from two different initial configurations:a random dispersed solution and a tensionless bilayer. It was found that the bilayer-vesicle transition was driven by the minimization of the water-tail hydrophobic interaction energy,and was accompanied with the increase of the position entropy due to the redistribution of water molecules. The bulk pressure was reduced during the bilayer-vesicle transition,suggesting the evolved vesicle morphology was at the relatively low free energy state. The membrane in the product vesicle was a two-dimensional fluid. It can be concluded that the membrane of a vesicle is not interdigitated and most of the bonds in lipid chains are inclined to orient along the radical axis of the vesicle.

  3. Simulating the DISAMATIC process using the discrete element method — a dynamical study of granular flow

    DEFF Research Database (Denmark)

    Hovad, Emil; Spangenberg, Jon; Larsen, P.

    2016-01-01

    The discrete element method (DEM) is applied to simulate the dynamics of the flow of green sand while filling a mould using the DISAMATIC process. The focus is to identify relevant physical experiments that can be used to characterize the material properties of green sand in the numerical model...

  4. Dynamic Mechanism of Single-Stranded DNA Encapsulated into Single-Wall Carbon Nanotubes: A Molecular Dynamics Simulation Study

    Science.gov (United States)

    Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang

    2014-02-01

    Hybrids of single-walled carbon nanotubes (SWCNTs) and biological molecules have been utilized for numerous applications in sensing, imaging, and drug delivery. By molecular dynamics simulation, we investigate the encapsulation of single-strand DNA (ssDNA) containing eight adenine bases with (17,17)-(12,12) SWCNTs. The effects of the diameter and length of SWCNTs on the encapsulation process are explored with the calculated curves of the center-of-mass distance, the van der Waals interaction between the ssDNA and SWCNT, the root-mean-square deviation of the ssDNA, and the radius of gyration of the ssDNA. The free energy of the encapsulated ssDNA for each SWCNT is also obtained via steered molecular dynamics simulation. The most suitable SWCNT for encapsulating the ssDNA is also suggested.

  5. Molecular dynamics simulation study of the melting and structural evolution of bimetallic Pd-Pt nanowires

    Science.gov (United States)

    Sankaranarayanan, Subramanian K. R. S.; Bhethanabotla, Venkat R.; Joseph, Babu

    2006-10-01

    Thermal characteristics of Pd-Pt metal nanowires with diameters ranging from 2.3 to 3.5nm and of several compositions were studied by molecular dynamics simulations utilizing the quantum Sutton-Chen potential function. Monte Carlo simulations employing bond order simulation model were used to generate the initial wire configurations that consisted of surface segregated structures. Melting temperatures were estimated based on variations in thermodynamic properties such as potential energy and specific heat capacity. We find that the melting transition temperatures for the nanowires are much lower than those of bulk alloys of the same composition and at least 100-200K higher than those of nanoclusters of the same diameter. Density distributions along the nanowire cross section and axis as well as components of shell-based diffusion coefficients and velocity autocorrelation functions were used to investigate the melting mechanism in these nanowires. Our findings indicate a surface-initiated melting process characterized by predominantly larger cross-sectional movement. This two-dimensional surface melting mechanism in nanowires differs from that in nanoclusters in which atomic movement is more isotropic in all three dimensions. Differences in the surface melting mechanism result in structural transformations from fcc-hcp type and lead to simulated phase boundaries for nanowires that are different from bulk alloys as well as from same-diameter nanoclusters. A composition and temperature dependent fcc-hcp transformation occurs prior to the melting transition in both nanowires and nanoclusters. Hcp phase occurs over a wider temperature range at Pd-rich compositions and a narrower range at low Pd compositions with the fcc-hcp and hcp-liquid transition temperatures showing a minimum at 25% Pt composition. In contrast, the nanoclusters exhibit a near-linear dependence of melting temperature on Pd composition with the hcp phase existing over a much narrower range of

  6. MOLECULAR DYNAMICS SIMULATION AND EXPERIMENTAL STUDIES OF GOLD NANOPARTICLE TEMPLATED HDL-LIKE NANOPARTICLES FOR CHOLESTEROL (POSTPRINT)

    Science.gov (United States)

    2016-12-21

    AFRL-RX-WP-JA-2017-0193 MOLECULAR DYNAMICS SIMULATION AND EXPERIMENTAL STUDIES OF GOLD NANOPARTICLE TEMPLATED HDL-LIKE NANOPARTICLES ...SIMULATION AND EXPERIMENTAL STUDIES OF GOLD NANOPARTICLE TEMPLATED HDL-LIKE NANOPARTICLES FOR CHOLESTEROL (POSTPRINT) 5a. CONTRACT NUMBER FA8650-15-2...removing excess cholesterol from arterial plaques. Gold nanoparticles (AuNPs) functionalized with apolipoprotein A-I and with the lipids 1,2

  7. Dynamic simulation of dispersed, grid-connected photovoltaic power systems: System studies

    Science.gov (United States)

    Wasynczuk, O.; Carroll, D. P.; Gareis, G. E.; Krause, P. C.; Ong, C. M.; Schwartz, R. J.

    1985-03-01

    To investigate the operating characteristics and dynamic behavior of photovoltaic (PV) power systems, four PV system configurations were selected as representative of those currently being used in PV applications. These included single and three phase, line and self commutated power conditioners with a flat plate PV array as the dc source. Detailed computer models of each of these systems were developed and incorporated into dynamic representations of typical primary and secondary distribution feeders. The dynamic electrical behavior of the PV and distribution systems following common network disturbances such as large load changes, PV system startup, and cloud cover transients are characterized. The dynamic behavior was also investigated during abnormal operating conditions following line faults, PV system malfunctions, and islanding or distribution systems containing significant levels of dispersed PV generation. Results of verification tests involving two of the single phase PV system configurations, in which the simulated response characteristics are compared with actual measurements, are also provided.

  8. STIFFNESS AND EXCLUDED VOLUME EFFECTS ON CONFORMATION AND DYNAMICS OF POLYMERS: A SIMULATION STUDY

    Institute of Scientific and Technical Information of China (English)

    An-bang Li; Yuan-gen Yao; Hong Xu

    2012-01-01

    This work investigates the effects of the excluded volume and especially those of the chain stiffness on the structural and dynamical properties of a model polymer chain.The theoretical framework is the same as in the recent works by Steinhauser et al.,where a Rouse approach is adopted.Our model differs in that our chains have a finite average bending angle.As in the works by Steinhauser et al.,Langevin dynamic simulations were performed without hydrodynamic interactions.Whereas this doesn't impact the static properties we obtain,it also allows us to compare our results on dynamic properties to those predicted by Rouse theory,where hydrodynamic interactions are also neglected.Our results show that the structural properties are very sensitive to the chain stiffness,whereas the dynamic scaling laws remain the same as those by Rouse theory,with the prefactor depending on the persistence length.

  9. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  10. The impact of ligands on the structure and flexibility of sulfotransferases: a molecular dynamics simulation study.

    Science.gov (United States)

    Zhao, Li; Zhang, Pupu; Long, Shiyang; Wang, Linlin; Tian, Pu

    2015-08-01

    Sulfotransferases catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to a large number of substrates. They play an important role in phase II metabolic process. The impact of the cofactor (PAPS) on the structure and flexibility of the enzyme has been studied extensively, and the response of the active-cap region to cofactor binding was proposed as the molecular basis for substrate selectivity. In this study, individual and cooperative effects of the cofactor and substrate on the structure and flexibility of the enzyme were investigated. Molecular dynamics simulations were performed for four systems, including free enzyme, binary complexes (cofactor or substrate bound enzyme) and ternary complex (both cofactor and substrate bound enzyme). The influence of ligands (the cofactor and the substrate) on the structure and flexibility of the enzyme, especially that of the active-site cap region, was analyzed. Moreover, mutual structural impact of the ligands was examined as well. The results show that the impact of both the cofactor and the substrate was significant. Our study indicated that the substrate, such as lithocholic acid (LCA), participated in regulating the structure and flexibility of the enzyme actively rather than merely being selected passively. Additionally, the observed synergistic effects of the cofactor and the substrate demonstrated the importance of examining both ligands in understanding enzymes.

  11. Solubility of cellulose in supercritical water studied by molecular dynamics simulations.

    Science.gov (United States)

    Tolonen, Lasse K; Bergenstråhle-Wohlert, Malin; Sixta, Herbert; Wohlert, Jakob

    2015-04-02

    The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 × 4 × 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.

  12. A system dynamics model for simulating the logistics demand dynamics of metropolitans: A case study of Beijing, China

    Directory of Open Access Journals (Sweden)

    Ying Qiu

    2015-05-01

    Full Text Available Purpose: We attempted to propose an approach to simulate the dynamics of Beijing’s logistics demand, which can do some help to find out the dynamics path of the needed storage and shipment, put forward with logistics policies and enhance logistics service. Design/methodology/approach: We present a paper with system dynamics (SD methodology, which was run by the software of Vensim®. Findings: With SD model, causal loop diagram and stock and flow diagram are constructed, as well as some experiments and policy analysis. The research findings revealed that the increase of average shipping capacity for a vehicle will bring a decrease in congestion and CO2 emission directly and the decrease of the average fuel use for a vehicle can help with the reduction of CO2 emission directly. Both the two parameters are the indirect causes of logistics demand dynamics in Beijing. Originality/value: Researches of this paper are aiming at handling logistics demand dynamics of Beijing, problems belonging to the area of complex systems, with SD model, where, to the best of our knowledge, no significant research has been done.

  13. Molecular Dynamics Simulation Study of Carbon Dioxide, Methane, and Their Mixture in the Presence of Brine

    KAUST Repository

    Yang, Yafan

    2017-10-03

    We perform molecular dynamics simulation study of CO2, methane, and their mixture in the presence of brine over a broad range of temperature (311–473 K), pressure (up to about 100 MPa), and NaCl concentration (up to about 14 wt %). The general decrease in the interfacial tension (IFT) values of the CH4–brine system with pressure and temperature is similar to that obtained for the corresponding CH4–water system. The IFT of methane and brine is a linearly increasing function of salt concentration, and the resulting slopes are dependent on the pressure. A similar behavior as methane is observed for such systems containing CO2 and CO2–CH4 mixture. The IFT of CO2 and brine increases linearly with increasing salt content; however, the resulting slopes are independent of pressure. The simulations show that the presence of CO2 decreases the IFT values of the CH4–water and CH4–brine systems, but the degree of reduction depends on the amount of CO2 in each sample, which is consistent with experimental evidence. These IFT values show a linear correlation with the amount of CO2, and the resulting slopes are dependent on the temperature and pressure. Furthermore, our results for the mole fractions of the different species in the CO2–CH4–water system at 323 K and 9 MPa are in agreement with those of experiments. The mole fractions of methane and CO2 in the water-rich phase decrease with increasing salt concentration, whereas that of H2O in the methane- or CO2-rich phases remains almost unaffected in all of the studied cases. Our results could be useful because of the importance of carbon dioxide sequestration and shale gas production.

  14. Water structure and dynamics in phosphate fluorosurfactant based reverse micelle: A computer simulation study

    Science.gov (United States)

    Senapati, Sanjib; Berkowitz, Max L.

    2003-01-01

    We performed a molecular dynamics simulation on a system containing a water pool inside the reverse micelle made up of an assembly of phosphate fluorosurfactant molecules dissolved in supercritical carbon dioxide. The water molecules in the first solvation shell of the headgroup lose the water to water tetrahedral hydrogen bonded network but are strongly bonded to the surfactant headgroups. This change in inter-water hydrogen bonding in connection with the confined geometry of the reverse micelle slows down the translational and especially the rotational dynamics of water.

  15. Parametric Study of ReaxFF Simulation Parameters for Molecular Dynamics Modeling of Reactive Carbon Gases.

    Science.gov (United States)

    Jensen, Benjamin D; Bandyopadhyay, Ananyo; Wise, Kristopher E; Odegard, Gregory M

    2012-09-11

    The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions.

  16. Study on numerical simulation and dynamic mechanism of winter- time circulation in the eastern China seas

    Institute of Scientific and Technical Information of China (English)

    HAN Dong; HOU Yijun; WEI Zexun; LIU Xingquan; ZHAO Xixi

    2004-01-01

    An MOM2 based 3-dimentional prognostic baroclinic Z-ordinate model was established to study the circulation in eastern China seas, considering the topography, inflow and outflow on the open boundary, wind stress, temperature and salinity exchange on the sea surface. The results were consistent with observation and showed that the Kuroshio intrudes in large scale into the East China Sea continental shelf East China, during which its water is exchanged ceaselessly with outer sea water along Ryukyu Island. The Tsushima Warm Current is derived from several sources, a branch of the Kuroshio, part of the Taiwan Warm Current, and Yellow Sea mixed water coming from the west of Cheju Island. The water from the west of Cheju Island contributes approximately 13% of the Isushima Warm Current total transport through the Korea Strait. The circulation in the Bohai Sea and Yellow Sea is basically cyclonic circulation, and is comprised of coastal currents and the Yellow Sea Warm Current. Besides simulation of the real circulation, numerical experiments were conducted to study the dynamic mechanism. The numerical experiments indicated that wind directly drives the East China Sea and Yellow Sea Coastal Currents, and strengthens the Korea Coastal Current and Yellow Sea Warm Current. In the no wind case, the kinetic energy of the coastal current area and main YSWC area is only 1% of that of the wind case. Numerical experiments also showed that the Tsushima Warm Current is of great importance to the formation of the Korea Coastal Current and Yellow Sea Warm Current.

  17. Studying the lateral chain packing in a ceramide bilayer with molecular dynamics simulations

    Science.gov (United States)

    Papadimitriou, N. I.; Karozis, S. N.; Kainourgiakis, M. E.; Charalambopoulou, G. Ch

    2015-01-01

    In this work, we present a novel technique, based on molecular dynamics simulations, that allows the study of the lateral chain packing in a lipid bilayer. It utilizes the radial distribution function of the alkyl chains to determine the arrangement of the chains along the bilayer plane. The positions of the mass centres of the chains are projected onto the bilayer plane and a 2D radial distribution function is calculated for these projections. The proposed technique can be particularly useful for lipid bilayers in the gel (solid) phase where the chains present a limited degree of mobility. As a case study, we have examined a bilayer that consists of ceramide NS 24:0. Ceramide bilayers can be found in the lipid domain of the skin where they have a significant role in its barrier function. The specific bilayer was found (at 300 K) to adopt a strictly hexagonal chain packing with a separation distance between the chains of 0.466 nm, in good agreement with the available experimental data.

  18. Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

    Science.gov (United States)

    Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay

    2017-02-01

    FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.

  19. Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Qianqian Yin

    2014-11-01

    Full Text Available Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.

  20. Towards New Insights in the Sterol/Amphotericin Nanochannels Formation: A Molecular Dynamic Simulation Study.

    Science.gov (United States)

    Boukari, Khaoula; Balme, Sébastien; Janot, Jean-Marc; Picaud, Fabien

    2016-06-01

    Amphotericin B (AmB) is a well-known polyene which self-organizes into membrane cell in order to cause the cell death. Its specific action towards fungal cell is not fully understood but was proved to become from sterol composition. The mechanism was shown experimentally to require the formation of stable sterol/polyene couples which could then organize in a nanochannel. This would allow the leakage of ions responsible for the death of fungal cells, only. In this present study, we investigate the arrangement of AmB/sterols in biological membrane using molecular dynamic simulations in order to understand the role of the sterol structure on the antifungal action of the polyene. We show in particular that the nanochannels tend to close up when cell was composed with cholesterol (animal cell) due to strong interaction between amphotericin and sterol. On the other side, with ergosterol (fungal cell) the largest interactions between amphotericin and lipid membrane lead to the appearance of large hole that could favor the important leakage of ions and thus, the fungal cell death. This work appears as a good complement in the extensive studies linked to the understanding of the antifungal molecules in membrane cells.

  1. Experimental and molecular dynamic simulation study of perfluorooctane sulfonate adsorption on soil and sediment components.

    Science.gov (United States)

    Zhang, Ruiming; Yan, Wei; Jing, Chuanyong

    2015-03-01

    Soil and sediment play a crucial role in the fate and transport of perfluorooctane sulfonate (PFOS) in the environment. However, the molecular mechanisms of major soil/sediment components on PFOS adsorption remain unclear. This study experimentally isolated three major components in soil/sediment: humin/kerogen, humic/fulvic acid (HA/FA), and inorganic component after removing organics, and explored their contributions to PFOS adsorption using batch adsorption experiments and molecular dynamic simulations. The results suggest that the humin/kerogen component dominated the PFOS adsorption due to its aliphatic features where hydrophobic effect and phase transfer are the primary adsorption mechanism. Compared with the humin/kerogen, the HA/FA component contributed less to the PFOS adsorption because of its hydrophilic and polar characteristics. The electrostatic repulsion between the polar groups of HA/FA and PFOS anions was attributable to the reduced PFOS adsorption. When the soil organic matter was extracted, the inorganic component also plays a non-negligible role because PFOS molecules might form surface complexes on SiO2 surface. The findings obtained in this study illustrate the contribution of organic matters in soils and sediments to PFOS adsorption and provided new perspective to understanding the adsorption process of PFOS on micro-interface in the environment. Copyright © 2014. Published by Elsevier B.V.

  2. Droplet formation and growth inside a polymer network: A molecular dynamics simulation study

    Science.gov (United States)

    Jung, Jiyun; Jang, Eunseon; Shoaib, Mahbubul Alam; Jo, Kyubong; Kim, Jun Soo

    2016-04-01

    We present a molecular dynamics simulation study that focuses on the formation and growth of nanoscale droplets inside polymer networks. Droplet formation and growth are investigated by the liquid-vapor phase separation of a dilute Lennard-Jones (LJ) fluid inside regularly crosslinked, polymer networks with varying mesh sizes. In a polymer network with small mesh sizes, droplet formation can be suppressed, the extent of which is dependent on the attraction strength between the LJ particles. When droplets form in a polymer network with intermediate mesh sizes, subsequent growth is significantly slower when compared with that in bulk without a polymer network. Interestingly, droplet growth beyond the initial nucleation stage occurs by different mechanisms depending on the mesh size: droplets grow mainly by diffusion and coalescence inside polymer networks with large mesh sizes (as observed in bulk), whereas Ostwald ripening becomes a more dominant mechanism for droplet growth for small mesh sizes. The analysis of droplet trajectories clearly reveals the obstruction effect of the polymer network on the movement of growing droplets, which leads to Ostwald ripening of droplets. This study suggests how polymer networks can be used to control the growth of nanoscale droplets.

  3. Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

    Science.gov (United States)

    2013-11-25

    New Mexico 87117 5776, United States ABSTRACT: Direct dynamics simulations and selected ion flow tube {SIFT) experiments were performed to study...0.04 0.51 0.49 500 0.48 ± 0.06 0.05 ± O.ot 0.47 ± 0.05 0.46 0.54 aSee footnote a in Table 2 and IVA . I Simulation Results concerning the [CH3 I OHt

  4. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    Science.gov (United States)

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  5. Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Jakse, N.; Pasturel, A. [Sciences et Ingénierie des Matériaux et Procédés, UMR CNRS 5266, Grenoble INP, BP 75, 38402 Saint-Martin d’Hères Cedex (France)

    2014-12-21

    In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

  6. Dynamic Value at Risk: A Comparative Study Between Heteroscedastic Models and Monte Carlo Simulation

    Directory of Open Access Journals (Sweden)

    José Lamartine Távora Junior

    2006-12-01

    Full Text Available The objective of this paper was to analyze the risk management of a portfolio composed by Petrobras PN, Telemar PN and Vale do Rio Doce PNA stocks. It was verified if the modeling of Value-at-Risk (VaR through the place Monte Carlo simulation with volatility of GARCH family is supported by hypothesis of efficient market. The results have shown that the statistic evaluation in inferior to dynamics, evidencing that the dynamic analysis supplies support to the hypothesis of efficient market of the Brazilian share holding market, in opposition of some empirical evidences. Also, it was verified that the GARCH models of volatility is enough to accommodate the variations of the shareholding Brazilian market, since the model is capable to accommodate the great dynamic of the Brazilian market.

  7. A comparative study of ibuprofen and ketoprofen glass-forming liquids by molecular dynamics simulations

    Science.gov (United States)

    Ottou Abe, M. T.; Correia, N. T.; Ndjaka, J. M. B.; Affouard, F.

    2015-10-01

    In this paper, structural and dynamical properties of ibuprofen and ketoprofen glass-forming liquids have been investigated by means of molecular dynamics simulations. Molecular mobility of both materials is analyzed with respect to the different inter-molecular linear/cyclic hydrogen bonding associations. For ibuprofen, the dominant organization is found to be composed of small hydrogen bonding aggregates corresponding to cyclic dimers through the carboxyl group. For ketoprofen, the propensity of cyclic dimers is significantly reduced by the formation of hydrogen bonds with the ketone oxygen of the molecule altering the hydrogen bond (HB) associating structures that can be formed and thus molecular dynamics. The issue of the presence/absence of the peculiar low frequency Debye-type process in dielectric relaxation spectroscopy (DRS) data in these materials is addressed. Results obtained from simulations confirm that the Debye process originates from the internal cis-trans conversion of the —COOH carboxyl group. It is shown that the specific intermolecular HB structures associated to a given profen control the main dynamical features of this conversion, in particular its separation from the α-process, which make it detectable or not from DRS. For ibuprofen, the possible role of the —CCCO torsion motion, more "local" than the —COOH motion since it is less influenced by the intermolecular HBs, is suggested in the microscopic origin of the quite intense secondary γ-relaxation process detected from DRS.

  8. Study and case simulation of a regional dust model coupled with a nonhydrostatic dynamics model

    Institute of Scientific and Technical Information of China (English)

    CHENG Conglan; WANG Yingchun; LIU Weidong; ZHANG Xiaoling; XU Xiaofeng; XIE Pu

    2004-01-01

    A new regional dust model suitable for simulation and forecasting of dust storms over northern China was described. The dust model was developed by coupling the mesoscale dynamics model MM5 (the Fifth-Generation NCAR/Penn State Mesoscale Model) with a set of mass conservation equations for the particles. The model includes all the atmospheric physical processes of dust storms including occurrence, lifting, transport, and dry and wet deposition. It considers the parameterization of dry and wet deposition, the dust size distribution and microphysical processes in detail. The dust flux from the surface is parameterized based on the friction velocity, which is provided by the mesoscale nonhydrostatic dynamics model, which takes account of the vegetation coverage, land use, soil category, and soil moisture. This new dust model is used to simulate the dust storm that occurred on 19-21 March, 2002 in North China. The results show that there is high dust concentration and its movement is consistent with the surface weather record and satellite monitoring images of the observed dust storm. The simulated dust concentration coincides with the observation data of the particulate concentration of PM10 (dust particles smaller than 10 μm in diameter). The new numerical model also successfully simulates the formation and migration of the dust storm of 6-8 April, 2002 in North China.

  9. The Ca(2+ influence on calmodulin unfolding pathway: a steered molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yong Zhang

    Full Text Available The force-induced unfolding of calmodulin (CaM was investigated at atomistic details with steered molecular dynamics. The two isolated CaM domains as well as the full-length CaM were simulated in N-C-terminal pulling scheme, and the isolated N-lobe of CaM was studied specially in two other pulling schemes to test the effect of pulling direction and compare with relevant experiments. Both Ca(2+-loaded CaM and Ca(2+-free CaM were considered in order to define the Ca(2+ influence to the CaM unfolding. The results reveal that the Ca(2+ significantly affects the stability and unfolding behaviors of both the isolated CaM domains and the full-length CaM. In Ca(2+-loaded CaM, N-terminal domain unfolds in priori to the C-terminal domain. But in Ca(2+-free CaM, the unfolding order changes, and C-terminal domain unfolds first. The force-extension curves of CaM unfolding indicate that the major unfolding barrier comes from conquering the interaction of two EF-hand motifs in both N- and C- terminal domains. Our results provide the atomistic-level insights in the force-induced CaM unfolding and explain the observation in recent AFM experiments.

  10. Effect of Strain Field on Threshold Displacement Energy of Tungsten Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Dong; Gao, Ning; Setyawan, W.; Kurtz, R. J.; Wang, Zhi-Guang; Gao, Xing; He, Wen-Hao; Pang, Li-Long

    2016-09-01

    The influence of strain field on defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten (W) has been studied with molecular dynamics simulations. Two different W potentials (Fikar and Juslin) were compared and the results indicate that the connection distance and selected function linking the short-range and long-range portions of the potentials affects the threshold displacement energy and its direction-specific values. The minimum Ed direction calculated with the Fikar-potential is <100> and with the Juslin-potential is <111>. Nevertheless, the most stable self-interstitial configuration is found to be a <111>-crowdion for both potentials. This stable configuration does not change with applied strain. Varying the strain from compression to tension increases the vacancy formation energy but decreases the self-interstitial formation energy. The formation energy of a self-interstitial changes more significantly than a vacancy such that Ed decreases with applied hydrostatic strain from compression to tension.

  11. Association of Multi-Chain Pentablock Ionomers in Solutions: A Molecular Dynamics Simulation Study

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Etampawala, Thusitha; Grest, Gary

    2014-03-01

    Ionic block copolymers in solutions are of interest due to their fascinating ability to self-assemble into a variety of ordered microscopic structures such as ionic domains and hydrocarbon domains. These polymers show unique properties such as chemical and mechanical stability that arise from incompatibility between individual blocks, proton conductivity, ion transportability, and hydrophilicity. Using molecular dynamics simulations we have studied the association of multi-chain pentablock copolymers (A-B-C-B-A) in a 1:1 mixture of cyclohexane and heptane (mutual solvent), and in water at 300K and 500K. The center block consists of randomly sulfonated polystyrene connected to a flexible poly (ethylene-r-propylene) bridge and end caped with poly (t-butyl styrene). We found that the pentablock in mutual solvent forms micelles in solutions with the sulfonated polystyrene in the core and chains of swollen flexible poly (ethylene-r-propylene) and poly (t-butyl styrene) in the corona. In water, the micelle remains quasi-spherical with the ionic groups located on the outer surface at both temperatures. These results are good agreement with those obtained from small angle neutron scattering (SANS). DOE DE-FG02-12ER46843.

  12. Dynamics of the in-run in ski jumping: a simulation study.

    Science.gov (United States)

    Ettema, Gertjan J C; Bråten, Steinar; Bobbert, Maarten F

    2005-08-01

    A ski jumper tries to maintain an aerodynamic position in the in-run during changing environmental forces. The purpose of this study was to analyze the mechanical demands on a ski jumper taking the in-run in a static position. We simulated the in-run in ski jumping with a 4-segment forward dynamic model (foot, leg, thigh, and upper body). The curved path of the in-run was used as kinematic constraint, and drag, lift, and snow friction were incorporated. Drag and snow friction created a forward rotating moment that had to be counteracted by a plantar flexion moment and caused the line of action of the normal force to pass anteriorly to the center of mass continuously. The normal force increased from 0.88 G on the first straight to 1.65 G in the curve. The required knee joint moment increased more because of an altered center of pressure. During the transition from the straight to the curve there was a rapid forward shift of the center of pressure under the foot, reflecting a short but high angular acceleration. Because unrealistically high rates of change of moment are required, an athlete cannot do this without changing body configuration which reduces the required rate of moment changes.

  13. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study.

    Science.gov (United States)

    do Canto, António M T M; Robalo, João R; Santos, Patrícia D; Carvalho, Alfredo J Palace; Ramalho, J P Prates; Loura, Luís M S

    2016-11-01

    Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Synthesis, Bioevaluation and Molecular Dynamic Simulation Studies of Dexibuprofen-Antioxidant Mutual Prodrugs.

    Science.gov (United States)

    Ashraf, Zaman; Alamgeer; Rasool, Raqiqatur; Hassan, Mubashir; Ahsan, Haseeb; Afzal, Samina; Afzal, Khurram; Cho, Hongsik; Kim, Song Ja

    2016-12-21

    Dexibuprofen-antioxidant conjugates were synthesized with the aim to reduce its gastrointestinal effects. The esters analogs of dexibuprofen 5a-c were obtained by reacting its -COOH group with chloroacetyl derivatives 3a-c. The in vitro hydrolysis data confirmed that synthesized prodrugs 5a-c were stable in stomach while undergo significant hydrolysis in 80% human plasma and thus release free dexibuprofen. The minimum reversion was observed at pH 1.2 suggesting that prodrugs are less irritating to stomach than dexibuprofen. The anti-inflammatory activity of 5c (p Molecular docking analysis showed that the prodrugs 5a-c interacts with the residues present in active binding sites of target protein. The stability of drug-target complexes is verified by molecular dynamic simulation study. It exhibited that synthesized prodrugs formed stable complexes with the COX-2 protein thus support our wet lab results. It is therefore concluded that the synthesized prodrugs have promising pharmacological activities with reduced gastrointestinal adverse effects than the parent drug.

  15. Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

    Science.gov (United States)

    Fuson, Michael M.

    2017-01-01

    Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

  16. Local structure and dynamics of benzene confined in the IRMOF-1 nanocavity as studied by molecular dynamics simulation.

    Science.gov (United States)

    Takakura, Kohei; Ueda, Takahiro; Miyakubo, Keisuke; Eguchi, Taro

    2013-01-07

    The local structure and dynamic behaviour of a benzene molecular assembly confined within the nano-cavities of a zinc-based metal-organic framework, [Zn(4)O(CO(2)C(6)H(4)CO(2))(3)](n) (IRMOF-1), were investigated by means of molecular dynamics (MD) simulations. The local structure of the confined benzene molecules was evaluated using radial distribution functions. The sites for adsorption of benzene in IRMOF-1 were well defined by the simulation. The diffusion coefficients at ambient temperature suggested that the mobility of the confined benzene was high, comparable to the bulk fluid. Decreasing the temperature gave rise to the aggregation of benzene in the IRMOF-1 frameworks. Molecular aggregation was attributed to the localization of benzene in the large and the small cavities of IRMOF-1, respectively. Both the translational diffusion coefficient and the trajectory of benzene provided evidence that the localization of benzene in the large and the small cavities takes place at ca. 200 K. Furthermore, at high benzene loading, the migration of benzene in the small cavities was prevented (frozen) below 135 K. Thus, the translational degree of freedom of the benzene molecules changed drastically, depending on the temperature.

  17. Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies.

    Science.gov (United States)

    Stepniewski, Michał; Pasenkiewicz-Gierula, Marta; Róg, Tomasz; Danne, Reinis; Orlowski, Adam; Karttunen, Mikko; Urtti, Arto; Yliperttula, Marjo; Vuorimaa, Elina; Bunker, Alex

    2011-06-21

    We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.

  18. Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

    2011-04-18

    An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.

  19. Preparation of nanoporous systems for the study of the mechanical properties of silica aerogels by Molecular Dynamics simulations

    Science.gov (United States)

    Rivas Murillo, John S.; Bachlechner, Martina E.; Barbero, Ever J.

    2009-03-01

    This presentation focuses on the application of the Molecular Dynamics technique to study the mechanical properties of silica aerogels through the simulation of a tension test. It covers multiple areas, including aspects related to the preparation of a well-relaxed nanoporous system from the expansion of an amorphous bulk sample and the influence of the initial configuration of the system on the final results of the simulated tension test. The results presented here will help to develop a more complete procedure to prepare a proper sample for the study of the mechanical properties of a nanoporous system by using Molecular Dynamics. Comparison of the simulation results and previously published experimental data is provided

  20. Grand canonical Molecular Dynamics Simulations

    CERN Document Server

    Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

    2011-01-01

    For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

  1. Study on the System Design of a Solar Assisted Ground Heat Pump System Using Dynamic Simulation

    Directory of Open Access Journals (Sweden)

    Min Gyung Yu

    2016-04-01

    Full Text Available Recently, the use of hybrid systems using multiple heat sources in buildings to ensure a stable energy supply and improve the system performance has gained attention. Among them, a heat pump system using both solar and ground heat was developed and various system configurations have been introduced. However, establishing a suitable design method for the solar-assisted ground heat pump (SAGHP system including a thermal storage tank is complicated and there are few quantitative studies on the detailed system configurations. Therefore, this study developed three SAGHP system design methods considering the design factors focused on the thermal storage tank. Using dynamic energy simulation code (TRNSYS 17, individual performance analysis models were developed and long-term quantitative analysis was carried out to suggest optimum design and operation methods. As a result, it was found that SYSTEM 2 which is a hybrid system with heat storage tank for only a solar system showed the highest average heat source temperature of 14.81 °C, which is about 11 °C higher than minimum temperature in SYSTEM 3. Furthermore, the best coefficient of performance (COP values of heat pump and system were 5.23 and 4.32 in SYSYEM 2, using high and stable solar heat from a thermal storage tank. Moreover, this paper considered five different geographical and climatic locations and the SAGHP system worked efficiently in having high solar radiation and cool climate zones and the system COP was 4.51 in the case of Winnipeg (Canada where the highest heating demand is required.

  2. The Plastic and Liquid Phases of CCl$_3$Br Studied by Molecular Dynamics Simulations

    CERN Document Server

    Caballero, Nirvana; Carignano, Marcelo; Serra, Pablo

    2013-01-01

    We present a molecular dynamics study of the liquid and plastic crystalline phases of CCl$_3$Br. We investigated the short-range orientational order using a recently developed classification method and we found that both phases behave in a very similar way. The only differences occur at very short molecular separations, which are shown to be very rare. The rotational dynamics was explored using time correlation functions of the molecular bonds. We found that the relaxation dynamics corresponds to an isotropic diffusive mode for the liquid phase, but departs from this behavior as the temperature is decreased and the system transitions into the plastic phase.

  3. Dynamic characterization for tumor- and deformation-induced thermal contrasts on breast surface: a simulation study

    Science.gov (United States)

    Jiang, Li; Zhan, Wang; Loew, Murray H.

    2009-02-01

    Understanding the complex relationship between the thermal contrasts on the breast surface and the underlying physiological and pathological factors is important for thermogram-based breast cancer detection. Our previous work introduced a combined thermal-elastic modeling method with improved ability to simultaneously characterize both elastic-deformation-induced and tumor-induced thermal contrasts on the breast. In this paper, the technique is further extended to investigate the dynamic behaviors of the breast thermal contrasts during cold stress and thermal recovery procedures in the practice of dynamic thermal imaging. A finite-element method (FEM) has been developed for dynamic thermal and elastic modeling. It is combined with a technique to address the nonlinear elasticity of breast tissues, as would arise in the large deformations caused by gravity. Our simulation results indicate that different sources of the thermal contrasts, such as the presence of a tumor, and elastic deformation, have different transient time courses in dynamic thermal imaging with cold-stress and thermal-recovery. Using appropriate quantifications of the thermal contrasts, we find that the tumor- and deformation-induced thermal contrasts show opposite changes in the initial period of the dynamic courses, whereas the global maxima of the contrast curves are reached at different time points during a cold-stress or thermal-recovery procedure. Moreover, deeper tumors generally lead to smaller peaks but have larger lags in the thermal contrast time course. These findings suggest that dynamic thermal imaging could be useful to differentiate the sources of the thermal contrast on breast surface and hence to enhance tumor detectability.

  4. Human motion simulation predictive dynamics

    CERN Document Server

    Abdel-Malek, Karim

    2013-01-01

    Simulate realistic human motion in a virtual world with an optimization-based approach to motion prediction. With this approach, motion is governed by human performance measures, such as speed and energy, which act as objective functions to be optimized. Constraints on joint torques and angles are imposed quite easily. Predicting motion in this way allows one to use avatars to study how and why humans move the way they do, given specific scenarios. It also enables avatars to react to infinitely many scenarios with substantial autonomy. With this approach it is possible to predict dynamic motion without having to integrate equations of motion -- rather than solving equations of motion, this approach solves for a continuous time-dependent curve characterizing joint variables (also called joint profiles) for every degree of freedom. Introduces rigorous mathematical methods for digital human modelling and simulation Focuses on understanding and representing spatial relationships (3D) of biomechanics Develops an i...

  5. Dynamic Stability of Passive Bipedal Walking on Rough Terrain:A Preliminary Simulation Study

    Institute of Scientific and Technical Information of China (English)

    Parsa Nassiri Afshar; Lei Ren

    2012-01-01

    A simplified 2D passive dynamic model was simulated to walk down on a rough slope surface defined by deterministic profiles to investigate how the walking stability changes with increasing surface roughness.Our results show that the passive walker can walk on rough surfaces subject to surface roughness up to approximately 0.1% of its leg length.This indicates that bipedal walkers based on passive dynamics may possess some intrinsic stability to adapt to rough terrains although the maximum roughness they can tolerate is small.Orbital stability method was used to quantify the walking stability before the walker started to fall over.It was found that the average maximum Floquet multiplier increases with surface roughness in a non-linear form.Although the passive walker remained orbitally stable for all the simulation cases,the results suggest that the possibility of the bipedal model moving away from its limit cycle increases with the surface roughness if subjected to additional perturbations.The number of consecutive steps before falling was used to measure the walking stability after the passive walker started to fall over.The results show that the number of steps before falling decreases exponentially with the increase in surface roughness.When the roughness magnitude approached to 0.73% of the walker's leg length,it fell down to the ground as soon as it entered into the uneven terrain.It was also found that shifting the phase angle of the surface profile has apparent affect on the system stability.This is probably because point contact was used to simulate the heel strikes and the resulted variations in system states at heel strikes may have pronounced impact on the passive gaits,which have narrow basins of attraction.These results would provide insight into how the dynamic stability of passive bipedal walkers evolves with increasing surface roughness.

  6. A study on dynamic response of slopes under wave action using simulation tests

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    After the erection of the Three Gorges Dam, the water level of Yangtze River will reach 175 m, and the average wave crest will be up to 1 m. Therefore the wave action cannot be neglected for the slope stability. Through simulation tests, the waveinduced dynamic response of the slope is analyzed. The soil body is taken as linear elastic body when it has a small deformation under the small wave action. Based on tests, the excess pore pressure and slope displacement under the loading in different wave period are analyzed. The ratio of dynamic strength and static strength to the breaking process of the slope is discussed. It is demonstrated that smaller wave period gives rise to a larger strain of the slope under the same stress. At different depth of water, different weakness effect on the stability of the soil slope is observed and the slope has an adaptability to the wave action to some extent.

  7. Deformation behavior of metallic glass composites reinforced with shape memory nanowires studied via molecular dynamics simulations

    Science.gov (United States)

    Şopu, D.; Stoica, M.; Eckert, J.

    2015-05-01

    Molecular dynamics simulations indicate that the deformation behavior and mechanism of Cu64Zr36 composite structures reinforced with B2 CuZr nanowires are strongly influenced by the martensitic phase transformation and distribution of these crystalline precipitates. When nanowires are distributed in the glassy matrix along the deformation direction, a two-steps stress-induced martensitic phase transformation is observed. Since the martensitic transformation is driven by the elastic energy release, the strain localization behavior in the glassy matrix is strongly affected. Therefore, the composite materials reinforced with a crystalline phase, which shows stress-induced martensitic transformation, represent a route for controlling the properties of glassy materials.

  8. Anharmonic resonance absorption of short laser pulses in clusters: A molecular dynamics simulation study

    Science.gov (United States)

    Mahalik, S. S.; Kundu, M.

    2016-12-01

    Linear resonance (LR) absorption of an intense 800 nm laser light in a nano-cluster requires a long laser pulse >100 fs when Mie-plasma frequency ( ω M ) of electrons in the expanding cluster matches the laser frequency (ω). For a short duration of the pulse, the condition for LR is not satisfied. In this case, it was shown by a model and particle-in-cell (PIC) simulations [Phys. Rev. Lett. 96, 123401 (2006)] that electrons absorb laser energy by anharmonic resonance (AHR) when the position-dependent frequency Ω [ r ( t ) ] of an electron in the self-consistent anharmonic potential of the cluster satisfies Ω [ r ( t ) ] = ω . However, AHR remains to be a debate and still obscure in multi-particle plasma simulations. Here, we identify AHR mechanism in a laser driven cluster using molecular dynamics (MD) simulations. By analyzing the trajectory of each MD electron and extracting its Ω [ r ( t ) ] in the self-generated anharmonic plasma potential, it is found that electron is outer ionized only when AHR is met. An anharmonic oscillator model, introduced here, brings out most of the features of MD electrons while passing the AHR. Thus, we not only bridge the gap between PIC simulations, analytical models, and MD calculations for the first time but also unequivocally prove that AHR process is a universal dominant collisionless mechanism of absorption in the short pulse regime or in the early time of longer pulses in clusters.

  9. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  10. Synthesis, Bioevaluation and Molecular Dynamic Simulation Studies of Dexibuprofen–Antioxidant Mutual Prodrugs

    Directory of Open Access Journals (Sweden)

    Zaman Ashraf

    2016-12-01

    Full Text Available Dexibuprofen–antioxidant conjugates were synthesized with the aim to reduce its gastrointestinal effects. The esters analogs of dexibuprofen 5a–c were obtained by reacting its –COOH group with chloroacetyl derivatives 3a–c. The in vitro hydrolysis data confirmed that synthesized prodrugs 5a–c were stable in stomach while undergo significant hydrolysis in 80% human plasma and thus release free dexibuprofen. The minimum reversion was observed at pH 1.2 suggesting that prodrugs are less irritating to stomach than dexibuprofen. The anti-inflammatory activity of 5c (p < 0.001 is more significant than the parent dexibuprofen. The prodrug 5c produced maximum inhibition (42.06% of paw-edema against egg-albumin induced inflammation in mice. Anti-pyretic effects in mice indicated that prodrugs 5a and 5b showed significant inhibition of pyrexia (p < 0.001. The analgesic activity of 5a is more pronounced compared to other synthesized prodrugs. The mean percent inhibition indicated that the prodrug 5a was more active in decreasing the number of writhes induced by acetic acid than standard dexibuprofen. The ulcerogenic activity results assured that synthesized prodrugs produce less gastrointestinal adverse effects than dexibuprofen. The ex vivo antiplatelet aggregation activity results also confirmed that synthesized prodrugs are less irritant to gastrointestinal mucosa than the parent dexibuprofen. Molecular docking analysis showed that the prodrugs 5a–c interacts with the residues present in active binding sites of target protein. The stability of drug–target complexes is verified by molecular dynamic simulation study. It exhibited that synthesized prodrugs formed stable complexes with the COX-2 protein thus support our wet lab results. It is therefore concluded that the synthesized prodrugs have promising pharmacological activities with reduced gastrointestinal adverse effects than the parent drug.

  11. Synthesis, Bioevaluation and Molecular Dynamic Simulation Studies of Dexibuprofen–Antioxidant Mutual Prodrugs

    Science.gov (United States)

    Ashraf, Zaman; Alamgeer; Rasool, Raqiqatur; Hassan, Mubashir; Ahsan, Haseeb; Afzal, Samina; Afzal, Khurram; Cho, Hongsik; Kim, Song Ja

    2016-01-01

    Dexibuprofen–antioxidant conjugates were synthesized with the aim to reduce its gastrointestinal effects. The esters analogs of dexibuprofen 5a–c were obtained by reacting its –COOH group with chloroacetyl derivatives 3a–c. The in vitro hydrolysis data confirmed that synthesized prodrugs 5a–c were stable in stomach while undergo significant hydrolysis in 80% human plasma and thus release free dexibuprofen. The minimum reversion was observed at pH 1.2 suggesting that prodrugs are less irritating to stomach than dexibuprofen. The anti-inflammatory activity of 5c (p < 0.001) is more significant than the parent dexibuprofen. The prodrug 5c produced maximum inhibition (42.06%) of paw-edema against egg-albumin induced inflammation in mice. Anti-pyretic effects in mice indicated that prodrugs 5a and 5b showed significant inhibition of pyrexia (p < 0.001). The analgesic activity of 5a is more pronounced compared to other synthesized prodrugs. The mean percent inhibition indicated that the prodrug 5a was more active in decreasing the number of writhes induced by acetic acid than standard dexibuprofen. The ulcerogenic activity results assured that synthesized prodrugs produce less gastrointestinal adverse effects than dexibuprofen. The ex vivo antiplatelet aggregation activity results also confirmed that synthesized prodrugs are less irritant to gastrointestinal mucosa than the parent dexibuprofen. Molecular docking analysis showed that the prodrugs 5a–c interacts with the residues present in active binding sites of target protein. The stability of drug–target complexes is verified by molecular dynamic simulation study. It exhibited that synthesized prodrugs formed stable complexes with the COX-2 protein thus support our wet lab results. It is therefore concluded that the synthesized prodrugs have promising pharmacological activities with reduced gastrointestinal adverse effects than the parent drug. PMID:28009827

  12. Safety and reliability analysis in a polyvinyl chloride batch process using dynamic simulator-case study: Loss of containment incident.

    Science.gov (United States)

    Rizal, Datu; Tani, Shinichi; Nishiyama, Kimitoshi; Suzuki, Kazuhiko

    2006-10-11

    In this paper, a novel methodology in batch plant safety and reliability analysis is proposed using a dynamic simulator. A batch process involving several safety objects (e.g. sensors, controller, valves, etc.) is activated during the operational stage. The performance of the safety objects is evaluated by the dynamic simulation and a fault propagation model is generated. By using the fault propagation model, an improved fault tree analysis (FTA) method using switching signal mode (SSM) is developed for estimating the probability of failures. The timely dependent failures can be considered as unavailability of safety objects that can cause the accidents in a plant. Finally, the rank of safety object is formulated as performance index (PI) and can be estimated using the importance measures. PI shows the prioritization of safety objects that should be investigated for safety improvement program in the plants. The output of this method can be used for optimal policy in safety object improvement and maintenance. The dynamic simulator was constructed using Visual Modeler (VM, the plant simulator, developed by Omega Simulation Corp., Japan). A case study is focused on the loss of containment (LOC) incident at polyvinyl chloride (PVC) batch process which is consumed the hazardous material, vinyl chloride monomer (VCM).

  13. The nociceptin receptor (NOPR) and its interaction with clinically important agonist molecules: a membrane molecular dynamics simulation study.

    Science.gov (United States)

    Kothandan, Gugan; Gadhe, Changdev G; Balupuri, Anand; Ganapathy, Jagadeesan; Cho, Seung Joo

    2014-12-01

    The nociceptin receptor (NOPR) is an orphan G protein-coupled receptor that contains seven transmembrane helices. NOPR has a distinct mechanism of activation, though it shares a significant homology with other opioid receptors. Previously there have been reports on homology modeling of NOPR and also molecular dynamics simulation studies for a short period. Recently the crystal structure of NOPR was reported. In this study, we analyzed the time dependent behavior of NOPR docked with clinically important agonist molecules such as NOP (natural agonist) peptide and compound 10 (SCH-221510 derivative) using molecular dynamics simulations (MDS) for 100 ns. Molecular dynamics simulations of NOPR-agonist complexes allowed us to refine the system and to also identify stable structures with better binding modes. Structure activity relationships (SAR) for SCH221510 derivatives were investigated and reasons for the activities of these derivatives were determined. Our molecular dynamics trajectory analysis of NOPR-peptide and NOPR-compound 10 complexes found residues to be crucial for binding. Mutagenesis studies on the residues identified from our analysis could prove useful. Our results could also provide useful information in the structure-based drug design of novel and potent agonists targeting NOPR.

  14. Molecular dynamics simulation of diffusivity

    Institute of Scientific and Technical Information of China (English)

    Juanfang LIU; Danling ZENG; Qin LI; Hong GAO

    2008-01-01

    Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.

  15. Study on Ultra-Short Laser Pulse Ablation of Metals by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    LIU Xuan; WANG Yang; ZHAO Li-jie

    2006-01-01

    The dynamical progresses involved in ultra-short laser pulse ablation of face-centered cubic metals under stress confinement condition are described completely using molecular dynamics method. The laser beam absorption and thermal energy turning into kinetics energy of atoms are taken into account to give a detailed picture of laser metal interaction. Superheating phenomenon is observed, and the phase change from solid to liquid is characterized by a destroyed atom configuration and a decreased number density. The steep velocity gradients are found in the systems of Cu and Ni after pulse in consequence of located heating and exponential decrease of fluences following the Lambert-Beer expression. The shock wave velocities are predicted to be about 5000m/s in Cu and 7200m/s in Ni. The higher ablation rates are obtained from simulations compared with experimental data as a result of a well-defined crystalline surface irradiated by a single pulse. Simulation results show that the main mechanisms of ablation are evaporation and thermoelastic stress due to located heating.

  16. A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

    Science.gov (United States)

    Oganesyan, Vasily S.; Chami, Fatima; White, Gaye F.; Thomson, Andrew J.

    2017-01-01

    EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.

  17. 3D dynamic rupture simulation and local tomography studies following the 2010 Haiti earthquake

    Science.gov (United States)

    Douilly, Roby

    The 2010 M7.0 Haiti earthquake was the first major earthquake in southern Haiti in 250 years. As this event could represent the beginning of a new period of active seismicity in the region, and in consideration of how vulnerable the population is to earthquake damage, it is important to understand the nature of this event and how it has influenced seismic hazards in the region. Most significantly, the 2010 earthquake occurred on the secondary Leogâne thrust fault (two fault segments), not the Enriquillo Fault, the major strike-slip fault in the region, despite it being only a few kilometers away. We first use a finite element model to simulate rupture along the Leogâne fault. We varied friction and background stress to investigate the conditions that best explain observed surface deformations and why the rupture did not to jump to the nearby Enriquillo fault. Our model successfully replicated rupture propagation along the two segments of the Leogâne fault, and indicated that a significant stress increase occurred on the top and to the west of the Enriquillo fault. We also investigated the potential ground shaking level in this region if a rupture similar to the Mw 7.0 2010 Haiti earthquake were to occur on the Enriquillo fault. We used a finite element method and assumptions on regional stress to simulate low frequency dynamic rupture propagation for the segment of the Enriquillo fault closer to the capital. The high-frequency ground motion components were calculated using the specific barrier model, and the hybrid synthetics were obtained by combining the low-frequencies ( 1Hz) from the stochastic simulation using matched filtering at a crossover frequency of 1 Hz. The average horizontal peak ground acceleration, computed at several sites of interest through Port-au-Prince (the capital), has a value of 0.35g. Finally, we investigated the 3D local tomography of this region. We considered 897 high-quality records from the earthquake catalog as recorded by

  18. Nonequilibrium study of the chiral magnetic effect from real-time simulations with dynamical fermions

    Science.gov (United States)

    Mace, Mark; Mueller, Niklas; Schlichting, Sören; Sharma, Sayantan

    2017-02-01

    We present a real-time lattice approach to study the nonequilibrium dynamics of vector and axial charges in S U (N )×U (1 ) gauge theories. Based on a classical description of the non-Abelian and Abelian gauge fields, we include dynamical fermions and develop operator definitions for (improved) Wilson and overlap fermions that allow us to study real-time manifestations of the axial anomaly from first principles. We present a first application of this approach to anomalous transport phenomena such as the chiral magnetic effect (CME) and the chiral separation effect (CSE) by studying the dynamics of fermions during and after a S U (N ) sphaleron transition in the presence of a U (1 ) magnetic field. We investigate the fermion mass and magnetic field dependence of the suggested signatures of the CME and the CSE and point out some important aspects which need to be accounted for in the macroscopic description of anomalous transport phenomena.

  19. A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface.

    Science.gov (United States)

    Yang, Hua; Lu, Zhong-Yuan; Li, Ze-Sheng; Sun, Chia-Chung

    2006-03-01

    Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid-liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. [Figure: see text].

  20. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  1. Molecular dynamics simulations of shock waves using the absorbing boundary condition: A case study of methane

    Science.gov (United States)

    Bolesta, Alexey V.; Zheng, Lianqing; Thompson, Donald L.; Sewell, Thomas D.

    2007-12-01

    We report a method that enables long-time molecular dynamics (MD) simulations of shock wave loading. The goal is to mitigate the severe interference effects that arise at interfaces or free boundaries when using standard nonequilibrium MD shock wave approaches. The essence of the method is to capture between two fixed pistons the material state at the precise instant in time when the shock front, initiated by a piston with velocity up at one end of the target sample, traverses the contiguous boundary between the target and a second, stationary piston located at the opposite end of the sample, at which point the second piston is also assigned velocity up and the simulation is continued. Thus, the target material is captured in the energy-volume Hugoniot state resulting from the initial shock wave, and can be propagated forward in time to monitor any subsequent chemistry, plastic deformation, or other time-dependent phenomena compatible with the spatial scale of the simulation. For demonstration purposes, we apply the method to shock-induced chemistry in methane based on the adaptive intermolecular reactive empirical bond order force field [S. J. Stuart , J. Chem. Phys. 112, 6472 (2000)].

  2. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: Quantum chemical calculation and molecular dynamics simulation studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghatee, Mohammad Hadi, E-mail: ghatee@susc.ac.ir; Sedghamiz, Tahereh

    2014-12-05

    Highlights: • Enantiomeric recognition of Propranolol studied by β-Cyclodextrin complexations. • Complexes characterized by PM3 and molecular dynamics (MD) simulation methods. • Results support more stability of R-enantiomer complex in gas and in aqueous solution phases. • Gas phase complexes are unlikely free-energy-wise, though solution phase’s are more likely. • Higher molecular diffusion in aqueous solution phase is inherent to S-enantiomer. - Abstract: Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree–Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.

  3. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: Quantum chemical calculation and molecular dynamics simulation studies

    Science.gov (United States)

    Ghatee, Mohammad Hadi; Sedghamiz, Tahereh

    2014-12-01

    Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree-Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.

  4. Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

    Science.gov (United States)

    Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

    2014-11-01

    The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

  5. Numerical simulation of trapped dipolar quantum gases: Collapse studies and vortex dynamics

    KAUST Repository

    Sparber, Christof

    2010-01-01

    We numerically study the three dimensional Gross-Pitaevskii equation for dipolar quantum gases using a time-splitting algorithm. We are mainly concerned with numerical investigations of the possible blow-up of solutions, i.e. collapse of the condensate, and the dynamics of vortices. © American Institute of Mathematical Sciences.

  6. Numerical simulation study of polar lows in Russian Arctic: dynamical characteristics

    Science.gov (United States)

    Verezemskaya, Polina; Baranyuk, Anastasia; Stepanenko, Victor

    2015-04-01

    Polar Lows (hereafter PL) are intensive mesoscale cyclones, appearing above the sea surface, usually behind the arctic front and characterized by severe weather conditions [1]. All in consequence of the global warming PLs started to emerge in the arctic water area as well - in summer and autumn. The research goal is to examine PLs by considering multisensory data and the resulting numerical mesoscale model. The main purpose was to realize which conditions induce PL development in such thermodynamically unusual season and region as Kara sea. In order to conduct the analysis we used visible and infrared images from MODIS (Aqua). Atmospheric water vapor V, cloud liquid water Q content and surface wind fields W were resampled by examining AMSR-E microwave radiometer data (Aqua)[2], the last one was additionally extracted from QuickSCAT scatterometer. We have selected some PL cases in Kara sea, appeared in autumn of 2007-2008. Life span of the PL was between 24 to 36 hours. Vortexes' characteristics were: W from 15m/s, Q and V values: 0.08-0.11 kg/m2 and 8-15 kg/m2 relatively. Numerical experiments were carried out with Weather Research and Forecasting model (WRF), which was installed on supercomputer "Lomonosov" of Research Computing Center of Moscow State University [3]. As initial conditions was used reanalysis data ERA-Interim from European Centre for Medium-Range Weather Forecasts. Numerical experiments were made with 5 km spatial resolution, with Goddard center microphysical parameterization and explicit convection simulation. Modeling fields were compared with satellite observations and shown good accordance. Than dynamic characteristics were analyzed: evolution of potential and absolute vorticity [4], surface heat and momentum fluxes, and CAPE and WISHE mechanisms realization. 1. Polar lows, J. Turner, E.A. Rasmussen, 612, Cambridge University press, Cambridge, 2003. 2. Zabolotskikh, E. V., Mitnik, L. M., & Chapron, B. (2013). New approach for severe marine

  7. Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Trueba, Alondra Torres [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); Kroon, Maaike C. [Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); Peters, Cor J. [Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); The Petroleum Institute, Chemical Engineering Department, P. O. Box 2533, Abu Dhabi (United Arab Emirates); Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A., E-mail: John.Ripmeester@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Alavi, Saman [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5 (Canada)

    2014-06-07

    Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH{sub 3}F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. {sup 13}C NMR chemical shifts of a CH{sub 3}F/CH{sub 4}/TBME sH hydrate and a temperature analysis of the {sup 2}H NMR powder lineshapes of a CD{sub 3}F/THF sII and CD{sub 3}F/TBME sH hydrate, displayed evidence that the populations of CH{sub 4} and CH{sub 3}F in the D and D{sup ′} cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH{sub 3}F and TBME/CH{sub 4} sH hydrates showed that the presence of CH{sub 3}F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH{sub 3}F and THF/CH{sub 4} sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH{sub 3}F molecules between adjacent small cages.

  8. Spontaneous assembly of HSP90 inhibitors at water/octanol interface: A molecular dynamics simulation study

    Science.gov (United States)

    Zolghadr, Amin Reza; Boroomand, Samaneh

    2017-02-01

    Drug absorption at an acceptable dose depends on the pair of solubility and permeability. There are many potent therapeutics that are not active in vivo, presumably due to the lack of capability to cross the cell membrane. Molecular dynamics simulation of radicicol, diol-radicicol, cyclopropane-radicicol and 17-DMAG were performed at water/octanol interface to suggest interfacial activity as a physico-chemical characteristic of these heat shock protein 90 (HSP90) inhibitors. We have observed that orally active HSP90 inhibitors form aggregates at the water/octanol and DPPC-lipid/water interfaces by starting from an initial configuration with HSP90 inhibitors embedded in the water matrix.

  9. Computational Fluid Dynamics Simulation Study of Active Power Control in Wind Plants

    Energy Technology Data Exchange (ETDEWEB)

    Fleming, Paul; Aho, Jake; Gebraad, Pieter; Pao, Lucy; Zhang, Yingchen

    2016-08-01

    This paper presents an analysis performed on a wind plant's ability to provide active power control services using a high-fidelity computational fluid dynamics-based wind plant simulator. This approach allows examination of the impact on wind turbine wake interactions within a wind plant on performance of the wind plant controller. The paper investigates several control methods for improving performance in waked conditions. One method uses wind plant wake controls, an active field of research in which wind turbine control systems are coordinated to account for their wakes, to improve the overall performance. Results demonstrate the challenge of providing active power control in waked conditions but also the potential methods for improving this performance.

  10. The Effect of Boron on the Properties of Glucomannan: An Experimental and Molecular Dynamics Simulation Study

    Institute of Scientific and Technical Information of China (English)

    PANG Jie; SUN Yu-Jing; LI Bin; TIAN Shi-Ping; CHEN Shao-Jun

    2005-01-01

    The effect of boron on the properties of Konjac Glucomanan (KGM) has been investigated by the method of experiment and molecular dynamic simulation. Upon analysis, the property and structure of KGM are apt to be affected by boron and structural reasons for property change were discussed. In detail, the addition low concentration borax can increase the systematic inherent viscosity, by contrast, high concentration borax has opposite effect on the viscosity. When adding borax, the micropores on KGM film surface decrease or disappear, leading to more compact and uniform on the film surface. The structure of KGM-Boron complex is described as the coor- dination reaction between KGM and boron. The main reaction points are hydroxyl group on C(6) position of sugar as well as those on C(2) and C(3) positions of mannose with two kinds of com- plexes formation: B-K2 and KB-K. And KB-K mainly consists of g-b-m.

  11. Study on adsorptive separation of berberine alkaloids in Coptis Japonica makino by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, D.; Sakoda, A.; Suzuki, M. [University of Tokyo, Tokyo (Japan). Institure of Industrial Science

    1997-12-01

    A calculation approach to discuss the solvent effect on liquid phase adsorption has been developed by using the molecular dynamics simulation method and solvophobic theory. The distinctive feature of the approach is that the calculations of the potential energy changes related to the solvent effect can be achieved on the basis of the molecular structure only, without using any experimental physicochemical property of the solute. This approach is applied to adsorption of five berberine alkaloids contained in Coptis japonica Makino onto the graphite surface from six solvents. Detailed analysis of the potential energy changes due to the solvent effect derived by molecular dynamics calculations yields an outline of the relative adsorption capacities of the alkaloids. Furthermore, the prediction of the preferential adsorption of alkaloids onto a graphite surface from the liquid phase and the eluent strength of solvents for desorption of the alkaloids from graphite surface were obtained. The calculated results are in good agreement with experimental data. 25 refs., 11 figs., 4 tabs.

  12. Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation.

    Science.gov (United States)

    Izanloo, Cobra

    2017-09-26

    An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ∼1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen-phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.

  13. Aspect of Dynamic Simulation and Experimental Research Studies on Hybrid Pneumatic Power System

    Directory of Open Access Journals (Sweden)

    K. David Huang

    2010-01-01

    Full Text Available A Hybrid Pneumatic Power System (HPPS has been developed for several years with the major aim of reducing the vehicle fuel consumption, environment pollution and enhancing the vehicle performance as well. Comparing with the conventional hybrid system, HPPS replaces the battery's electrochemical energy with a high-pressure air storage tank and enables the internal combustion engine (ICE to function at its sweet spot. Besides, the HPPS, which effectively merges both the high-pressure air flow from the storage tank and the recycled exhaust flow from the ICE, thereby increases the thermal efficiency of the ICE and transforms the merged flow energy into mechanical energy using a high-efficiency turbine. This paper focuses on the major research process into HPPSs, including overall dynamic simulation and experimental validation. By using the simulation tool ITI-Sim, this research demonstrates an experiment which can be operated precisely according to the requirements of various driving conditions under which a car actually runs on the road in accordance with the regulated running vehicle test mode. HPPS is expected to increase the performance of the entire system from 15% to 39%, and is likely to replace the traditional system in the coming years.

  14. Supramolecular polymerization of benzene-1,3,5-tricarboxamide: a molecular dynamics simulation study.

    Science.gov (United States)

    Bejagam, Karteek K; Fiorin, Giacomo; Klein, Michael L; Balasubramanian, Sundaram

    2014-05-15

    Supramolecular polymerization in the family of benzene-1,3,5-tricarboxamide (BTA) has been investigated using atomistic molecular dynamics (MD) simulations. Gas phase calculations using a nonpolarizable force field reproduce the cooperativity in binding energy and intermolecular structure seen in quantum chemical calculations. Both quantum chemical and force field based calculations suggest that the ground state structure of the BTA dimer contains two donor hydrogen bonds and one acceptor hydrogen bond rather than the conjectured three-donor and zero-acceptor hydrogen-bonded state. MD simulations of BTA molecules in a realistic solvent, n-nonane, demonstrate the self-assembly process. The free energy (FE) of dimerization and of solvation has been determined. The solvated dimer of BTA with hexyl tails is more stable than two monomers by about 13 kcal/mol. Furthermore, the FE of association of a BTA molecule to an oligomer exhibits a dependence on the oligomer size, which is a robust signature of cooperative self-assembly.

  15. Effect of strain field on displacement cascade in tungsten studied by molecular dynamics simulation

    Science.gov (United States)

    Wang, D.; Gao, N.; Wang, Z. G.; Gao, X.; He, W. H.; Cui, M. H.; Pang, L. L.; Zhu, Y. B.

    2016-10-01

    Using atomistic methods, the coupling effect of strain field and displacement cascade in body-centered cubic (BCC) tungsten is directly simulated by molecular dynamics (MD) simulations at different temperatures. The values of the hydrostatic and uniaxial (parallel or perpendicular to primary knock-on atom (PKA) direction) strains are from -2% to 2% and the temperature is from 100 to 1000 K. Because of the annealing effect, the influence of strain on radiation damage at low temperature has been proved to be more significant than that at high temperature. When the cascade proceeds under the hydrostatic strain, the Frenkel Pair (FP) production, the fraction of defect in cluster and the average size of the defect cluster, all increase at tensile state and decrease at compressive state. When the cascade is under uniaxial strain, the effect of strain parallel to PKA direction is less than the effect of hydrostatic strain, while the effect of strain perpendicular to PKA direction can be negligible. Under the uniaxial strain along direction, the SIA and SIA cluster is observed to orientate along the strain direction at tensile state and the uniaxial compressive strain with direction perpendicular to has led to the similar preferred nucleation. All these results indicate that under irradiation, the tensile state should be avoided for materials used in nuclear power plants.

  16. Dynamic Simulation for Missile Erection System

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to study the dynamic characteristics of the missile erection system, it can be considered as a rigid-flexible coupling multi-body system. Firstly, the actual system is abstracted as an equal and simplified one and then the forces applied to it are analyzed. Secondly, the rigid-flexible coupling dynamic simulation for erection system is accomplished by use of the system simulation software, for example Pro/E, ADAMS, ANSYS, MATLAB/Simulink, etc. Finally, having the aid of simulation results, the kinetic and dynamic characteristics of the flexible bodies in erection system are analyzed.The simulation considering the erection system as a rigid-flexible coupling system can provide valuable results to the research of its kinetic, dynamic and vibrational characteristics.

  17. Non-adiabatic and intersystem crossing dynamics in SO2. II. The role of triplet states in the bound state dynamics studied by surface-hopping simulations.

    Science.gov (United States)

    Mai, Sebastian; Marquetand, Philipp; González, Leticia

    2014-05-28

    The importance of triplet states in the photorelaxation dynamics of SO2 is studied by mixed quantum-classical dynamics simulations. Using the SHARC method, standing for Surface Hopping including ARbitrary Couplings, intersystem crossing (ISC) processes caused by spin-orbit coupling are found occurring on an ultrafast time scale (few 100 fs) and thus competing with internal conversion. While in the singlet-only dynamics only oscillatory population transfer between the (1)B1 and (1)A2 states is observed, in the dynamics including singlet and triplet states we find additionally continuous ISC to the (3)B2 state and to a smaller extent to the (3)B1/(3)A2 coupled states. The populations obtained from the dynamics are discussed with respect to the overall nuclear motion and in the light of recent TRPEPICO studies [I. Wilkinson, A. E. Boguslavskiy, J. Mikosch, D. M. Villeneuve, H.-J. Wörner, M. Spanner, S. Patchkovskii, and A. Stolow, "Excited state dynamics in SO2. I. Bound state relaxation studied by time-resolved photoelectron-photoion coincidence spectroscopy," J. Chem. Phys. 140, 204301 (2014)].

  18. Simulational studies of epitaxial semiconductor superlattices: Quantum dynamical phenomena in ac and dc electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Reynolds, Joseph [Iowa State Univ., Ames, IA (United States)

    1997-10-08

    Using high-accuracy numerical methods the author investigates the dynamics of independent electrons in both ideal and realistic superlattices subject to arbitrary ac and/or dc electric fields. For a variety of superlattice potentials, optically excited initial wave packets, and combinations of ac and dc electric fields, he numerically solves the time-dependent Schroedinger equation. In the case of ideal periodic superlattice potentials, he investigates a long list of dynamical phenomena involving multiple miniband transitions and time-dependent electric fields. These include acceleration effects associated with interminiband transitions in strong fields, Zener resonances between minibands, dynamic localization with ac fields, increased single-miniband transport with an auxiliary resonant ac field, and enhanced or suppressed interminiband probability exchange using an auxiliary ac field. For all of the cases studied, the resulting time-dependent wave function is analyzed by projecting the data onto convenient orthonormal bases. This allows a detailed comparison with approximately analytic treatments. In an effort to explain the rapid decay of experimentally measured Bloch oscillation (BO) signals the author incorporates a one-dimensional representation of interface roughness (IR) into their superlattice potential. He shows that as a result of IR, the electron dynamics can be characterized in terms of many discrete, incommensurate frequencies near the Block frequency. Chapters 2, 3, 4 and 5 have been removed from this report and will be processed separately.

  19. Numerical simulations through first order nonlinear difference equation to study highly ductile symmetric fold (HDSF dynamics: A conceptual study

    Directory of Open Access Journals (Sweden)

    B. S. Sagar

    1998-01-01

    Full Text Available Changes in morphology of a geological fold are due to stress and internally exerting forces (IEFs. Such morphological changes can be quantified in terms of fractal dimensions. Stress and the fractal dimension are depicted in normalized scale as dimensionless parameters.Incorporating these parameters in a first order nonlinear difference equation that has physical relevance as the simplest viable model of a symmetric fold sustaining morphological changes,numerical simulations are carried out which are analogous to creep experiments. In the first experiment, the constant stress (λ is employed to model the morphological dynamical behaviour of highly ductile symmetric folds (HDSFs that are postulated as they are precarious to stress and IEF, and will not supervene the state of brittleness during the evolution. In the second experiment, the time dependent stress that is changed according to a dynamical rule is used to model distinct dynamical behaviors of these HDSFs.The results arrived through computer simulations are the attractor interlimb angles (AIAs.Bifurcation diagrams are also depicted to show the dynamical behaviors concerning the change in the stress dynamics.

  20. Equilibrium Molecular Dynamics (MD Simulation Study of Thermal Conductivity of Graphene Nanoribbon: A Comparative Study on MD Potentials

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    Asir Intisar Khan

    2015-12-01

    Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.

  1. Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study

    Science.gov (United States)

    de Oliveira, César Augusto F.; Hamelberg, Donald; McCammon, J. Andrew

    2007-11-01

    Molecular dynamics (MD) simulation is the standard computational technique used to obtain information on the time evolution of the conformations of proteins and many other molecular systems. However, for most biological systems of interest, the time scale for slow conformational transitions is still inaccessible to standard MD simulations. Several sampling methods have been proposed to address this issue, including the accelerated molecular dynamics method. In this work, we study the extent of sampling of the phi/psi space of alanine dipeptide in explicit water using accelerated molecular dynamics and present a framework to recover the correct kinetic rate constant for the helix to beta-strand transition. We show that the accelerated MD can drastically enhance the sampling of the phi/psi conformational phase space when compared to normal MD. In addition, the free energy density plots of the phi/psi space show that all minima regions are accurately sampled and the canonical distribution is recovered. Moreover, the kinetic rate constant for the helix to beta-strand transition is accurately estimated from these simulations by relating the diffusion coefficient to the local energetic roughness of the energy landscape. Surprisingly, even for such a low barrier transition, it is difficult to obtain enough transitions to accurately estimate the rate constant when one uses normal MD.

  2. Impact of ionic liquids in aqueous solution on bacterial plasma membranes studied with molecular dynamics simulations.

    Science.gov (United States)

    Lim, Geraldine S; Zidar, Jernej; Cheong, Daniel W; Jaenicke, Stephan; Klähn, Marco

    2014-09-04

    The impact of five different imidazolium-based ionic liquids (ILs) diluted in water on the properties of a bacterial plasma membrane is investigated using molecular dynamics (MD) simulations. Cations considered are 1-octyl-3-methylimidazolium (OMIM), 1-octyloxymethyl-3-methylimidazolium (OXMIM), and 1-tetradecyl-3-methylimidazolium (TDMIM), as well as the anions chloride and lactate. The atomistic model of the membrane bilayer is designed to reproduce the lipid composition of the plasma membrane of Gram-negative Escherichia coli. Spontaneous insertion of cations into the membrane is observed in all ILs. Substantially more insertions of OMIM than of OXMIM occur and the presence of chloride reduces cation insertions compared to lactate. In contrast, anions do not adsorb onto the membrane surface nor diffuse into the bilayer. Once inserted, cations are oriented in parallel to membrane lipids with cation alkyl tails embedded into the hydrophobic membrane core, while the imidazolium-ring remains mostly exposed to the solvent. Such inserted cations are strongly associated with one to two phospholipids in the membrane. The overall order of lipids decreased after OMIM and OXMIM insertions, while on the contrary the order of lipids in the vicinity of TDMIM increased. The short alkyl tails of OMIM and OXMIM generate voids in the bilayer that are filled by curling lipids. This cation induced lipid disorder also reduces the average membrane thickness. This effect is not observed after TDMIM insertions due to the similar length of cation alkyl chain and the fatty acids of the lipids. This lipid-mimicking behavior of inserted TDMIM indicates a high membrane affinity of this cation that could lead to an enhanced accumulation of cations in the membrane over time. Overall, the simulations reveal how cations are inserted into the bacterial membrane and how such insertions change its properties. Moreover, the different roles of cations and anions are highlighted and the fundamental

  3. Three-Dimensional Muscle Architecture and Comprehensive Dynamic Properties of Rabbit Gastrocnemius, Plantaris and Soleus: Input for Simulation Studies.

    Directory of Open Access Journals (Sweden)

    Tobias Siebert

    Full Text Available The vastly increasing number of neuro-muscular simulation studies (with increasing numbers of muscles used per simulation is in sharp contrast to a narrow database of necessary muscle parameters. Simulation results depend heavily on rough parameter estimates often obtained by scaling of one muscle parameter set. However, in vivo muscles differ in their individual properties and architecture. Here we provide a comprehensive dataset of dynamic (n = 6 per muscle and geometric (three-dimensional architecture, n = 3 per muscle muscle properties of the rabbit calf muscles gastrocnemius, plantaris, and soleus. For completeness we provide the dynamic muscle properties for further important shank muscles (flexor digitorum longus, extensor digitorum longus, and tibialis anterior; n = 1 per muscle. Maximum shortening velocity (normalized to optimal fiber length of the gastrocnemius is about twice that of soleus, while plantaris showed an intermediate value. The force-velocity relation is similar for gastrocnemius and plantaris but is much more bent for the soleus. Although the muscles vary greatly in their three-dimensional architecture their mean pennation angle and normalized force-length relationships are almost similar. Forces of the muscles were enhanced in the isometric phase following stretching and were depressed following shortening compared to the corresponding isometric forces. While the enhancement was independent of the ramp velocity, the depression was inversely related to the ramp velocity. The lowest effect strength for soleus supports the idea that these effects adapt to muscle function. The careful acquisition of typical dynamical parameters (e.g. force-length and force-velocity relations, force elongation relations of passive components, enhancement and depression effects, and 3D muscle architecture of calf muscles provides valuable comprehensive datasets for e.g. simulations with neuro-muscular models, development of more realistic

  4. Dynamics of Pickering Emulsions in the Presence of an Interfacial Reaction: A Simulation Study.

    Science.gov (United States)

    Zhao, Shuangliang; Zhan, Bicai; Hu, Yaofeng; Fan, Zhaoyu; Pera-Titus, Marc; Liu, Honglai

    2016-12-13

    Pickering emulsions combining surface-active and catalytic properties offer a promising platform for conducting interfacial reactions between immiscible reagents. Despite the significant progress in the design of Pickering interfacial catalysts for a broad panel of reactions, the dynamics of Pickering emulsions under reaction conditions is still poorly understood. Herein, using benzene hydroxylation with aqueous H2O2 as a model system, we explored the dynamics of benzene/water Pickering emulsions during reaction by dissipative particle dynamics. Our study points out that the surface wettability of the silica nanoparticles is affected to a higher extent by the degree of polymer grafting rather than an increase of the chain length of hydrophobic polymer moieties. A remarkable decline of the oil-in-water (O/W) interfacial tension was observed when increasing the yield of the reaction product (phenol), affecting the emulsion stability. However, phenol did not alter to an important extent the distribution of immiscible reagents around the nanoparticles sitting at the benzene/water interface. A synergistic effect between phenol and silica nanoparticles on the O/W interfacial tension of the biphasic system could be ascertained.

  5. Effect of temperature, pressure, and cosolvents on structural and dynamic properties of the hydration shell of SNase: a molecular dynamics computer simulation study.

    Science.gov (United States)

    Smolin, Nikolai; Winter, Roland

    2008-01-24

    It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.

  6. Simulation study on dynamics transition in neuronal activity during sleep cycle by using asynchronous and symmetry neural network model.

    Science.gov (United States)

    Nakao, M; Takahashi, T; Mizutani, Y; Yamamoto, M

    1990-01-01

    We have found that single neuronal activities in different regions in the brain commonly exhibit the distinct dynamics transition during sleep-waking cycle in cats. Especially, power spectral densities of single neuronal activities change their profiles from the white to the 1/f along with sleep cycle from slow wave sleep (SWS) to paradoxical sleep (PS). Each region has different neural network structure and physiological function. This suggests a globally working mechanism may be underlying the dynamics transition we concern. Pharmacological studies have shown that a change in a wide-spread serotonergic input to these regions possibly causes the neuronal dynamics transition during sleep cycle. In this paper, based on these experimental results, an asynchronous and symmetry neural network model including inhibitory input, which represents the role of the serotonergic system, is utilized to examine the reality of our idea that the inhibitory input level varying during sleep cycle induce that transition. Simulation results show that the globally applied inhibitory input can control the dynamics of single neuronal state evolution in the artificial neural network: 1/f-like power spectral density profiles result under weak inhibition, which possibly corresponds to PS, and white profiles under strong inhibition, which possibly corresponds to SWS. An asynchronous neural network is known to change its state according to its energy function. The geometrical structure of network energy function is thought to vary along with the change in inhibitory level, which is expected to cause the dynamics transition of neuronal state evolution in the network model. These simulation results support the possibility that the serotonergic system is essential for the dynamics transition of single neuronal activities during sleep cycle.

  7. The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Pu-pu; Zhao, Li; Long, Shi-yang; Tian, Pu

    2015-04-01

    Human cytosolic sulfotransferases (hSULTs) are important phase II metabolic enzymes. They catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the hydroxyl or primary amine moieties of a large number of endogenous and xenobiotic substrates. Broad selectivity and specificity of binding and activity within the sulfortransferases family could be detected by thermal denaturation assays, which have been made more and more suitable for high throughput screening based on recent technical advances. Here molecular dynamics simulations were used to explore the effect of the cofactor (PAPS) and substrate (LCA) on the thermal stability of the enzyme. It was found that the apo-enzyme unfolded fastest upon heating. The holo-enzyme with bound substrate LCA unfolded slowest. This thermo-denaturation order is consistent with that observed in experiments. Further it was found that the cofactor and substrate will pronouncedly increase the thermal stability of the active pocket regions that interact directly with the ligands. In addition, cofactor and substrate show noticeable synergy effect on the thermal stability of the enzyme.

  8. Ice Storage Air-Conditioning System Simulation with Dynamic Electricity Pricing: A Demand Response Study

    Directory of Open Access Journals (Sweden)

    Chi-Chun Lo

    2016-02-01

    Full Text Available This paper presents an optimal dispatch model of an ice storage air-conditioning system for participants to quickly and accurately perform energy saving and demand response, and to avoid the over contact with electricity price peak. The schedule planning for an ice storage air-conditioning system of demand response is mainly to transfer energy consumption from the peak load to the partial-peak or off-peak load. Least Squares Regression (LSR is used to obtain the polynomial function for the cooling capacity and the cost of power consumption with a real ice storage air-conditioning system. Based on the dynamic electricity pricing, the requirements of cooling loads, and all technical constraints, the dispatch model of the ice-storage air-conditioning system is formulated to minimize the operation cost. The Improved Ripple Bee Swarm Optimization (IRBSO algorithm is proposed to solve the dispatch model of the ice storage air-conditioning system in a daily schedule on summer. Simulation results indicate that reasonable solutions provide a practical and flexible framework allowing the demand response of ice storage air-conditioning systems to demonstrate the optimization of its energy savings and operational efficiency and offering greater energy efficiency.

  9. A Langevin dynamics simulation study of the tribology of polymer loop brushes.

    Science.gov (United States)

    Yin, Fang; Bedrov, Dmitry; Smith, Grant D; Kilbey, S Michael

    2007-08-28

    The tribology of surfaces modified with doubly bound polymer chains (loops) has been investigated in good solvent conditions using Langevin dynamics simulations. The density profiles, brush interpenetration, chain inclination, normal forces, and shear forces for two flat substrates modified by doubly bound bead-necklace polymers and equivalent singly bound polymers (twice as many polymer chains of 12 the molecular weight of the loop chains) were determined and compared as a function of surface separation, grafting density, and shear velocity. The doubly bound polymer layers showed less interpenetration with decreasing separation than the equivalent singly bound layers. Surprisingly, this difference in interpenetration between doubly bound polymer and singly bound polymer did not result in decreased friction at high shear velocity possibly due to the decreased ability of the doubly bound chains to deform in response to the applied shear. However, at lower shear velocity, where deformation of the chains in the flow direction is less pronounced and the difference in interpenetration is greater between the doubly bound and singly bound chains, some reduction in friction was observed.

  10. The interaction between electrolyte and surfaces decorated with charged groups: A molecular dynamics simulation study.

    Science.gov (United States)

    Calero, Carles; Faraudo, Jordi

    2010-01-14

    In this paper, we perform molecular dynamics simulations of an interface containing charged functional groups of different valences in contact with 2:1 ionic solution. We take into account both the finite sizes of the ions in solution and the functional groups but we neglect the structural details of the solvent (primitive model). We show that the distribution of ions and the electrostatic properties of the system depend strongly on the valence of the interfacial charged groups. In the case of surfaces containing well-separated charged interfacial groups, we observe counterion binding at these groups induced by electrostatic interactions. A detailed analysis of the potential of mean force between interfacial charged groups and ions reveals significant features not anticipated by present theories of electrolytes near interfaces. Overall, our results show that, in primitive models of the ion-interface interaction, not only the ionic size and valence are important but the size and valence of the interfacial charged groups also have a significant impact.

  11. Spectroscopic, docking and molecular dynamics simulation studies on the interaction of two Schiff base complexes with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Fani, N. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Bordbar, A.K., E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Ghayeb, Y. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of)

    2013-09-15

    This study was designed to examine the interaction of two Schiff base complexes with human serum albumin (HSA), by different kinds of spectroscopic and molecular modeling techniques. Fluorescence quenching and absorption spectra were investigated in order to estimate the binding parameters. The analysis of absorption data at different temperatures were done in order to estimate the thermodynamics parameters of interactions between Schiff base complexes and HSA. The experimental data suggested that both complexes demonstrated a significant binding affinity to HSA and the process is enthalpy driven. Molecular docking study indicated that both Schiff base complexes bind to polar and apolar residues located in the subdomain IB of HSA. Molecular dynamics (MD) simulations were also performed with the GROMACS program package to study the characters of HSA in binding states. Molecular dynamics results suggested that both Schiff base complexes can interact with HSA, without affecting the secondary structure of HSA but probably with a slight modification of its tertiary structure. All the molecular docking and molecular dynamics results kept in good consistence with experimental data. -- Highlights: • The fluorescence of HSA quenched due to reacting with Schiff base complexes. • The absorbance of Schiff base complexes in the presence of HSA changed. • Binding parameters and the pose of the molecules in the binding site were estimated. • Both complexes can interact with HSA, without affecting the secondary structure. • Simulation results predicted slight compactness of tertiary structure for HSA.

  12. Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.

    Science.gov (United States)

    Debolt, Stephen Edward

    Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

  13. Urea induced unfolding dynamics of flavin adenine dinucleotide (FAD): spectroscopic and molecular dynamics simulation studies from femto-second to nanosecond regime.

    Science.gov (United States)

    Sengupta, Abhigyan; Singh, Reman K; Gavvala, Krishna; Koninti, Raj Kumar; Mukherjee, Arnab; Hazra, Partha

    2014-02-20

    Here, we investigate the effect of urea in the unfolding dynamics of flavin adenine dinucleotide (FAD), an important enzymatic cofactor, through steady state, time-resolved fluorescence spectroscopic and molecular dynamics (MD) simulation studies. Steady state results indicate the possibility of urea induced unfolding of FAD, inferred from increasing emission intensity of FAD with urea. The TCSPC and up-conversion results suggest that the stack-unstack dynamics of FAD severely gets affected in the presence of urea and leads to an increase in the unstack conformation population from 15% in pure water to 40% in 12 M urea. Molecular dynamics simulation was employed to understand the nature of the interaction between FAD and urea at the molecular level. Results depict that urea molecules replace many of the water molecules around adenine and isoalloxazine rings of FAD. However, the major driving force for the stability of this unstack conformations arises from the favorable stacking interaction of a significant fraction of the urea molecules with adenine and isoalloxazine rings of FAD, which overcomes the intramolecular stacking interaction between themselves observed in pure water.

  14. The study of Cu/Nb interface diffusion using molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Ivan V. Nelasov

    2016-06-01

    Full Text Available The peculiarities of interfacial boundary diffusion where the boundary goes between nonmiscible metals with body-centered cubic (BCC and face-centered cubic (FCC lattices have been studied taking, as a case in point, the Cu/Nb system, and using the molecular dynamics method. The diffusion atomic displacements were shown to occur mainly near the mismatch dislocations and their intersections. The diffusion of the high-melting component was found to be characterized by high anisotropy with the predominant atomic displacement along the dense-packed direction in the interfacial boundary plane being common to FCC and BCC lattices with the Kurdyumov–Sachs mutual orientation.

  15. Experimental and molecular dynamics simulation study of structure of liquid and amorphous Ni62Nb38 alloy

    Science.gov (United States)

    Zhang, Y.; Ashcraft, R.; Mendelev, M. I.; Wang, C. Z.; Kelton, K. F.

    2016-11-01

    The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate the AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni-Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. The analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to Tg and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni62Nb38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.

  16. Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

    Energy Technology Data Exchange (ETDEWEB)

    Ravi Kumar, Venkatraman; Umapathy, Siva, E-mail: umapathy@ipc.iisc.ernet.in, E-mail: chandra@bii.a-star.edu.sg [Inorganic and Physical Chemistry Department, Indian Institute of Science, Bangalore 560012 (India); Verma, Chandra, E-mail: umapathy@ipc.iisc.ernet.in, E-mail: chandra@bii.a-star.edu.sg [Bioinformatics Institute - A*STAR, 30 Biopolis Street, # 07-01 Matrix, Singapore 138671 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)

    2016-02-14

    Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm{sup −1} blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1{sup 1}nπ{sup ∗} (band I) and 1{sup 1}ππ{sup ∗} (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm{sup −1}), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to

  17. Cooling rate dependence of solidification for liquid aluminium: a large-scale molecular dynamics simulation study.

    Science.gov (United States)

    Hou, Z Y; Dong, K J; Tian, Z A; Liu, R S; Wang, Z; Wang, J G

    2016-06-29

    The effect of the cooling rate on the solidification process of liquid aluminium is studied using a large-scale molecular dynamics method. It is found that there are various types of short-range order (SRO) structures in the liquid, among which the icosahedral (ICO)-like structures are dominant. These SRO structures are in dynamic fluctuation and transform each other. The effect of the cooling rate on the microstructure is very weak at high temperatures and in supercooled liquids, and it appears only below the liquid-solid transition temperature. Fast cooling rates favour the formation of amorphous structures with ICO-like features, while slow cooling rates favour the formation of FCC crystalline structures. Furthermore, FCC and HCP structures can coexist in crystalline structures. It is also found that nanocrystalline aluminium can be achieved at appropriate cooling rates, and its formation mechanism is thoroughly investigated by tracing the evolution of nanoclusters. The arrangement of FCC and HCP atoms in the nanograins displays various twinned structures as observed using visualization analysis, which is different from the layering or phase separation structures observed in the solidification of Lennard-Jones fluids and some metal liquids.

  18. Dynamic Simulation of the Green Roofs Impact on Building Energy Performance, Case Study of Antananarivo, Madagascar

    Directory of Open Access Journals (Sweden)

    Hery Tiana Rakotondramiarana

    2015-05-01

    Full Text Available Green roofs improve building energy performance and constitute an alternative to sustainable buildings. A green roof model is dynamically coupled with a building thermal model to assess its energy performance that takes into account the indoor air temperature dynamic changes. Under the climate conditions in Antananarivo, we compared green and conventional roofs. The present study shows that green roofs protect the roof structure under extreme temperature and large temperature fluctuations. For the case of Antananarivo, the amplitude of the temperature fluctuations at the top face of the support is reduced by 28 °C when using green roof. The impact of the green roof on indoor air temperature and energy demand is investigated. The vegetation decreases the maximum indoor air temperature and improves the building thermal comfort during summer days. It has no effect on the minimum indoor air temperature, but additional soil thickness can increase it. In addition, a global sensitivity analysis, which is carried out on the proposed model without considering any specific weather data, allows us to identify the most influential parameters on the energy demand. It has been found that green roofs have almost insignificant thermal impact in insulated buildings; however, their potential prevails over the building envelope and weather characteristics in the case of non-insulated building.

  19. The data system dynamic simulation /DSDS/

    Science.gov (United States)

    Hooper, J. W.; Piner, J. R.

    1978-01-01

    The paper describes the development by NASA of the data system dynamic simulation (DSDS) which provides a data system simulation capability for a broad range of programs, with the capability to model and simulate all or any portion of an end-to-end data system to multiple levels of fidelity. Versatility is achieved by specifying parameters which define the performance characteristics of data system components, and by specifying control and data paths in a data system. DSDS helps reduce overall simulation cost and the time required for obtaining a data systems analysis, and helps provide both early realistic representations of data systems and the flexibility to study design changes and operating strategies.

  20. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation.

    Science.gov (United States)

    Chen, Lin; Li, Xue; Wang, Ruige; Fang, Fengqin; Yang, Wanli; Kan, Wei

    2016-07-01

    The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic Thermoytoga maritima RBP (tmRBP) and mesophilic Escherichia coli homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologs and the ecRBP unfolds faster than the hyperthermophilic homologs at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different directions of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.

  1. Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-12-10

    In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  2. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

    Science.gov (United States)

    Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

    2017-01-01

    The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis. PMID:28192428

  3. Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Arkundato, Artoto [Physics Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Su' ud, Zaki [Physics Department, Faculty of Mathematical and Natural Sciences, Bandung Institute of Technology, Jl. Ganesha 10, Bandung (Indonesia); Sudarko [Chemistry Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Shafii, Mohammad Ali [Physics Department, Faculty of Mathematical and Natural Sciences, Andalas University, Padang (Indonesia); Celino, Massimo [ENEA, CR Casaccia, Via Anguillarese 301, Rome (Italy)

    2014-09-30

    Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal.

  4. Three-dimensional ordering of cold ion beams in a storage ring: A molecular-dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Yuri, Yosuke, E-mail: yuri.yosuke@jaea.go.jp [Takasaki Advanced Radiation Research Institute, Japan Atomic Energy Agency, 1233 Watanuki-machi Takasaki, Gunma 370-1292 Japan (Japan)

    2015-06-29

    Three-dimensional (3D) ordering of a charged-particle beams circulating in a storage ring is systematically studied with a molecular-dynamics simulation code. An ion beam can exhibit a 3D ordered configuration at ultralow temperature as a result of powerful 3D laser cooling. Various unique characteristics of the ordered beams, different from those of crystalline beams, are revealed in detail, such as the single-particle motion in the transverse and longitudinal directions, and the dependence of the tune depression and the Coulomb coupling constant on the operating points.

  5. Phase behavior and molecular dynamics simulation studies of new aqueous two-phase separation systems induced by HEPES buffer.

    Science.gov (United States)

    Taha, Mohamed; Khoiroh, Ianatul; Lee, Ming-Jer

    2013-01-17

    Here, for the first time, we show that with addition of a biological buffer, 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES), into aqueous solutions of tetrahydrofuran (THF), 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone, the organic solvent can be excluded from water to form a new liquid phase. The phase diagrams have been determined at ambient temperature. In order to understand why and how a zwitterion solute (HEPES) induced phase separation of the investigated systems, molecular dynamics (MD) simulation studies are performed for HEPES + water + THF system. The MD simulations were conducted for the aqueous mixtures with 12 different compositions. The reliability of the simulation results of HEPES in pure water and beyond the phase separation mixtures was justified by comparing the densities obtained from MD with the experimental values. The simulation results of HEPES in pure THF and in a composition inside the phase separation region were justified qualitatively. Interestingly, all HEPES molecules entirely aggregated in pure THF. This reveals that HEPES is insoluble in pure THF, which is consistent with the experimental results. Even more interestingly, the MD simulation for the mixture with composition inside the phase separation region showed the formation of two phases. The THF molecules are squeezed out from the water network into a new liquid phase. The hydrogen bonds (HBs), HB lifetime, HB Gibbs energy (ΔG), radial distribution functions (RDFs), coordination numbers (CNs), electrostatic interactions, and the van der Waals interactions between the different species have been analyzed. Further, MD simulations for the other phase separation systems by choosing a composition inside the two liquids region for each system were also simulated. Our findings will therefore pave the way for designing new benign separation auxiliary agents.

  6. Molecular Dynamics Simulation Study of Atomic Segregation of (PdPt)147 during the Heating Process

    Science.gov (United States)

    Xiao, X. Y.; Cheng, Z. F.; Xia, J. H.

    Research on the influence of alloy concentration and distribution on bimetallic cluster plays a key role in exploring new structural material. This paper studies the melting process of icosahedral bimetallic cluster (PdPt)147 with different Pt concentrations and different atomic distributions by using molecular dynamics with an embedded atom method. The results indicate that the mixed Pd-Pt cluster shows an irregular phenomenon between 580 and 630 K, i.e. the atomic energy decreases with the increase of temperature. This is because the surface energy of Pd is lower than that of Pt; the decreased energy due to Pd atomic segregation is larger than the increased energy due to heating during the segregation process. In addition, the temperature of Pd atomic segregation is strongly related to Pt concentration. This leads to that Pd atoms prefer to remain on the surface even after the cluster melted.

  7. Steady-state and dynamic simulation study on boil-off gas minimization and recovery strategies at LNG exporting terminals

    Science.gov (United States)

    Kurle, Yogesh

    Liquefied natural gas (LNG) is becoming one of the prominent clean energy sources with its abundance, high calorific value, low emission, and price. Vapors generated from LNG due to heat leak are called boil-off gas (BOG). As world-wide LNG productions are increasing fast, BOG generation and handling problems are becoming more critical. Also, due to stringent environmental regulations, flaring of BOG is not a viable option. In this study, typical Propane-and-Mixed-Refrigerant (C3-MR) process, storage facilities, and loading facilities are modeled and simulated to study BOG generation at LNG exporting terminals, including LNG processing, storage, and berth loading areas. Factors causing BOG are presented, and quantities of BOG generated due to each factor at each location are calculated under different LNG temperatures. Various strategies to minimize, recover, and reuse BOG are also studied for their feasibility and energy requirements. Rate of BOG generation during LNG loading---Jetty BOG (JBOG)---changes significantly with loading time. In this study, LNG vessel loading is simulated using dynamic process simulation software to obtain JBOG generation profile and to study JBOG recovery strategies. Also, fuel requirements for LNG plant to run steam-turbine driven compressors and gas-turbine driven compressors are calculated. Handling of JBOG generated from multiple loadings is also considered. The study would help proper handling of BOG problems in terms of minimizing flaring at LNG exporting terminals, and thus reducing waste, saving energy, and protecting surrounding environments.

  8. Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2

    Science.gov (United States)

    Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori

    2005-07-01

    An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.

  9. Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

    Science.gov (United States)

    Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

    2013-08-01

    In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

  10. Study of structural and conformational change in cytochrome, C through molecular dynamic simulation in presence of gold nanoparticles

    Science.gov (United States)

    Moudgil, Lovika; Singh, Baljinder; Kaura, Aman; Singh, Gurinder; Tripathi, S. K.; Saini, G. S. S.

    2017-05-01

    Proteins are the most abundant organic molecules in living system having diverse structures and various functions than the other classes of macromolecules. We have done Molecular Dynamics (MD) simulation of the Cytochrome,C (Cyt,c) protein found in plants, animals and many unicellular animals in the presence of gold nanoparticles (Au NPs). MD results helped to recognize the amino acids that play important role to make the interaction possible between protein and gold surface. In the present study we have examined the structural change of protein in the presence of gold surface and its adsorption on the surface through MD simulations with the help of Gold-Protein (GolP) force field. Results were further analyzed to understand the protein interaction up to molecular level.

  11. Study of dynamic structure and heat and mass transfer of a vertical ceramic tiles dryer using CFD simulations

    Science.gov (United States)

    Kriaa, Wassim; Bejaoui, Salma; Mhiri, Hatem; Le Palec, Georges; Bournot, Philippe

    2014-02-01

    In this study, we developed a two-dimensional Computational Fluid Dynamics (CFD) model to simulate dynamic structure and heat and mass transfer of a vertical ceramic tiles dryer (EVA 702). The carrier's motion imposed the choice of a dynamic mesh based on two methods: "spring based smoothing" and "local remeshing". The dryer airflow is considered as turbulent ( Re = 1.09 × 105 at the dryer inlet), therefore the Re-Normalization Group model with Enhanced Wall Treatment was used as a turbulence model. The resolution of the governing equation was performed with Fluent 6.3 whose capacities do not allow the direct resolution of drying problems. Thus, a user defined scalar equation was inserted in the CFD code to model moisture content diffusion into tiles. User-defined functions were implemented to define carriers' motion, thermo-physical properties… etc. We adopted also a "two-step" simulation method: in the first step, we follow the heat transfer coefficient evolution (Hc). In the second step, we determine the mass transfer coefficient (Hm) and the features fields of drying air and ceramic tiles. The found results in mixed convection mode (Fr = 5.39 at the dryer inlet) were used to describe dynamic and thermal fields of airflow and heat and mass transfer close to the ceramic tiles. The response of ceramic tiles to heat and mass transfer was studied based on Biot numbers. The evolutions of averages temperature and moisture content of ceramic tiles were analyzed. Lastly, comparison between experimental and numerical results showed a good agreement.

  12. Vehicle dynamics modeling and simulation

    CERN Document Server

    Schramm, Dieter; Bardini, Roberto

    2014-01-01

    The authors examine in detail the fundamentals and mathematical descriptions of the dynamics of automobiles. In this context different levels of complexity will be presented, starting with basic single-track models up to complex three-dimensional multi-body models. A particular focus is on the process of establishing mathematical models on the basis of real cars and the validation of simulation results. The methods presented are explained in detail by means of selected application scenarios.

  13. Molecular dynamics simulation of pyridine

    Science.gov (United States)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

  14. Multibody dynamic simulation of knee contact mechanics.

    Science.gov (United States)

    Bei, Yanhong; Fregly, Benjamin J

    2004-11-01

    Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multibody knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer's CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously.

  15. Molecular dynamics simulation and molecular docking studies of Angiotensin converting enzyme with inhibitor lisinopril and amyloid Beta Peptide.

    Science.gov (United States)

    Jalkute, Chidambar Balbhim; Barage, Sagar Hindurao; Dhanavade, Maruti Jayram; Sonawane, Kailas Dasharath

    2013-06-01

    Angiotensin converting enzyme (ACE) cleaves amyloid beta peptide. So far this cleavage mechanism has not been studied in detail at atomic level. Keeping this view in mind, we performed molecular dynamics simulation of crystal structure complex of testis truncated version of ACE (tACE) and its inhibitor lisinopril along with Zn(2+) to understand the dynamic behavior of active site residues of tACE. Root mean square deviation results revealed the stability of tACE throughout simulation. The residues Ala 354, Glu 376, Asp 377, Glu 384, His 513, Tyr 520 and Tyr 523 of tACE stabilized lisinopril by hydrogen bonding interactions. Using this information in subsequent part of study, molecular docking of tACE crystal structure with Aβ-peptide has been made to investigate the interactions of Aβ-peptide with enzyme tACE. The residues Asp 7 and Ser 8 of Aβ-peptide were found in close contact with Glu 384 of tACE along with Zn(2+). This study has demonstrated that the residue Glu 384 of tACE might play key role in the degradation of Aβ-peptide by cleaving peptide bond between Asp 7 and Ser 8 residues. Molecular basis generated by this attempt could provide valuable information towards designing of new therapies to control Aβ concentration in Alzheimer's patient.

  16. Hydration effects and antifouling properties of poly(vinyl chloride-co-PEGMA) membranes studied using molecular dynamics simulations

    Science.gov (United States)

    Shaikh, Abdul Rajjak; Rajabzadeh, Saeid; Matsuo, Ryuichi; Takaba, Hiromitsu; Matsuyama, Hideto

    2016-04-01

    Polyvinyl chloride (PVC) membranes are widely used in water treatment because of their low cost and chemical stability. However, PVC membranes can become fouled, and this restricts their applications in membrane technology. In order to enhance the antifouling property of PVC membranes, copolymers such as poly(vinyl chloride-co-poly(ethylene glycol)methyl ether methacrylate) (poly(VC-co-PEGMA)) with different PEGMA segment percentages were synthesized in our previous work. Experimentally, it was observed that the poly(VC-co-PEGMA) copolymer has better antifouling properties than those of PVC membranes. Here, we explore effect of the PEGMA segment percentage on the surface hydration properties of poly(VC-co-PEGMA) copolymers. Density functional theory calculations and molecular dynamics simulations were carried out to understand the interactions between PVC and PEGMA. Model structures of these systems were validated by comparing the simulated values of their volumetric properties with the experimental values. MD studies showed that increasing PEGMA percentage in the copolymer increases the interaction with water molecules, leading to improved resistance to fouling. The antifouling mechanism is also discussed with respect to surface hydration and water dynamicity. This study could form a basis for the systematic studies of polymeric membranes as well as their stability from the extent of solvent-polymer, solvent-solvent, and polymer-polymer interactions.

  17. 横针机构的动态仿真研究%Study on Dynamic Simulation of Transverse Needle Mechanism

    Institute of Scientific and Technical Information of China (English)

    李瑞琴; 邹慧君; 郭为忠

    2004-01-01

    This paper studied dynamic simulation of transverse needle mechanism that was used for the multi-purpose sewing machine. The simulation software of transverse needle mechanism was programmed, which can dynamically input all structure parameters and realize dynamic simulation. This software can rapidly get the pattern cam contour according to the design requirements for the transverse stitch length. Through different transverse stitch length and different straight stitch length cooperate, multi-purpose sewing machines can realize to sew arbitrary thread trace. The parameters of the pattern cam contours can be used as the design parameters of pattern electronic cam. This paper provides design basis for the mechatronic transverse needle mechanism.%对用于多功能缝纫机中的横针机构进行了动态仿真研究.编制的横针机构的仿真软件实现了全部结构参数的动态输入,动态仿真.并可根据对横针距的设计要求,快速反求花模凸轮的轮廓.不同的横针距与直针距相配合,可以实现任意给定的缝纫线迹.求出的花模凸轮的廓线数据,可作为花模电子凸轮的设计参数,为横针机构的机电一体化提供了设计基础.

  18. The Value of Optimization in Dynamic Ride-Sharing: a Simulation Study in Metro Atlanta

    NARCIS (Netherlands)

    N.A.H. Agatz (Niels); A. Erera (Alan); M.W.P. Savelsbergh (Martin); X. Wang (Xing)

    2010-01-01

    textabstractSmartphone technology enables dynamic ride-sharing systems that bring together people with similar itineraries and time schedules to share rides on short-notice. This paper considers the problem of matching drivers and riders in this dynamic setting. We develop optimization-based approac

  19. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    Energy Technology Data Exchange (ETDEWEB)

    Arthur, Carly W. [Univ. of California, Davis, CA (United States). Dept. of Civil and Environmental Engineering; Goto, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-11-30

    This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

  20. Molecular dynamics simulation of benzene

    Science.gov (United States)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  1. Dynamic simulations of tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E. [and others

    1996-02-01

    The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.

  2. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

    Science.gov (United States)

    Stadlbauer, Petr; Krepl, Miroslav; Cheatham, Thomas E.; Koča, Jaroslav; Šponer, Jiří

    2013-01-01

    Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales. PMID:23700306

  3. Molecular Dynamics Simulation Study of the Early Stages of Nucleation of Iron Oxyhydroxide Nanoparticles in Aqueous Solutions.

    Science.gov (United States)

    Zhang, Hengzhong; Waychunas, Glenn A; Banfield, Jillian F

    2015-08-20

    Nucleation is a fundamental step in crystal growth. Of environmental and materials relevance are reactions that lead to nucleation of iron oxyhydroxides in aqueous solutions. These reactions are difficult to study experimentally due to their rapid kinetics. Here, we used classical molecular dynamics simulations to investigate nucleation of iron hydroxide/oxyhydroxide nanoparticles in aqueous solutions. Results show that in a solution containing ferric ions and hydroxyl groups, iron-hydroxyl molecular clusters form by merging ferric monomers, dimers, and other oligomers, driven by strong affinity of ferric ions to hydroxyls. When deprotonation reactions are not considered in the simulations, these clusters aggregate to form small iron hydroxide nanocrystals with a six-membered ring-like layered structure allomeric to gibbsite. By comparison, in a solution containing iron chloride and sodium hydroxide, the presence of chlorine drives cluster assembly along a different direction to form long molecular chains (rather than rings) composed of Fe-O octahedra linked by edge sharing. Further, in chlorine-free solutions, when deprotonation reactions are considered, the simulations predict ultimate formation of amorphous iron oxyhydroxide nanoparticles with local atomic structure similar to that of ferrihydrite nanoparticles. Overall, our simulation results reveal that nucleation of iron oxyhydroxide nanoparticles proceeds via a cluster aggregation-based nonclassical pathway.

  4. A molecular dynamics simulation study of temperature and depth effect on helium bubble releasing from Ti surface

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Li; Ma, Mingwang; Xiang, Wei; Wang, Yuan; Cheng, Yanlin; Tan, Xiaohua, E-mail: caepiee@163.com

    2015-10-05

    Highlights: • Features of helium bubble at varied depths in Ti are researched by MD simulation. • Effect of Temperature on helium bubble in Ti is researched by MD simulation. • The mechanism of helium bubble releasing from metal is clarified. - Abstract: Using molecular dynamics simulation, the effect of environment temperature and depth of helium bubble on its volume, pressure and releasing process in metal Ti is researched. First, through studying the statuses of helium bubble at different depths at 300 K, the regularity of helium bubble shape, volume and pressure is acquired. The results show that with depth augmenting, the pressure increases gradually, while the volume decreases, but these two parameters keep around some level when depth is greater than 2.6 nm. Then, the evolution of model system with helium bubble at various temperatures is simulated. On the whole, the critical releasing temperature increases with depth. Finally, the mechanism of helium bubble releasing from Ti surface is explained. It is found that the bubble would tear the Ti film above it when its pressure is greater than the tensile strength of metal film, and then helium atoms will release from the metal.

  5. Towards Four-Flavour Dynamical Simulations

    CERN Document Server

    Herdoiza, Gregorio

    2010-01-01

    The inclusion of physical effects from sea quarks has been one of the main advances in lattice QCD simulations over the last few years. We report on recent studies with four flavours of dynamical quarks and address some of the potential issues arising in this new setup. First results for physical observables in the light, strange and charm sectors are presented together with the status of dedicated simulations to perform the non-perturbative renormalisation in mass-independent schemes.

  6. Towards four-flavour dynamical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Herdoiza, Gregorio [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC; Univ. Autonoma de Madrid (Spain). Dept. de Fisica Teorica e Inst. de Fiscia Teorica

    2011-03-15

    The inclusion of physical effects from sea quarks has been one of the main advances in lattice QCD simulations over the last few years. We report on recent studies with four flavours of dynamical quarks and address some of the potential issues arising in this new setup. First results for physical observables in the light, strange and charm sectors are presented together with the status of dedicated simulations to perform the non-perturbative renormalisation in mass-independent schemes. (orig.)

  7. Composition Dependence of Dynamic Heterogeneity Time- and Length Scales in [Omim][BF4]/Water Binary Mixtures: Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Pal, Tamisra; Biswas, Ranjit

    2015-12-24

    Composition dependence of four-point dynamic susceptibilities, overlap functions, and other dynamic heterogeneity (DH) parameters have been investigated by using all-atom molecular dynamics simulations for aqueous solutions of the ionic liquid (IL), 1-octyl-3-methyl imidazolium tetrafluoroborate ([Omim][BF4]) covering the pure-to-pure range. Upon addition of water in the IL, the DH time scales become faster and the four-point dynamic susceptibility time scale softens. Evidences for jump motions for both water and ions have been found from the simulated single particle displacements that show strong deviation from Gaussian distribution. Estimated dynamic correlation length for water reflects effects of IL, whereas those for ions remain largely insensitive to the mixture composition. Simulated structural aspects and DH time scales provide microscopic explanations to the existing experimental observations from time-resolved fluorescence and Kerr spectroscopic measurements.

  8. Systematic comparison of position and time dependent macroparticle simulations in beam dynamics studies

    Directory of Open Access Journals (Sweden)

    Ji Qiang

    2002-06-01

    Full Text Available Macroparticle simulation plays an important role in modern accelerator design and operation. Most linear rf accelerators have been designed based on macroparticle simulations using longitudinal position as the independent variable. In this paper, we have done a systematic comparison between using longitudinal position as the independent variable and using time as the independent variable in macroparticle simulations. We have found that, for an rms-matched beam, the maximum relative moment difference for second, fourth moments and beam maximum amplitudes between these two types of simulations is 0.25% in a 10 m reference transport system with physical parameters similar to the Spallation Neutron Source linac design. The maximum z-to- t transform error in the space-charge force calculation of the position dependent simulation is about 0.1% in such a system. This might cause a several percent error in a complete simulation of a linac with a length of hundreds of meters. Furthermore, the error may be several times larger in simulations of mismatched beams. However, if such errors are acceptable to the linac designer, then one is justified in using position dependent macroparticle simulations in this type of linac design application.

  9. Atomistic simulation studies on the dynamics and thermodynamics of nonpolar molecules within the zeolite imidazolate framework-8.

    Science.gov (United States)

    Pantatosaki, Evangelia; Pazzona, Federico G; Megariotis, Gregory; Papadopoulos, George K

    2010-02-25

    Statistical-mechanics-based simulation studies at the atomistic level of argon (Ar), methane (CH(4)), and hydrogen (H(2)) sorbed in the zeolite imidazolate framework-8 (ZIF-8) are reported. ZIF-8 is a product of a special kind of chemical process, recently termed as reticular synthesis, which has generated a class of materials of critical importance as molecular binders. In this work, we explore the mechanisms that govern the sorption thermodynamics and kinetics of nonpolar sorbates possessing different sizes and strength of interactions with the metal-organic framework to understand the outstanding properties of this novel class of sorbents, as revealed by experiments published elsewhere. For this purpose, we have developed an in-house modeling procedure involving calculations of sorption isotherms, partial internal energies, various probability density functions, and molecular dynamics for the simulation of the sorbed phase over a wide range of occupancies and temperatures within a digitally reconstructed unit cell of ZIF-8. The results showed that sorbates perceive a marked energetic inhomogeneity within the atomic framework of the metal-organic material under study, resulting in free energy barriers that give rise to inflections in the sorption isotherms and guide the dynamics of guest molecules.

  10. The effect of C-terminal helix on the stability of FF domain studied by molecular dynamics simulation.

    Science.gov (United States)

    Zhao, Liling; Cao, Zanxia; Wang, Jihua

    2012-01-01

    To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.

  11. Investigation of dynamic SPECT measurements of the arterial input function in human subjects using simulation, phantom and human studies

    Science.gov (United States)

    Winant, Celeste D.; Aparici, Carina Mari; Zelnik, Yuval R.; Reutter, Bryan W.; Sitek, Arkadiusz; Bacharach, Stephen L.; Gullberg, Grant T.

    2012-01-01

    Computer simulations, a phantom study and a human study were performed to determine whether a slowly rotating single-photon computed emission tomography (SPECT) system could provide accurate arterial input functions for quantification of myocardial perfusion imaging using kinetic models. The errors induced by data inconsistency associated with imaging with slow camera rotation during tracer injection were evaluated with an approach called SPECT/P (dynamic SPECT from positron emission tomography (PET)) and SPECT/D (dynamic SPECT from database of SPECT phantom projections). SPECT/P simulated SPECT-like dynamic projections using reprojections of reconstructed dynamic 94Tc-methoxyisobutylisonitrile (94Tc-MIBI) PET images acquired in three human subjects (1 min infusion). This approach was used to evaluate the accuracy of estimating myocardial wash-in rate parameters K1 for rotation speeds providing 180° of projection data every 27 or 54 s. Blood input and myocardium tissue time-activity curves (TACs) were estimated using spatiotemporal splines. These were fit to a one-compartment perfusion model to obtain wash-in rate parameters K1. For the second method (SPECT/D), an anthropomorphic cardiac torso phantom was used to create real SPECT dynamic projection data of a tracer distribution derived from 94Tc-MIBI PET scans in the blood pool, myocardium, liver and background. This method introduced attenuation, collimation and scatter into the modeling of dynamic SPECT projections. Both approaches were used to evaluate the accuracy of estimating myocardial wash-in parameters for rotation speeds providing 180° of projection data every 27 and 54 s. Dynamic cardiac SPECT was also performed in a human subject at rest using a hybrid SPECT/CT scanner. Dynamic measurements of 99mTc-tetrofosmin in the myocardium were obtained using an infusion time of 2 min. Blood input, myocardium tissue and liver TACs were estimated using the same spatiotemporal splines. The spatiotemporal maximum

  12. Investigation of dynamic SPECT measurements of the arterial input function in human subjects using simulation, phantom and human studies.

    Science.gov (United States)

    Winant, Celeste D; Aparici, Carina Mari; Zelnik, Yuval R; Reutter, Bryan W; Sitek, Arkadiusz; Bacharach, Stephen L; Gullberg, Grant T

    2012-01-21

    Computer simulations, a phantom study and a human study were performed to determine whether a slowly rotating single-photon computed emission tomography (SPECT) system could provide accurate arterial input functions for quantification of myocardial perfusion imaging using kinetic models. The errors induced by data inconsistency associated with imaging with slow camera rotation during tracer injection were evaluated with an approach called SPECT/P (dynamic SPECT from positron emission tomography (PET)) and SPECT/D (dynamic SPECT from database of SPECT phantom projections). SPECT/P simulated SPECT-like dynamic projections using reprojections of reconstructed dynamic (94)Tc-methoxyisobutylisonitrile ((94)Tc-MIBI) PET images acquired in three human subjects (1 min infusion). This approach was used to evaluate the accuracy of estimating myocardial wash-in rate parameters K(1) for rotation speeds providing 180° of projection data every 27 or 54 s. Blood input and myocardium tissue time-activity curves (TACs) were estimated using spatiotemporal splines. These were fit to a one-compartment perfusion model to obtain wash-in rate parameters K(1). For the second method (SPECT/D), an anthropomorphic cardiac torso phantom was used to create real SPECT dynamic projection data of a tracer distribution derived from (94)Tc-MIBI PET scans in the blood pool, myocardium, liver and background. This method introduced attenuation, collimation and scatter into the modeling of dynamic SPECT projections. Both approaches were used to evaluate the accuracy of estimating myocardial wash-in parameters for rotation speeds providing 180° of projection data every 27 and 54 s. Dynamic cardiac SPECT was also performed in a human subject at rest using a hybrid SPECT/CT scanner. Dynamic measurements of (99m)Tc-tetrofosmin in the myocardium were obtained using an infusion time of 2 min. Blood input, myocardium tissue and liver TACs were estimated using the same spatiotemporal splines. The

  13. Solvation structure and dynamics of cis- and trans-1,2 dichloroethene isomers in supercritical carbon dioxide. A molecular dynamics simulation study.

    Science.gov (United States)

    Dellis, Dimitris; Skarmoutsos, Ioannis; Samios, Jannis

    2011-10-27

    Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for state points along a near-critical isotherm (1.02 T(c)) over a wide range of densities, using new developed optimized potential models for both isomers. The similarities and differences in the solvation structures around each isomer have been presented and discussed. The local density augmentation and enhancement factors of CO(2) around the isomers have been found significantly larger than the corresponding values for pure supercritical CO(2). The dynamic local density reorganization has been investigated and related to previously proposed relaxation mechanisms. The density dependence of the calculated self-diffusion coefficients has revealed the existence of a plateau in the region of 0.7-1.1 ρ(c), where the local density augmentation exhibits the maximum value. The reorientational dynamics of the C═C bond vector have been also studied, exhibiting significant differences between the two isomers in the case of the second-order Legendre time correlation functions.

  14. Study of lattice thermal conductivity of alpha-zirconium by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Wu Tian-Yu; Lai Wen-Sheng; Fu Bao-Qin

    2013-01-01

    The non-equilibrium molecular dynamics method is adapted to calculate the phonon thermal conductivity of alphazirconium.By exchanging velocities of atoms in different regions,the stable heat flux and the temperature gradient are established to calculate the thermal conductivity.The phonon thermal conductivities under different conditions,such as different heat exchange frequencies,different temperatures,different crystallographic orientations,and crossing grain boundary (GB),are studied in detail with considering the finite size effect.It turns out that the phonon thermal conductivity decreases with the increase of temperature,and displays anisotropies along different crystallographic orientations.The phonon thermal conductivity in [0001] direction (close-packed plane) is largest,while the values in other two directions of [2(1)(1)0] and [01 (1)0] are relatively close.In the region near GB,there is a sharp temperature drop,and the phonon thermal conductivity is about one-tenth of that of the single crystal at 550 K,suggesting that the GB may act as a thermal barrier in the crystal.

  15. Dynamic performance of accommodating intraocular lenses in a negative feedback control system: a simulation-based study.

    Science.gov (United States)

    Schor, Clifton M; Bharadwaj, Shrikant R; Burns, Christopher D

    2007-07-01

    A dynamic model of ocular accommodation is used to simulate the stability and dynamic performance of accommodating intraocular lenses (A-IOLs) that replace the hardened natural ocular lens that is unable to change focus. Accommodation simulations of an older eye with A-IOL materials having biomechanical properties of a younger eye illustrate overshoots and oscillations resulting from decreased visco-elasticity of the A-IOL. Stable dynamics of an A-IOL are restored by adaptation of phasic and tonic neural-control properties of accommodation. Simulations indicate that neural control must be recalibrated to avoid unstable dynamic accommodation with A-IOLs. An interactive web-model of A-IOL illustrating these properties is available at http://schorlab.berkeley.edu.

  16. Molecular docking and dynamic simulation studies evidenced plausible immunotherapeutic anticancer property by Withaferin A targeting indoleamine 2,3-dioxygenase.

    Science.gov (United States)

    Reddy, S V G; Reddy, K Thammi; Kumari, V Valli; Basha, Syed Hussain

    2015-01-01

    Indoleamine 2,3-dioxygenase (IDO) is emerging as an important new therapeutic drug target for the treatment of cancer characterized by pathological immune suppression. IDO catalyzes the rate-limiting step of tryptophan degradation along the kynurenine pathway. Reduction in local tryptophan concentration and the production of immunomodulatory tryptophan metabolites contribute to the immunosuppressive effects of IDO. Presence of IDO on dentritic cells in tumor-draining lymph nodes leading to the activation of T cells toward forming immunosuppressive microenvironment for the survival of tumor cells has confirmed the importance of IDO as a promising novel anticancer immunotherapy drug target. On the other hand, Withaferin A (WA) - active constituent of Withania Somnifera ayurvedic herb has shown to be having a wide range of targeted anticancer properties. In the present study conducted here is an attempt to explore the potential of WA in attenuating IDO for immunotherapeutic tumor arresting activity and to elucidate the underlying mode of action in a computational approach. Our docking and molecular dynamic simulation results predict high binding affinity of the ligand to the receptor with up to -11.51 kcal/mol of energy and 3.63 nM of IC50 value. Further, de novo molecular dynamic simulations predicted stable ligand interactions with critically important residues SER167; ARG231; LYS377, and heme moiety involved in IDO's activity. Conclusively, our results strongly suggest WA as a valuable small ligand molecule with strong binding affinity toward IDO.

  17. Molecular dynamic simulations of ocular tablet dissolution.

    Science.gov (United States)

    Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

    2013-11-25

    Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.

  18. Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-06-01

    In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  19. Numerical simulation study of the dynamical behavior of the Niedermayer algorithm

    CERN Document Server

    Girardi, D

    2010-01-01

    We calculate the dynamic critical exponent for the Niedermayer algorithm applied to the two-dimensional Ising and XY models, for various values of the free parameter $E_0$. For $E_0=-1$ we regain the Metropolis algorithm and for $E_0=1$ we regain the Wolff algorithm. For $-1\\widetilde{L}$, the Niedermayer algorithm is equivalent to the Metropolis one, i.e, they have the same dynamic exponent. For $E_0>1$, the autocorrelation time is always greater than for $E_0=1$ (Wolff) and, more important, it also grows faster than a power of $L$. Therefore, we show that the best choice of cluster algorithm is the Wolff one, when compared to the Nierdermayer generalization. We also obtain the dynamic behavior of the Wolff algorithm: although not conclusive, we propose a scaling law for the dependence of the autocorrelation time on $L$.

  20. Dynamics modeling and simulation of flexible airships

    Science.gov (United States)

    Li, Yuwen

    The resurgence of airships has created a need for dynamics models and simulation capabilities of these lighter-than-air vehicles. The focus of this thesis is a theoretical framework that integrates the flight dynamics, structural dynamics, aerostatics and aerodynamics of flexible airships. The study begins with a dynamics model based on a rigid-body assumption. A comprehensive computation of aerodynamic effects is presented, where the aerodynamic forces and moments are categorized into various terms based on different physical effects. A series of prediction approaches for different aerodynamic effects are unified and applied to airships. The numerical results of aerodynamic derivatives and the simulated responses to control surface deflection inputs are verified by comparing to existing wind-tunnel and flight test data. With the validated aerodynamics and rigid-body modeling, the equations of motion of an elastic airship are derived by the Lagrangian formulation. The airship is modeled as a free-free Euler-Bernoulli beam and the bending deformations are represented by shape functions chosen as the free-free normal modes. In order to capture the coupling between the aerodynamic forces and the structural elasticity, local velocity on the deformed vehicle is used in the computation of aerodynamic forces. Finally, with the inertial, gravity, aerostatic and control forces incorporated, the dynamics model of a flexible airship is represented by a single set of nonlinear ordinary differential equations. The proposed model is implemented as a dynamics simulation program to analyze the dynamics characteristics of the Skyship-500 airship. Simulation results are presented to demonstrate the influence of structural deformation on the aerodynamic forces and the dynamics behavior of the airship. The nonlinear equations of motion are linearized numerically for the purpose of frequency domain analysis and for aeroelastic stability analysis. The results from the latter for the

  1. Granular dynamics, contact mechanics and particle system simulations a DEM study

    CERN Document Server

    Thornton, Colin

    2015-01-01

    This book is devoted to the Discrete Element Method (DEM) technique, a discontinuum modelling approach that takes into account the fact that granular materials are composed of discrete particles which interact with each other at the microscale level. This numerical simulation technique can be used both for dispersed systems in which the particle-particle interactions are collisional and compact systems of particles with multiple enduring contacts. The book provides an extensive and detailed explanation of the theoretical background of DEM. Contact mechanics theories for elastic, elastic-plastic, adhesive elastic and adhesive elastic-plastic particle-particle interactions are presented. Other contact force models are also discussed, including corrections to some of these models as described in the literature, and important areas of further research are identified. A key issue in DEM simulations is whether or not a code can reliably simulate the simplest of systems, namely the single particle oblique impact wit...

  2. Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2011-03-31

    The loss of the insulin-producing β-cells in the pancreatic islets of Langerhans, responsible for type-II diabetes, is associated with islet amyloid deposits. The main component of these deposits is the amyloid fibrils formed by the 37-residue human islet amyloid polypeptide (hIAPP also known as amylin). Although the fibrils are well characterized by cross β structure, the structure of the transient oligomers formed in the early stage of aggregation remains elusive. In this study, we apply the Hamiltonian-temperature replica exchange molecular dynamics to characterize the structure and thermodynamics of a full-length hIAPP dimer in both the presence and the absence of the Cys2-Cys7 disulfide bond. We compare these results with those obtained on the monomeric and dimeric forms of rat IAPP (rIAPP) with a disulfide bridge which differ from the hIAPP by 6 amino acids in the C-terminal region, but it is unable to form fibrils. Using a coarse-grained protein force field (OPEP-the Optimized Potential for Efficient peptide structure Prediction) running for a total of 10-28 μs per system studied, we show that sequences sample α-helical structure in the N-terminal region but that the length of this secondary element is shorter and less stable for the chains without the disulfide bridge (residues 5-16 for hIAPP with the bridge vs 10-16 for hIAPP without the bridge). This α-helix is known to be an important transient stage in the formation of oligomers. In the C-terminal, the amyloidogenic region of hIAPP, β-strands are seen for residues 17-26 and 30-35. On the contrary, no significant β-sheet content in the C-terminal is observed for either the monomeric or the dimeric rIAPP. These numerical results are fully consistent with recent experimental findings that the N-terminal residues are not part of the fibril by forming α-helical structure but rather play a significant role in stabilizing the amyloidogenic region available for the fibrillation.

  3. Modeling sorption and diffusion of organic sorbate in hexadecyltrimethylammonium-modified clay nanopores - a molecular dynamics simulation study.

    Science.gov (United States)

    Zhao, Qian; Burns, Susan E

    2013-03-19

    Organoclays are highly sorptive engineered materials that can be used as amendments in barrier systems or geosynthetic liners. The performance of confining and isolating the nonpolar organic contaminants by those barrier/lining systems is essentially controlled by the process of organic contaminant mass transport in nanopores of organoclays. In this article, we use molecular dynamics (MD) simulations to study the sorption and diffusion of organic sorbates in interlayers of sodium montmorillonite and hexadecyltrimethylammonium (HDTMA(+))-modified montmorillonite clays. Simulated system consisted of the clay framework, interlayer organic cation, water, and organic sorbate. Their interactions were addressed by the combined force field of ClayFF, constant-valence force field, and SPC water model. Simulation results indicated that in HDTMA coated clay nanopores, diffusion of nonpolar species benzene was slowed because they were subjected to influence of both the pore wall and the HDTMA surfactant. This suggested the nonpolar organic compound diffusion in organophilic clays can be affected by molecular size of diffusive species, clay pore size, and organic surfactant loading. Additionally, a model that connected the diffusion rate of organic compounds in the bulk organoclay matrix with macropores and nanopores was established. The impact of intercalated organic cations on the diffusion dominated mass transport of organic compounds yielded insight into the prediction of the apparent diffusion behavior of organic compounds in organic-modified clays.

  4. Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex.

    Science.gov (United States)

    Blessy, J Jino; Sharmila, D Jeya Sundara

    2015-01-01

    Cholera toxin (CT) is an AB5 protein complex secreted by the pathogen Vibrio cholera, which is responsible for cholera infection. N-acetylneuraminic acid (NeuNAc) is a derivative of neuraminic acid with nine-carbon backbone. NeuNAc is distributed on the cell surface mainly located in the terminal components of glycoconjugates, and also plays an important role in cell-cell interaction. In our current study, molecular docking and molecular dynamic (MD) simulations were implemented to identify the potent NeuNAc analogs with high-inhibitory activity against CT protein. Thirty-four NeuNAc analogs, modified in different positions C-1/C-2/C-4/C-5/C-7/C-8/C-9, were modeled and docked against the active site of CT protein. Among the 34 NeuNAc analogs, the analog Neu5Gc shows the least extra precision glide score of -9.52 and glide energy of -44.71 kcal/mol. NeuNAc analogs block the CT active site residues HIS:13, ASN:90, LYS:91, GLN:56, GLN:61, and TRP:88 through intermolecular hydrogen bonding. The MD simulation for CT-Neu5Gc docking complex was performed using Desmond. MD simulation of CT-Neu5Gc complex reveals the stable nature of docking interaction.

  5. A 5D computational phantom for pharmacokinetic simulation studies in dynamic emission tomography

    NARCIS (Netherlands)

    Kotasidis, Fotis A.; Tsoumpas, Charalampos; Polycarpou, Irene; Zaidi, Habib

    2014-01-01

    Introduction: Dynamic image acquisition protocols are increasingly used in emission tomography for drug development and clinical research. As such, there is a need for computational phantoms to accurately describe both the spatial and temporal distribution of radiotracers, also accounting for period

  6. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies

    Science.gov (United States)

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala

    2017-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo.

  7. Study on two-dimensional equilibrium structure of magnetized complex plasmas based on a Langevin dynamics simulation

    Science.gov (United States)

    Kong, Wei; Yang, Fang; Liu, Songfen; Shi, Feng

    2016-10-01

    A Langevin dynamics simulation method is used to study the two-dimensional (2D) equilibrium structure of complex plasmas while considering an external magnetic field. The traditional Yukawa potential and a modified Yukawa potential according to Shukla et al. [Phys. Lett. A 291, 413 (2001); Shukla and Mendonca, Phys. Scr. T113 82 (2004)] and Salimullah et al. [Phys. Plasmas 10, 3047 (2003)] respectively, are employed to account for the interaction of the charged dust particles. It is found that the collisions between neutral gas and charged dust particles have minor effects on the 2D equilibrium structure of the system. Based on the modified Yukawa potential, studies on the 2D equilibrium structure show that the traditional Yukawa potential is still suitable for describing the magnetized complex plasmas, even if the shielding distance of charged dust particles is affected by the strong external magnetic field.

  8. Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

    Science.gov (United States)

    Xie, Jing; Kohale, Swapnil C; Hase, William L; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A

    2013-12-27

    Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of

  9. Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: a combined dynamic fluorescence and all-atom molecular dynamics simulation study.

    Science.gov (United States)

    Guchhait, Biswajit; Biswas, Ranjit; Ghorai, Pradip K

    2013-03-28

    Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements.

  10. Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Jensen, T.R.; Kjær, Kristian

    2002-01-01

    Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely...... characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a Computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different...... orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain...

  11. Numerical simulation study of the dynamical behavior of the Niedermayer algorithm

    Science.gov (United States)

    Girardi, D.; Branco, N. S.

    2010-04-01

    We calculate the dynamic critical exponent for the Niedermayer algorithm applied to the two-dimensional Ising and XY models, for various values of the free parameter E0. For E0 = - 1 we regain the Metropolis algorithm and for E0 = 1 we regain the Wolff algorithm. For - 1 clusters of (possibly) turned spins initially grows with the linear size of the lattice, L, but eventually saturates at a given lattice size \\widetilde {L} , which depends on E0. For L\\gt \\widetilde {L} , the Niedermayer algorithm is equivalent to the Metropolis one, i.e., they have the same dynamic exponent. For E0 > 1, the autocorrelation time is always greater than for E0 = 1 (Wolff) and, more important, it also grows faster than a power of L. Therefore, we show that the best choice of cluster algorithm is the Wolff one, when comparing against the Niedermayer generalization. We also obtain the dynamic behavior of the Wolff algorithm: although not conclusively, we propose a scaling law for the dependence of the autocorrelation time on L.

  12. Integration of Inhibition Kinetics and Molecular Dynamics Simulations: A Urea-Mediated Folding Study on Acetaldehyde Dehydrogenase 1.

    Science.gov (United States)

    Xu, Yingying; Lee, Jinhyuk; Lü, Zhi-Rong; Mu, Hang; Zhang, Qian; Park, Yong-Doo

    2016-07-01

    Understanding the mechanism of acetaldehyde dehydrogenase 1 (ALDH1) folding is important because this enzyme is directly involved in several types of cancers and other diseases. We investigated the urea-mediated unfolding of ALDH1 by integrating kinetic inhibition studies with computational molecular dynamics (MD) simulations. Conformational changes in the enzyme structure were also analyzed using intrinsic and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence measurements. Kinetic studies revealed that the direct binding of urea to ALDH1 induces inactivation of ALDH1 in a manner of mixed-type inhibition. Tertiary structural changes associated with regional hydrophobic exposure of the active site were observed. The urea binding regions on ALDH1 were predicted by docking simulations and were partly shared with active site residues of ALDH1 and with interface residues of the oligomerization domain for tetramer formation. The docking results suggest that urea prevents formation of the ALDH1 normal shape for the tetramer state as well as entrance of the substrate into the active site. Our study provides insight into the structural changes that accompany urea-mediated unfolding of ALDH1 and the catalytic role associated with conformational changes.

  13. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models.

    Science.gov (United States)

    Rebič, Matúš; Laaksonen, Aatto; Šponer, Jiří; Uličný, Jozef; Mocci, Francesca

    2016-08-04

    Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew

  14. Study of the Plasma Turbulence Dynamics by Measurements of Diagnostic Stimulated Electromagnetic Emission. Part II. Results of Numerical Simulation

    Science.gov (United States)

    Sergeev, E. N.; Grach, S. M.

    2017-07-01

    The data on measured dynamic characteristics of diagnostic stimulated electromagnetic emission (SEE) of the ionosphere are presented. Numerical simulations of the SEE evolution within the framework of a theoretical model of the broad-continuum SEE feature with the use of improved (3D) empirical model of the spatial spectrum of artificial irregularities of the HF pumped ionospheric plasma are performed and compared with the measurement data. Possible applications of such a comparison for determining the spectrum parameters and studying the evolution of the geomagnetic field-aligned artificial irregularities (striations) are discussed. It is concluded that changes in the intensity and spectrum shape of the striations, mainly for transverse scales l ⊥ 2-18 m, play the decisive role in the observed variations of the magnitude and temporal characteristics of the overshoot effect (formation of the intensity maximum followed by the suppression of the ionospheric SEE intensity).

  15. Blood-brain barrier transport studies, aggregation, and molecular dynamics simulation of multiwalled carbon nanotube functionalized with fluorescein isothiocyanate.

    Science.gov (United States)

    Shityakov, Sergey; Salvador, Ellaine; Pastorin, Giorgia; Förster, Carola

    2015-01-01

    In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT-FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood-brain barrier. The results indicated that the MWCNT-FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell(®) system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT-FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT-FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCNT-FITC rapid dissociation as an intermediate phase.

  16. Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow

    CERN Document Server

    Archereau, Aurelien Y M; Willmott, Geoff R

    2016-01-01

    We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.

  17. Numerical simulation study of the dynamical behavior of the Niedermayer algorithm

    OpenAIRE

    Girardi, D.; Branco, N. S.

    2010-01-01

    We calculate the dynamic critical exponent for the Niedermayer algorithm applied to the two-dimensional Ising and XY models, for various values of the free parameter $E_0$. For $E_0=-1$ we regain the Metropolis algorithm and for $E_0=1$ we regain the Wolff algorithm. For $-11$, the autocorrelation time is always greater than for $E_0=1$ (Wolff) and, more important, it also grows faster than a power of $L$. Therefore, we show that the best choice of cluster algorithm is the Wolff one, when com...

  18. Humanoid robot simulator: a realistic dynamics approach

    OpenAIRE

    Lima, José; Gonçalves, José; Costa, Paulo; Moreira, António

    2008-01-01

    This paper describes a humanoid robot simulator with realistic dynamics. As simulation is a powerful tool for speeding up the control software development, the suggested accurate simulator allows to accomplish this goal. The simulator, based on the Open Dynamics Engine and GLScene graphics library, provides instant visual feedback and allows the user to test any control strategy without damaging the real robot in the early stages of the development. The proposed simulator also captures some c...

  19. Study of Interfacial Tension between an Organic Solvent and Aqueous Electrolyte Solutions Using Electrostatic Dissipative Particle Dynamics Simulations

    CERN Document Server

    Mayoral, E; 10.1063/1.4766456

    2012-01-01

    The study of the modification of interfacial properties between an organic solvent and aqueous electrolyte solutions is presented by using electrostatic Dissipative Particle Dynamics (DPD) simulations. In this article the parametrization for the DPD repulsive parameters aij for the electrolyte components is calculated considering the dependence of the Flory-Huggins \\c{hi} parameter on the concentration and the kind of electrolyte added, by means of the activity coefficients. In turn, experimental data was used to obtain the activity coefficients of the electrolytes as a function of their concentration in order to estimate the \\c{hi} parameters and then the aij coefficients. We validate this parametrization through the study of the interfacial tension in a mixture of n-dodecane and water, varying the concentration of different inorganic salts (NaCl, KBr, Na2SO4 and UO2Cl2). The case of HCl in the mixture n-dodecane/water was also analyzed and the results presented. Our simulations reproduce the experimental da...

  20. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  1. On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: A molecular dynamics simulation study

    Science.gov (United States)

    Shao, Qiang

    2013-09-01

    The structure stability of three α-helix bundle (the B domain of protein A) in an imidazolium-based ionic liquid (1-butyl-3-methylimidazolium chloride (BMIM-Cl)) is studied by molecular dynamics simulations. Consistent with previous experiments, the present simulation results show that the native structure of the protein is consistently stabilized in BMIM-Cl solutions with different concentrations. It is observed that BMIM+ cations have a strong tendency to accumulate on protein surface whereas Cl- anions are expelled from protein. BMIM+ cations cannot only have electrostatic interactions with the carbonyl groups on backbone and the carboxylate groups on negatively charged side chains, but also have hydrophobic interactions with the side chains of non-polar residues. In the meanwhile, the accumulation of large-size BMIM+ cations on protein surface could remove the surrounding water molecules, reduce the hydrogen bonding from water to protein, and thus stabilize the backbone hydrogen bonds. In summary, the present study could improve our understanding of the molecular mechanism of the impact of water-miscible ionic liquid on protein structure.

  2. Solvation structure and dynamics of Na+ in liquid ammonia studied by ONIOM-XS MD simulations

    Science.gov (United States)

    Sripradite, Jarukorn; Tongraar, Anan; Kerdcharoen, Teerakiat

    2015-12-01

    The molecular dynamics (MD) technique based on the ONIOM-XS method, known as the ONIOM-XS MD, has been applied to investigate the solvation structure and dynamics of Na+ in liquid ammonia. Regarding the ONIOM-XS MD results, it is observed that Na+ is able to order the surrounding ammonia molecules to form its specific first and second solvation shells with the average coordination numbers of 5.1 and 11.2, respectively. The first solvation shell of Na+ is rather well-defined, forming a preferred 5-fold coordinated complex with a distorted square pyramidal geometry. In this respect, the most preferential Na+(NH3)5 species could convert back and forth to the lower probability Na+(NH3)6 and Na+(NH3)4 configurations. The second solvation shell of Na+ is detectable, in which a number of ammonia molecules, ranging from 7 to 14, are involved in this layer and they are arranged according to recognizable influence of the ion.

  3. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.

  4. A simulation study of flow dynamics of erythrocytes through diverging and converging bifurcations

    Science.gov (United States)

    Wang, Tong; Xing, Zhongwen

    2015-03-01

    A numerical model has been developed to predict the cells deformation and motion in a symmetric diverging and converging bifurcation of a microchannel. Fluid dynamics and membrane mechanics are incorporated. The model was utilized to evaluate the effect of different biophysical parameters, such as: initial cell position, membrane stiffness and shape of the cells on deformation and motion of the erythrocytes in the bifurcating curved microchannel. The numerical results demonstrate that erythrocytes in microvessels blunt velocity profiles in both straight section and daughter branches, and the transit velocity of erythrocytes is strongly influenced by cell deformability, shape of the cells, and the vessel geometry. These results may provide fundamental knowledge for a better understanding of hemodynamic behavior of microscale blood flow. The authors acknowledge the support of the State Key Program for Basic Researches of China (2014CB921103 and 2010CB923404), the National ``Climbing'' Program of China (91021003), and the National Science Foundation of Jiangsu Province (BK2010012).

  5. Theoretical studies on FGFR isoform selectivity of FGFR1/FGFR4 inhibitors by molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Fu, Weitao; Chen, Lingfeng; Wang, Zhe; Kang, Yanting; Wu, Chao; Xia, Qinqin; Liu, Zhiguo; Zhou, Jianmin; Liang, Guang; Cai, Yuepiao

    2017-02-01

    The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4. In this study, conventional molecular dynamics (MD) simulations, molecular mechanics/generalized Born surface area (MM/GBSA) free energy calculations and umbrella sampling (US) simulations were carried out to reveal the principle of the binding preference of ponatinib and AZD4547 towards FGFR4/FGFR1. The results provided by MM/GBSA illustrate that ponatinib has similar binding affinities to FGFR4 and FGFR1, while AZD4547 has much stronger binding affinity to FGFR1 than to FGFR4. A comparison of the individual energy terms suggests that the selectivity of AZD4547 towards FGFR1 versus FGFR4 is primarily controlled by the variation of the van der Waals interactions. The US simulations reveal that the PMF profile of FGFR1/AZD4547 has more peaks and valleys compared with that of FGFR4/AZD4547, suggesting that the dissociation process of AZD4547 from FGFR1 are easily trapped into local minima. Moreover, it is observed that FGFR1/AZD4547 has much higher PMF depth than FGFR4/AZD4547, implying that it is more difficult for AZD4547 to escape from FGFR1 than from FGFR4. The physical principles provided by this study extend our understanding of the binding mechanisms and provide valuable guidance for the rational design of FGFR isoform selective inhibitors.

  6. Molecular dynamics simulation and linear interaction energy study of D-Glu-based inhibitors of the MurD ligase.

    Science.gov (United States)

    Perdih, Andrej; Wolber, Gerhard; Solmajer, Tom

    2013-08-01

    The biosynthetic pathway of the bacterial peptidoglycan, where MurD is an enzyme involved at the intracellular stage of its construction, represents a collection of highly selective macromolecular targets for novel antibacterial drug design. In this study as part of our investigation of the MurD bacterial target two recently discovered classes of the MurD ligase inhibitors were investigated resulting from the lead optimization phases of the N-sulfonamide D-Glu MurD inhibitors. Molecular dynamics simulations, based on novel structural data, in conjunction with the linear interaction energy (LIE) method suggested the transferability of our previously obtained LIE coefficients to further D-Glu based classes of MurD inhibitors. Analysis of the observed dynamical behavior of these compounds in the MurD active site was supported by static drug design techniques. These results complement the current knowledge of the MurD inhibitory mechanism and provide valuable support for the D-Glu paradigm of the inhibitor design.

  7. Decision support for green supply chain operations by integrating dynamic simulation and LCA indicators: diaper case study.

    Science.gov (United States)

    Adhitya, Arief; Halim, Iskandar; Srinivasan, Rajagopalan

    2011-12-01

    As the issue of environmental sustainability is becoming an important business factor, companies are now looking for decision support tools to assess the fuller picture of the environmental impacts associated with their manufacturing operations and supply chain (SC) activities. Lifecycle assessment (LCA) is widely used to measure the environmental consequences assignable to a product. However, it is usually limited to a high-level snapshot of the environmental implications over the product value chain without consideration of the dynamics arising from the multitiered structure and the interactions along the SC. This paper proposes a framework for green supply chain management by integrating a SC dynamic simulation and LCA indicators to evaluate both the economic and environmental impacts of various SC decisions such as inventories, distribution network configuration, and ordering policy. The advantages of this framework are demonstrated through an industrially motivated case study involving diaper production. Three distinct scenarios are evaluated to highlight how the proposed approach enables integrated decision support for green SC design and operation.

  8. Effect of graphene oxide on the conformational transitions of amyloid beta peptide: A molecular dynamics simulation study.

    Science.gov (United States)

    Baweja, Lokesh; Balamurugan, Kanagasabai; Subramanian, Venkatesan; Dhawan, Alok

    2015-09-01

    The interactions between nanomaterials (NMs) and amyloid proteins are central to the nanotechnology-based diagnostics and therapy in neurodegenerative disorders such as Alzheimer's and Parkinson's. Graphene oxide (GO) and its derivatives have shown to modulate the aggregation pattern of disease causing amyloid beta (Aβ) peptide. However, the mechanism is still not well understood. Using molecular dynamics simulations, the effect of graphene oxide (GO) and reduced graphene oxide (rGO) having carbon:oxygen ratio of 4:1 and 10:1, respectively, on the conformational transitions (alpha-helix to beta-sheet) and the dynamics of the peptide was investigated. GO and rGO decreased the beta-strand propensity of amino acid residues in Aβ. The peptide displayed different modes of adsorption on GO and rGO. The adsorption on GO was dominated by electrostatic interactions, whereas on rGO, both van der Waals and electrostatic interactions contributed in the adsorption of the peptide. Our study revealed that the slight increase in the hydrophobic patches on rGO made it more effective inhibitor of conformational transitions in the peptide. Alpha helix-beta sheet transition in Aβ peptide could be one of the plausible mechanism by which graphene oxide may inhibit amyloid fibrillation.

  9. Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase

    Science.gov (United States)

    Perdih, Andrej; Wolber, Gerhard; Solmajer, Tom

    2013-08-01

    The biosynthetic pathway of the bacterial peptidoglycan, where MurD is an enzyme involved at the intracellular stage of its construction, represents a collection of highly selective macromolecular targets for novel antibacterial drug design. In this study as part of our investigation of the MurD bacterial target two recently discovered classes of the MurD ligase inhibitors were investigated resulting from the lead optimization phases of the N-sulfonamide d-Glu MurD inhibitors. Molecular dynamics simulations, based on novel structural data, in conjunction with the linear interaction energy (LIE) method suggested the transferability of our previously obtained LIE coefficients to further d-Glu based classes of MurD inhibitors. Analysis of the observed dynamical behavior of these compounds in the MurD active site was supported by static drug design techniques. These results complement the current knowledge of the MurD inhibitory mechanism and provide valuable support for the d-Glu paradigm of the inhibitor design.

  10. Molecular Dynamics Simulation and Experimental Studies of Gold Nanoparticle Templated HDL-like Nanoparticles for Cholesterol Metabolism Therapeutics.

    Science.gov (United States)

    Lai, Cheng-Tsung; Sun, Wangqiang; Palekar, Rohun U; Thaxton, C Shad; Schatz, George C

    2017-01-18

    High-density lipoprotein (HDL) plays an important role in the transport and metabolism of cholesterol. Mimics of HDL are being explored as potentially powerful therapeutic agents for removing excess cholesterol from arterial plaques. Gold nanoparticles (AuNPs) functionalized with apolipoprotein A-I and with the lipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[3-(2-pyridyldithio)propionate] have been demonstrated to be robust acceptors of cellular cholesterol. However, detailed structural information about this functionalized HDL AuNP is still lacking. In this study, we have used X-ray photoelectron spectroscopy and lecithin/cholesterol acyltransferase activation experiments together with coarse-grained and all-atom molecular dynamics simulations to model the structure and cholesterol uptake properties of the HDL AuNP construct. By simulating different apolipoprotein-loaded AuNPs, we find that lipids are oriented differently in regions with and without apoA-I. We also show that in this functionalized HDL AuNP, the distribution of cholesteryl ester maintains a reverse concentration gradient that is similar to the gradient found in native HDL.

  11. Intramolecular diffusive motion in alkane monolayers studied by high-resolution quasielastic neutron scattering and molecular dynamics simulations

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D;

    2004-01-01

    Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence that these rel...

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

    Science.gov (United States)

    Mori, Yukie; Masuda, Yuichi

    2015-09-01

    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 CCl4, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17O and 1H nuclei monitoring the nuclear magnetic relaxation times of 1H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the

  13. Coupling calcium dynamics and mitochondrial bioenergetic: an in silico study to simulate cardiomyocyte dysfunction.

    Science.gov (United States)

    Das, Phonindra Nath; Pedruzzi, Gabriele; Bairagi, Nandadulal; Chatterjee, Samrat

    2016-03-01

    The coupling of intracellular Ca(2+) dynamics with mitochondrial bioenergetic is crucial for the functioning of cardiomyocytes both in healthy and disease conditions. The pathophysiological signature of the Cardiomyocyte Dysfunction (CD) is commonly related to decreased ATP production due to mitochondrial functional impairment and to an increased mitochondrial calcium content ([Ca(2+)]m). These features advanced the therapeutic approaches which aim to reduce [Ca(2+)]m. But whether [Ca(2+)]m overload is the pathological trigger for CD or a physiological consequence, remained controversial. We addressed this issue in silico and showed that [Ca(2+)]m might not directly cause CD. Through model parameter recalibration, we demonstrated how mitochondria cope up with functionally impaired processes and consequently accumulate calcium. A strong coupling of the [Ca(2+)]m oscillations with the ATP synthesis rate ensures robust calcium cycling and avoids CD. We suggested a cardioprotective role of the mitochondrial calcium uniporter and predicted that a mitochondrial sodium calcium exchanger could be a potential therapeutic target to restore the normal functioning of the cardiomyocyte.

  14. Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study.

    Science.gov (United States)

    Hassan, Mubashir; Abbas, Qamar; Ashraf, Zaman; Moustafa, Ahmed A; Seo, Sung-Yum

    2017-06-01

    Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis. The 3D structures of PPO1 and PPO2 were built through homology modeling, while the 3D crystal structures of PPO3 and PPO4 were retrieved from PDB. Pharmacophore modeling was performed using LigandScout 3.1 software and top five models were selected to screen the libraries (2601 of Aurora and 727, 842 of ZINC). Top 10 hit compounds (C1-10) were short-listed having strong binding affinities for PPO1-4. Drug and synthetic accessibility (SA) scores along with absorption, distribution, metabolism, excretion and toxicity (ADMET) assessment were employed to scrutinize the best lead hit. C4 (name) hit showed the best predicted SA score (5.75), ADMET properties and drug-likeness behavior among the short-listed compounds. Furthermore, docking simulations were performed to check the binding affinity of C1-C10 compounds against target proteins (PPOs). The binding affinity values of complex between C4 and PPOs were higher than those of other complexes (-11.70, -12.1, -9.90 and -11.20kcal/mol with PPO1, PPO2, PPO3, or PPO4, respectively). From comparative docking energy and binding analyses, PPO2 may be considered as better target for melanogenesis than others. The potential binding modes of C4, C8 and C10 against PPO2 were explored using molecular dynamics simulations. The root mean square deviation and fluctuation (RMSD/RMSF) graphs results depict the significance of C4 over the other compounds

  15. Dynamic switching mechanisms of a CC chemokine, CCL5 (RANTES). A simulation study

    Science.gov (United States)

    Peter, Emanuel; Pivkin, Igor

    CCL5 (RANTES) belongs to the class of pro-inflammatory chemokines which are part of the human immune-response. It is known to activate leukocytes through its associated chemokine receptor 5 (CCR5) and plays a key role in several malignancies, including HIV-1 infections and cancer. In this talk, we present our results from enhanced sampling simulations of the CCL5 (RANTES) monomer. We find that this protein can adopt 2 different conformations : a globular form, with an orthogonal alignment of the N-terminal part, and a 'cis' form, in which the N-terminus is aligned parallel to the β-strand interface. A detailed analysis of the structure reveals that each of these states is stabilized by salt-bridges along the sequence, and corresponds to a defined dihedral-geometry of the 2 disulfide bridges Cys10-34 and Cys11-50. We derive a uniform distribution of transitions from the globular form of CCL5 (RANTES), and find that each of the main conformers adopts different electrostatic patterns.

  16. Host behavior alters spiny lobster-viral disease dynamics: a simulation study.

    Science.gov (United States)

    Dolan, Thomas W; Butler, Mark J; Shields, Jeffrey D

    2014-08-01

    Social behavior confers numerous benefits to animals but also risks, among them an increase in the spread of pathogenic diseases. We examined the trade-off between risk of predation and disease transmission under different scenarios of host spatial structure and disease avoidance behavior using a spatially explicit, individual-based model of the host pathogen interaction between juvenile Caribbean spiny lobster (Panulirus argus) and Panulirus argus Virus 1 (PaV1). Spiny lobsters are normally social but modify their behavior to avoid diseased conspecifics, a potentially effective means of reducing transmission but one rarely observed in the wild. We found that without lobster avoidance of diseased conspecifics, viral outbreaks grew in intensity and duration in simulations until the virus was maintained continuously at unrealistically high levels. However, when we invoked disease avoidance at empirically observed levels, the intensity and duration of outbreaks was reduced and the disease extirpated within five years. Increased lobster (host) spatial aggregation mimicking that which occurs when sponge shelters for lobsters are diminished by harmful algal blooms, did not significantly increase PaV1 transmission or persistence in lobster populations. On the contrary, behavioral aversion of diseased conspecifics effectively reduced viral prevalence, even when shelters were limited, which reduced shelter availability for all lobsters but increased predation, especially of infected lobsters. Therefore, avoidance of diseased conspecifics selects against transmission by contact, promotes alternative modes of transmission, and results in a more resilient host-pathogen system.

  17. Study and simulation of carbon impurity dynamics near the ergodic divertor in Tore Supra

    Energy Technology Data Exchange (ETDEWEB)

    Giannella, R.; Cordier, J.J.; Corre, Y.; Ghendrih, P.; Guirlet, R.; Gunn, J. [Association Euratom-CEA, CEA/Cadarache, Dept. de Recherches sur la Fusion Controlee (DRFC), 13 - Saint-Paul-lez-Durance (France); Hogan, J. [Oak Ridge National Lab., TN (United States)

    1999-10-15

    In the past few years, effects induced by the ergodic dive such as impurity screening and transport modifications in the plasma edge have been used to achieve high radiation, low contamination regimes. A crucial issue in understanding these effects is that of impurity generation and propagation across the plasma edge, especially in the vicinity of the Ergodic Divertor (ED) neutralizer plates. A variety of diagnostic tools and techniques are used for this purpose. In the case of Tore Supra, interpretation of spectroscopic data is strongly complicated by the complex geometry of the ED, leading among other effects to the total lack of uniformity of the sources. Indeed, due to the specific pattern of impurity sources on the neutralizers and to their particular orientation with respect to the local magnetic field, densities of lowly ionised impurities are deeply modulated on the sub-centimeter scale in both directions perpendicular to the magnetic field. Because of this, accurate 3-D simulations are essential for the evaluation of experimental signals. (authors)

  18. 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 on an ex......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...

  19. 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

  20. Preparation, temperature dependent structural, molecular dynamics simulations studies and electrochemical properties of LiFePO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Rao, R. Prasada, E-mail: mserpr@nus.edu.sg [Department of Materials Science and Engineering, National University of Singapore, 117576 (Singapore); Reddy, M.V. [Department of Materials Science and Engineering, National University of Singapore, 117576 (Singapore); Department of Physics, National University of Singapore, 117542 (Singapore); Adams, S. [Department of Materials Science and Engineering, National University of Singapore, 117576 (Singapore); Chowdari, B.V.R. [Department of Physics, National University of Singapore, 117542 (Singapore)

    2015-06-15

    Highlights: • LiFePO{sub 4} compound was prepared by carbothermal reduction method. • In-situ XRD studies were carried out on LiFePO{sub 4} at various temperatures. • Dedicated imperial potentials used to explain the variation of lattice constants. • It exhibited reversible capacity of 140 (±5) mAh g{sup −1}, stable up to 400 cycles. - Abstract: LiFePO{sub 4} was prepared using carbothermal reduction method. In-situ temperature dependent structural studies were carried using X-ray diffraction. Molecular dynamics simulations were conducted for the LiFePO{sub 4} using empirical potentials developed using bond valence approach to investigate the structural variations. Electrochemical behaviour of LiFePO{sub 4} was evaluated using cyclic voltammetry and galvanostatic cycling studies at room temperature. Charge–discharge cycling studies showed a reversible capacities 140 (±5) mAh g{sup −1} at the end of 50th cycle and these capacity values were stable up to 400 cycles and almost nil capacity fade between 50 and 400 cycles, showing excellent capacity retention, low capacity fading. The cyclic voltammetry studies showed a main cathodic and anodic redox peaks at 3.34 and 3.5 V vs. Li, respectively.

  1. Mesoscopic Simulation Methods for Polymer Dynamics

    Science.gov (United States)

    Larson, Ronald

    2015-03-01

    We assess the accuracy and efficiency of mesoscopic simulation methods, namely Brownian Dynamics (BD), Stochastic Rotation Dynamics (SRD) and Dissipative Particle Dynamics (DPD), for polymers in solution at equilibrium and in flows in microfluidic geometries. Both SRD and DPD use solvent ``particles'' to carry momentum, and so account automatically for hydrodynamic interactions both within isolated polymer coils, and with other polymer molecules and with nearby solid boundaries. We assess quantitatively the effects of artificial particle inertia and fluid compressibility and show that they can be made small with appropriate choice of simulation parameters. We then use these methods to study flow-induced migration of polymer chains produced by: 1) hydrodynamic interactions, 2) streamline curvature or stress-gradients, and 3) convection of wall depletion zones. We show that huge concentration gradients can be produced by these mechanisms in microfluidic geometries that can be exploited for separation of polymers by size in periodic contraction-expansion geometries. We also assess the range of conditions for which BD, SRD or DPD is preferable for mesoscopic simulations. Finally, we show how such methods can be used to simulate quantitatively the swimming of micro-organisms such as E. coli. In collaboration with Lei Jiang and Tongyang Zhao, University of Michigan, Ann Arbor, MI.

  2. Dynamic simulator for PEFC propulsion plant

    Energy Technology Data Exchange (ETDEWEB)

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao [Mitsui Engineering & Shipbuilding Co., Ltd., Tokyo (Japan)] [and others

    1996-12-31

    This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.

  3. Dynamic simulation of flywheel-type fuses

    OpenAIRE

    Editorial Office

    1996-01-01

    Rounds of ammunition are normally armed with a fuse. In this study, a fuse is developed which uses a flywheel-type mechanism controlled by time or distance. Due to its simplicity of operation and construction, the concept is expected to have high reliabil­ity. The dynamic response of all the components of this flywheel-type fuse is mathematically modelled. Simulation software was developed which connects the mathematical models of the various components. With the definition of boundary value...

  4. A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles.

    Science.gov (United States)

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Parastar, Hadi

    2013-10-05

    The interaction of quercetin with β-casein nanoparticle micelle was studied at various temperatures in order to do a complete thermodynamic and molecular analysis on the binding process. The results of fluorescence studies showed the possibility of fluorescence energy transfer between excited tryptophan and quercetin. The determined values of critical transfers distance and the mean distance of ligand from Trp-143 residues in β-casein micelle represents a non-radiative energy transfer mechanism for quenching and the existence of a significant interaction between this flavonoid and β-casein nanoparticle. The equilibrium binding of quercetin with β-casein micelle at different temperatures was studied by using UV-Vis absorption spectroscopy. The chemometric analysis (principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods) on spectrophotometric data revealed the existence of two components in solution (quercetin and β-casein-quercetin complex) and resolved their pure concentration and spectral profiles. This information let us to calculate the equilibrium binding constant at various temperatures and the relevant thermodynamic parameters of interaction (enthalpy, entropy and Gibbs free energy) with low uncertainty. The negative values of entropy and enthalpy changes represent the predominate role of hydrogen binding and van der Waals interactions in the binding process. Docking calculations showed the probable binding site of quercetin is located in the hydrophobic core of β-casein where the quercetin molecule is lined by hydrophobic residues and make five hydrogen bonds and several van der Waals contacts with them. Moreover, molecular dynamic (MD) simulation results suggested that this flavonoid can interact with β-casein, without affecting the secondary structure of β-casein. Simulations, molecular docking and experimental data reciprocally supported each other. Copyright © 2013 Elsevier B.V. All

  5. Synthesis, structure and properties of hierarchical nanostructured porous materials studied by molecular dynamics simulations

    Science.gov (United States)

    Chae, Kisung

    For applications of porous materials in many fields of technological importance, such as catalysis, filtration, separation, energy storage and conversion, the efficiency is often limited by chemical kinetics, and/or diffusion of reactants and products to and from the active sites. Hierarchical nanostructured porous materials (HNPMs) that possess both mesopores (2 nm size size size and the pore wall roughness as well as the microporous structure such as the density and the graphitic pore walls can be independently controlled by synthesis parameters, such as the size of the template, the interaction strength between the template and carbon source, the initial carbon density and the quench rate, respectively. These atomic models allowed us to quantify the structure-mechanical properties relation in aligned carbon nanotubes/amorphous porous carbon nanocomposites. Our study shows that there is an optimum balance between the crystallinity of CNTs and the number bridging bonds between CNTs and the microporous matrix in order for the nanocomposites to have desired mechanical properties such as high stiffness and high buckling resistance under compressive loading. We further used these models to study the effects of the mesopore size and the pore wall roughness on the transport behaviors of methane in HNPCs. Our study shows that some defects in the mesopore walls do not have a significant effect on transport properties, especially in large channels. However, when the walls of small channels become rough, adsorption and transport behaviors change dramatically. Our study shows that the enhanced flow in CNTs observed in experiments is mainly due to the smooth potential energy surface of CNTs with high quality of graphitic walls. In order to carry out a systematic study on pressure-driven gas transport in HNPCs, a computationally efficient reflecting particle method (RPM) together with a perturbation-relaxation loop was developed in this work to make the pressure drop

  6. Structural insights into the interactions of xpt riboswitch with novel guanine analogues: a molecular dynamics simulation study.

    Science.gov (United States)

    Jain, Swapan S; Sonavane, Uddhavesh B; Uppuladinne, Mallikarjunachari V N; McLaughlin, Emily C; Wang, Weiqing; Black, Sheneil; Joshi, Rajendra R

    2015-01-01

    Ligand recognition in purine riboswitches is a complex process requiring different levels of conformational changes. Recent efforts in the area of purine riboswitch research have focused on ligand analogue binding studies. In the case of the guanine xanthine phosphoribosyl transferase (xpt) riboswitch, synthetic analogues that resemble guanine have the potential to tightly bind and subsequently influence the genetic expression of xpt mRNA in prokaryotes. We have carried out 25 ns Molecular Dynamics (MD) simulation studies of the aptamer domain of the xpt G-riboswitch in four different states: guanine riboswitch in free form, riboswitch bound with its cognate ligand guanine, and with two guanine analogues SJ1 and SJ2. Our work reveals novel interactions of SJ1 and SJ2 ligands with the binding core residues of the riboswitch. The ligands proposed in this work bind to the riboswitch with greater overall stability and lower root mean square deviations and fluctuations compared to guanine ligand. Reporter gene assay data demonstrate that the ligand analogues, upon binding to the RNA, lower the genetic expression of the guanine riboswitch. Our work has important implications for future ligand design and binding studies in the exciting field of riboswitches.

  7. Discovery of Potential Inhibitors of Aldosterone Synthase from Chinese Herbs Using Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulation Studies

    Science.gov (United States)

    Lu, Fang; Qiao, Liansheng; Chen, Xi; Li, Gongyu

    2016-01-01

    Aldosterone synthase (CYP11B2) is a key enzyme for the biosynthesis of aldosterone, which plays a significant role for the regulation of blood pressure. Excess aldosterone can cause the dysregulation of the renin-angiotensin-aldosterone system (RAAS) and lead to hypertension. Therefore, research and development of CYP11B2 inhibitor are regarded as a novel approach for the treatment of hypertension. In this study, the pharmacophore models of CYP11B2 inhibitors were generated and the optimal model was used to identify potential CYP11B2 inhibitors from the Traditional Chinese Medicine Database (TCMD, Version 2009). The hits were further refined by molecular docking and the interactions between compounds and CYP11B2 were analyzed. Compounds with high Fitvalue, high docking score, and expected interactions with key residues were selected as potential CYP11B2 inhibitors. Two most promising compounds, ethyl caffeate and labiatenic acid, with high Fitvalue and docking score were reserved for molecular dynamics (MD) study. All of them have stability of ligand binding which suggested that they might perform the inhibitory effect on CYP11B2. This study provided candidates for novel drug-like CYP11B2 inhibitors by molecular simulation methods for the hypertension treatment. PMID:27781210

  8. Discovery of Potential Inhibitors of Aldosterone Synthase from Chinese Herbs Using Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulation Studies

    Directory of Open Access Journals (Sweden)

    Ganggang Luo

    2016-01-01

    Full Text Available Aldosterone synthase (CYP11B2 is a key enzyme for the biosynthesis of aldosterone, which plays a significant role for the regulation of blood pressure. Excess aldosterone can cause the dysregulation of the renin-angiotensin-aldosterone system (RAAS and lead to hypertension. Therefore, research and development of CYP11B2 inhibitor are regarded as a novel approach for the treatment of hypertension. In this study, the pharmacophore models of CYP11B2 inhibitors were generated and the optimal model was used to identify potential CYP11B2 inhibitors from the Traditional Chinese Medicine Database (TCMD, Version 2009. The hits were further refined by molecular docking and the interactions between compounds and CYP11B2 were analyzed. Compounds with high Fitvalue, high docking score, and expected interactions with key residues were selected as potential CYP11B2 inhibitors. Two most promising compounds, ethyl caffeate and labiatenic acid, with high Fitvalue and docking score were reserved for molecular dynamics (MD study. All of them have stability of ligand binding which suggested that they might perform the inhibitory effect on CYP11B2. This study provided candidates for novel drug-like CYP11B2 inhibitors by molecular simulation methods for the hypertension treatment.

  9. Study of fluid flow behavior in smooth and rough nanochannels through oscillatory wall by molecular dynamics simulation

    Science.gov (United States)

    Rahmatipour, Hamed; Azimian, Ahmad-Reza; Atlaschian, Omid

    2017-01-01

    The method of molecular dynamics simulation is applied in order to study the behavior of liquid Argon flow within oscillatory Couette flows, in both smooth and rough nanochannels. To accomplish this study, the fluid velocity and the fluid slip in oscillatory Couette flows were used to assess the effects of: oscillatory velocity amplitude, speed frequency rate, channel height, wall density, and the amount of interaction between fluid and wall particles. Both smooth and rough walls were modelled in order to investigate the effect on the fluid patterns as well. Rectangular and triangular wall roughnesses in different dimensions were used to study this effect. The results indicate that an increase in the velocity amplitude increases the fluid slip, and decreases the fluid velocity fluctuations near the walls. Similar to the steady-state Couette flow, in oscillatory flow we observe a decrease in fluid slip by reducing the wall density. Moreover, by reducing the energy parameter between the fluid and wall, the fluid slip increases, and by reducing the length parameter the fluid slip decreases. Implementing the rectangular and triangular roughness to the bottom wall in the oscillatory flow results in a decrease in fluid slip, which is also similar to the usual non-oscillating flows.

  10. Structure, interfacial properties, and dynamics of the sodium alkyl sulfate type surfactant monolayer at the water/trichloroethylene interface: a molecular dynamics simulation study.

    Science.gov (United States)

    Shi, Wen-Xiong; Guo, Hong-Xia

    2010-05-20

    In this work, we perform a series of molecular dynamics (MD) simulations on the category of sodium alkyl sulfate (SDS-type) surfactant monolayers at the water/trichloroethylene (TCE) interface. Three separate tail-length SDS-type molecules are used. We investigate the conformation of surfactant chain (i.e., packing, orientation, and order), interfacial properties (i.e., interfacial thickness, interfacial tension, area compressibility, and bending modulus), their dependence on the chain length, and the average area per surfactant chain. We also examine the behavior of the surfactant monolayer in the metastable regime of negative surface tension with reference to collapse. The simulation has clearly shown that the very dilute monolayer is well described as a two-dimensional gas. With the increase of interfacial surfactant coverage, the monolayer is in the liquid-expanded (LE) phase. The surfactant tails at the interface become straighter, more ordered, and thicker at higher surfactant coverage. At the same time, interfacial tension of long-tail systems is always lower than that of short-tail systems. In the LE phase, the area compressibility modulus and the bending modulus increase with an increase in tail length. With a further decrease in molecular areas, the monolayer with large negative surface tension becomes unstable. Our simulations show that buckling of the monolayers is of dynamic nature as a response to mechanical instability. The further transformation pathway from buckling to bud can be controlled by the bending modulus, which depends crucially on the tail length and interfacial surfactant coverage. At a given area per molecule, the short tail chain makes the monolayer softer, and the budding process becomes more probable. For the supersaturated softer SDS monolayer, the collapse transition is initiated by the buckling of monolayers, followed primarily by budding and detachment of the nanoscale swollen micelle from the monolayer. Despite a number of

  11. Theoretical study on the mechanism of double proton transfer in porphycene by path-integral molecular dynamics simulations

    Science.gov (United States)

    Yoshikawa, Takehiro; Sugawara, Shuichi; Takayanagi, Toshiyuki; Shiga, Motoyuki; Tachikawa, Masanori

    2010-08-01

    Full-dimensional path-integral molecular dynamics simulations were performed to determine whether the double proton transfer tautomerization of porphycene is a concerted or a stepwise process. We employed an on-the-fly direct dynamics technique at the semiempirical PM6 method whose parameters were determined so as that the relative energies of the stationary points approximately reproduce previously reported electronic structure calculations. It was found that double proton transfer occurs dominantly through the concerted pathway via the second-order saddle point structure and that contribution of the stepwise mechanism increases with a temperature increase. Nuclear quantum effects play essential roles in determining the proton transfer mechanism.

  12. Molecular dynamics simulation studies of GLUT4: substrate-free and substrate-induced dynamics and ATP-mediated glucose transport inhibition.

    Directory of Open Access Journals (Sweden)

    Suma Mohan

    Full Text Available BACKGROUND: Glucose transporter 4 (GLUT4 is an insulin facilitated glucose transporter that plays an important role in maintaining blood glucose homeostasis. GLUT4 is sequestered into intracellular vesicles in unstimulated cells and translocated to the plasma membrane by various stimuli. Understanding the structural details of GLUT4 will provide insights into the mechanism of glucose transport and its regulation. To date, a crystal structure for GLUT4 is not available. However, earlier work from our laboratory proposed a well validated homology model for GLUT4 based on the experimental data available on GLUT1 and the crystal structure data obtained from the glycerol 3-phosphate transporter. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, the dynamic behavior of GLUT4 in a membrane environment was analyzed using three forms of GLUT4 (apo, substrate and ATP-substrate bound states. Apo form simulation analysis revealed an extracellular open conformation of GLUT4 in the membrane favoring easy exofacial binding of substrate. Simulation studies with the substrate bound form proposed a stable state of GLUT4 with glucose, which can be a substrate-occluded state of the transporter. Principal component analysis suggested a clockwise movement for the domains in the apo form, whereas ATP substrate-bound form induced an anti-clockwise rotation. Simulation studies suggested distinct conformational changes for the GLUT4 domains in the ATP substrate-bound form and favor a constricted behavior for the transport channel. Various inter-domain hydrogen bonds and switching of a salt-bridge network from E345-R350-E409 to E345-R169-E409 contributed to this ATP-mediated channel constriction favoring substrate occlusion and prevention of its release into cytoplasm. These data are consistent with the biochemical studies, suggesting an inhibitory role for ATP in GLUT-mediated glucose transport. CONCLUSIONS/SIGNIFICANCE: In the absence of a crystal structure for any

  13. Surface films of short fluorocarbon-hydrocarbon diblocks studied by molecular dynamics simulations: Spontaneous formation of elongated hemimicelles.

    Science.gov (United States)

    Piñeiro, Angel; Prieto, Gerardo; Ruso, Juan M; Verdes, Pedro V; Sarmiento, Félix

    2009-01-15

    Using grazing incidence small-angle X-ray scattering (GISAXS), and atomic force microscopy (AFM) it has been recently demonstrated that linear fluorocarbon-hydrocarbon diblocks (FnHm) self-assemble in water/air interfaces forming elongated and circular hemimicelles. Those structures have been observed for diblocks with at least eight fluorinated carbons. Based on the lack of a collapse pressure for F6H16, and due to the fact that no stable surface pressure values are reached under compression, it has been concluded that these molecules do not form stable monolayers. It has been also suggested that F6H16 and shorter diblocks desorb from the water surface under compression. It is not easy to accept that a significant concentration of so hydrophobic molecules can be stable in aqueous solution even when the employed experimental techniques were not able to clearly detect a well defined structure on the interface. In the present work the adsorption and arrangement of F6H16 and F6H10 at the water surface are studied by molecular dynamics (MD) simulations as a function of the available area per molecule. Starting from a random mixture, the spontaneous formation of elongated hemimicelles is observed for both systems when the area per molecule is higher than approximately 50 A(2). For intermediate areas two pseudo-phases, one rich in hydrocarbons and the other with higher fluorocarbon concentration, are formed. For the systems with less than approximately 30 A(2) available per molecule the formation of multilayers is observed. This is the first time that the dynamics and structure of perfluoroalkane (PFA) films, and in particular of hemimicelles on a liquid surface, are observed and characterized at atomic level.

  14. Allosteric analysis of glucocorticoid receptor-DNA interface induced by cyclic Py-Im polyamide: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yaru Wang

    Full Text Available BACKGROUND: It has been extensively developed in recent years that cell-permeable small molecules, such as polyamide, can be programmed to disrupt transcription factor-DNA interfaces and can silence aberrant gene expression. For example, cyclic pyrrole-imidazole polyamide that competes with glucocorticoid receptor (GR for binding to glucocorticoid response elements could be expected to affect the DNA dependent binding by interfering with the protein-DNA interface. However, how such small molecules affect the transcription factor-DNA interfaces and gene regulatory pathways through DNA structure distortion is not fully understood so far. METHODOLOGY/PRINCIPAL FINDINGS: In the present work, we have constructed some models, especially the ternary model of polyamides+DNA+GR DNA-binding domain (GRDBD dimer, and carried out molecular dynamics simulations and free energy calculations for them to address how polyamide molecules disrupt the GRDBD and DNA interface when polyamide and protein bind at the same sites on opposite grooves of DNA. CONCLUSIONS/SIGNIFICANCE: We found that the cyclic polyamide binding in minor groove of DNA can induce a large structural perturbation of DNA, i.e. a >4 Å widening of the DNA minor groove and a compression of the major groove by more than 4 Å as compared with the DNA molecule in the GRDBD dimer+DNA complex. Further investigations for the ternary system of polyamides+DNA+GRDBD dimer and the binary system of allosteric DNA+GRDBD dimer revealed that the compression of DNA major groove surface causes GRDBD to move away from the DNA major groove with the initial average distance of ∼4 Å to the final average distance of ∼10 Å during 40 ns simulation course. Therefore, this study straightforward explores how small molecule targeting specific sites in the DNA minor groove disrupts the transcription factor-DNA interface in DNA major groove, and consequently modulates gene expression.

  15. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties.

  16. Rotational Brownian Dynamics simulations of clathrin cage formation

    Energy Technology Data Exchange (ETDEWEB)

    Ilie, Ioana M.; Briels, Wim J. [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Otter, Wouter K. den, E-mail: w.k.denotter@utwente.nl [Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

    2014-08-14

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

  17. Rotational Brownian dynamics simulations of clathrin cage formation.

    Science.gov (United States)

    Ilie, Ioana M; den Otter, Wouter K; Briels, Wim J

    2014-08-14

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

  18. Regularization of rupture dynamics along bi-material interfaces: a parametric study and simulations of the Tohoku earthquake

    Science.gov (United States)

    Scala, Antonio; Festa, Gaetano; Vilotte, Jean-Pierre

    2015-04-01

    Faults are often interfaces between materials with different elastic properties. This is generally the case of plate boundaries in subduction zones, where the ruptures extend for many kilometers crossing materials with strong impedance contrasts (oceanic crust, continental crust, mantle wedge, accretionary prism). From a physical point of view, several peculiar features emerged both from analogic experiments and numerical simulations for a rupture propagating along a bimaterial interface. The elastodynamic flux at the rupture tip breaks its symmetry, inducing normal stress changes and an asymmetric propagation. This latter was widely shown for rupture velocity and slip rate (e.g. Xia et al, 2005) and was supposed to generate an asymmetric distribution of the aftershocks (Rubin and Ampuero, 2007). The bimaterial problem coupled with a Coulomb friction law is ill-posed for a wide range of impedance contrasts, due to a missing length scale in the instantaneous response to the normal traction changes. The ill-posedness also results into simulations no longer independent of the grid size. A regularization can be introduced by delaying the tangential traction from the normal traction as suggested by Cochard and Rice (2000) and Ranjith and Rice (2000) δσeff α|v|+-v* δt = δσ (σn - σeff) where σeff represents the effective normal stress to be used in the Coulomb friction. This regularization introduces two delays depending on the slip rate and on a fixed time scale. In this study we performed a large number of 2D numerical simulations of in plane rupture with the spectral element method dynamic and we systematically investigated the effect of parameter selection on the rupture propagation, dissipation and radiation, by also performing a direct comparison with solutions provided by numerical and experimental results. We found that a purely time-dependent regularization requires a fine tuning rapidly jumping from a too fast, ineffective delay to a slow, invasive

  19. Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite.

    Science.gov (United States)

    Wang, Xiao-Lin; Lu, Zhong-Yuan; Li, Ze-Sheng; Sun, Chia-Chung

    2007-01-16

    Molecular dynamics simulations are applied to study the adsorption of polyethylene with different chain lengths on patterned graphite surfaces that contain nanoscale protrusions. The influence of the nanostructure on the strong attractive interaction inherently in the hydrophobic polyethylene and hydrophobic graphite system is investigated by modifying the top surface area and the height and the shape of the protrusions. The results are analyzed in terms of the chain configuration, the adsorption energy, the global orientational order parameter, and the normalized surface-chain contacting pair number in the first adsorption layer. When the size of the protrusion increases, the adsorption energy, the order parameter, and the normalized surface-chain contacting pair number decrease at a fixed chain length. When the size of the protrusion is fixed, the average adsorption energy per monomer and the order parameter decrease with increasing chain length because of the stronger intramolecular interactions between the monomers. Changing the protrusion shape in a suitable way will effectively reduce the strong surface-chain interaction.

  20. Molecular modeling and molecular dynamics simulation studies on the interactions of hydroxylated polychlorinated biphenyls with estrogen receptor-β.

    Science.gov (United States)

    Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Shi, Wei; Qian, XiangPing; Zhu, YongLiang; Yu, HongXia

    2013-10-01

    Endocrine-disrupting chemicals have attracted great concern. As major metabolites of polychlorinated biphenyls (PCBs), hydroxylated polychlorinated biphenyls (HO-PCBs) may disrupt estrogen hormone status because of their structural similarity to estrogen endogenous compounds. However, interactions between HO-PCBs and estrogen receptors (ERs) are not fully understood. In the present work, a molecular modeling study combining molecular docking, molecular dynamics simulations, and binding free energy calculations was performed to characterize the interactions of three HO-PCBs (4'-HO-PCB50, 2'-HO-PCB65, and 4'-HO-PCB69) having much different estrogenic activities with ERβ. Docking results showed that binding between ligands and ERβ was stabilized by hydrogen bond and hydrophobic interactions. The binding free energies of three ligands with ERβ were calculated, and further binding free energy decomposition analysis indicated that the dominating driving force of the binding between the ligands and ERβ was the van der Waals interaction. Some key residues, such as Leu298, Phe356, Gly472, His475, and Leu476, played important roles in ligand-receptor interactions by forming hydrophobic and hydrogen bond interactions with ligands. The results may be beneficial to increase understanding of the interactions between HO-PCBs and ERβ.

  1. Molecular dynamics simulations and Kelvin probe force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

    Science.gov (United States)

    Drolle, E.; Bennett, W. F. D.; Hammond, K.; Lyman, E.; Karttunen, M.; Leonenko, Z.

    The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

  2. Coupling effect of Brownian motion and laminar shear flow on colloid coagulation: a Brownian dynamics simulation study

    Institute of Scientific and Technical Information of China (English)

    Xu Sheng-Hua; Sun Zhi-Wei; Li Xu; Jin Tong Wang

    2012-01-01

    Simultaneous orthokinetic and perikinetic coagulations(SOPCs)are studied for small and large Peclet numbers(Pe)using Brownian dynamics simulation.The results demonstrate that the contributions of the Brownian motion and the shear flow to the overall coagulation rate are basically not additive.At the early stages of coagulation with small Peclet numbers,the ratio of overall coagulation rate to the rate of pure perikinetic coagulation is proportional to Pe1/2,while with high Peclet numbers,the ratio of overall coagulation rate to the rate of pure orthokinetic coagulation is proportional to pe-1/2.Moreover,our results show that the aggregation rate generally changes with time for the SOPC,which is different from that for pure preikinetic and pure orthokinetic coagulations.By comparing the SOPC with pure preikinetic and pure orthokinetic coagulations,we show that the redistribution of particles due to Brownian motion can play a very important role in the SOPC.In addition,the effects of redistribution in the directions perpendicular and parallel to the shear flow direction are different.This perspective explains the behavior of coagulation due to the joint effects of the Brownian motion(perikinetic)and the fluid motion(orthokinetic).

  3. QSAR, docking, dynamic simulation and quantum mechanics studies to explore the recognition properties of cholinesterase binding sites.

    Science.gov (United States)

    Correa-Basurto, J; Bello, M; Rosales-Hernández, M C; Hernández-Rodríguez, M; Nicolás-Vázquez, I; Rojo-Domínguez, A; Trujillo-Ferrara, J G; Miranda, René; Flores-Sandoval, C A

    2014-02-25

    A set of 84 known N-aryl-monosubstituted derivatives (42 amides: series 1 and 2, and 42 imides: series 3 an 4, from maleic and succinic anhydrides, respectively) that display inhibitory activity toward both acetylcholinesterase and butyrylcholinesterase (ChEs) was considered for Quantitative structure-activity relationship (QSAR) studies. These QSAR studies employed docking data from both ChEs that were previously submitted to molecular dynamics (MD) simulations. Donepezil and galanthamine stereoisomers were included to analyze their quantum mechanics properties and for validating the docking procedure. Quantum parameters such as frontier orbital energies, dipole moment, molecular volume, atomic charges, bond length and reactivity parameters were measured, as well as partition coefficients, molar refractivity and polarizability were also analyzed. In order to evaluate the obtained equations, four compounds: 1a (4-oxo-4-(phenylamino)butanoic acid), 2a ((2Z)-4-oxo-4-(phenylamino)but-2-enoic acid), 3a (2-phenylcyclopentane-1,3-dione) and 4a (2-phenylcyclopent-4-ene-1,3-dione) were employed as independent data set, using only equations with r(m(test))²>0.5. It was observed that residual values gave low value in almost all series, excepting in series 1 for compounds 3a and 4a, and in series 4 for compounds 1a, 2a and 3a, giving a low value for 4a. Consequently, equations seems to be specific according to the structure of the evaluated compound, that means, series 1 fits better for compound 1a, series 3 or 4 fits better for compounds 3a or 4a. Same behavior was observed in the butyrylcholinesterase (BChE). Therefore, obtained equations in this QSAR study could be employed to calculate the inhibition constant (Ki) value for compounds having a similar structure as N-aryl derivatives described here. The QSAR study showed that bond lengths, molecular electrostatic potential and frontier orbital energies are important in both ChE targets. Docking studies revealed that

  4. Influence of B{sub 1}-inhomogeneity on pharmacokinetic modeling of dynamic contrast-enhanced MRI: A simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Park, Bun Woo [Dept. of Radiology, Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Choi, Byung Se [Dept. of Radiology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam (Korea, Republic of); and others

    2017-08-01

    To simulate the B1-inhomogeneity-induced variation of pharmacokinetic parameters on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). B1-inhomogeneity-induced flip angle (FA) variation was estimated in a phantom study. Monte Carlo simulation was performed to assess the FA-deviation-induced measurement error of the pre-contrast R1, contrast-enhancement ratio, Gd-concentration, and two-compartment pharmacokinetic parameters (Ktrans, ve, and vp). B1-inhomogeneity resulted in −23–5% fluctuations (95% confidence interval [CI] of % error) of FA. The 95% CIs of FA-dependent % errors in the gray matter and blood were as follows: −16.7–61.8% and −16.7–61.8% for the pre-contrast R1, −1.0–0.3% and −5.2–1.3% for the contrast-enhancement ratio, and −14.2–58.1% and −14.1–57.8% for the Gd-concentration, respectively. These resulted in −43.1–48.4% error for Ktrans, −32.3–48.6% error for the ve, and −43.2–48.6% error for vp. The pre-contrast R1 was more vulnerable to FA error than the contrast-enhancement ratio, and was therefore a significant cause of the Gd-concentration error. For example, a −10% FA error led to a 23.6% deviation in the pre-contrast R1, −0.4% in the contrast-enhancement ratio, and 23.6% in the Gd-concentration. In a simulated condition with a 3% FA error in a target lesion and a −10% FA error in a feeding vessel, the % errors of the pharmacokinetic parameters were −23.7% for Ktrans, −23.7% for ve, and −23.7% for vp. Even a small degree of B1-inhomogeneity can cause a significant error in the measurement of pharmacokinetic parameters on DCE-MRI, while the vulnerability of the pre-contrast R1 calculations to FA deviations is a significant cause of the miscalculation.

  5. Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r

    NARCIS (Netherlands)

    Boek, E.S.; Briels, W.J.

    1993-01-01

    Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary

  6. Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3'-oxime from molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Bing; Tan, Vincent B C; Lim, Kian Meng; Tay, Tong Earn; Zhuang, Shulin

    2007-01-01

    Molecular dynamics simulations were performed to elucidate the interactions of CDK2 and CDK5 complexes with three inhibitors: R-roscovitine, S-roscovitine, and indirubin-3'-oxime. The preference of the two complexes for R-roscovitine over the S enantiomer, as reported by the experiment, was also found by the simulations. More importantly, the simulations showed that the cause of the stronger affinity for the R enantiomer is the presence of an important hydrogen bond between R-roscovitine and the kinases not found with S-roscovitine. The simulations also showed two amino acid mutations in the active site of CDK5/R-roscovitine that favor binding-enhanced electrostatic contributions, making the inhibitor more effective for CDK5 than for CDK2. This suggests that the effectiveness of roscovitine-like inhibitors can be improved by enhancing their electrostatic interaction with the kinases. Finally, molecular mechanics-Possion-Boltzmann/surface area calculations of the CDK5/indirubin-3'-oxime system in both water-excluded and water-included environments gave significantly different electrostatic contributions to the binding. The simulations detected the displacement of a water molecule in the active site of the water-included CDK/indirubin-3'-oxime system. This resulted in a more conserved binding pattern than the water-excluded structure. Hence, in the design of new indirubin-like inhibitors, it is important to include the water molecule in the analysis.

  7. Energy loss and surface temperature effects in ab initio molecular dynamics simulations: N adsorption on Ag(111) as a case study

    Science.gov (United States)

    Novko, Dino; Lončarić, Ivor; Blanco-Rey, María; Juaristi, J. Iñaki; Alducin, Maite

    2017-08-01

    We study surface temperature effects on the adsorption and relaxation of N atoms on Ag(111). To this aim, we perform ab initio molecular dynamics simulations with electronic friction, in which the surface is coupled to a thermostat that fixes the desired surface temperature. Simulations performed at 80 and 700 K show that the surface temperature has minor effects on magnitudes such as the initial adsorption probability, the relaxation rate of the adsorbing N, and the energy lost in electronic excitations. Slight differences are identified in the adsorption paths with the appearance of subsurface absorption events at 700 K that are not observed at 80 K. Furthermore, we perform additional simulations without a thermostat in order to examine the validity of commonly used ab initio molecular dynamics simulations in which no heat dissipation from the simulation cell is allowed. Our results show that such a methodology may not suffice to simulate the low-temperature regime since the surface becomes unphysically heated within a few picoseconds upon adsorption of the N atom. However, neither in this unfavorable case are the magnitudes defining the dynamics of the adsorbates at the same time scale significantly modified from those obtained at constant surface temperature.

  8. Simulating Effects of Long Term Use of Wastewater on Farmers Health Using System Dynamics Modeling (Case Study: Varamin Plain

    Directory of Open Access Journals (Sweden)

    Hamzehali Alizadeh

    2017-06-01

    Full Text Available Introduction: Agricultural activity in Varamin plain has been faced with many challenges in recent years, due to vicinity to Tehran the capital of Iran (competition for Latian dam reservoir, and competition with Tehran south network in allocation of Mamlou dam reservoir and treated wastewater of south wastewater treatment plant. Mamlou and Latian dam reservoirs, due to increase of population and industry sectors, allocated to urban utilization of Tehran. Based on national policy, the treated wastewater should be replaced with Latian dam reservoir water to supply water demand of agricultural sector. High volume transmission of wastewater to Varamin plain, will be have economical, environmental, and social effects. Several factors effect on wastewater management and success of utilization plans and any change in these factors may have various feedbacks on the other elements of wastewater use system. Hence, development of a model with capability of simulation of all factors, aspects and interactions that affect wastewater utilization is very necessary. The main objective of present study was development of water integrated model to study long-term effects of irrigation with Tehran treated wastewater, using system dynamics modeling (SD approach. Materials and Methods: Varamin Plain is one of the most important agricultural production centers of the country due to nearness to the large consumer market of Tehran and having fertile soil and knowledge of agriculture. The total agricultural irrigated land in Varamin Plain is 53486 hectares containing 17274 hectares of barley, 16926 hectares of wheat, 3866 hectares of tomato, 3521 hectares of vegetables, 3556 hectares of alfalfa, 2518 hectares of silage maize, 1771 hectares of melon, 1642 hectares of cotton, 1121 hectares of cucumber and 1291 hectares of other crops. In 2006 the irrigation requirement of the crop pattern was about 690 MCM and the actual agriculture water consumption was about 620 MCM

  9. Dynamic simulation of regulatory networks using SQUAD

    Directory of Open Access Journals (Sweden)

    Xenarios Ioannis

    2007-11-01

    Full Text Available Abstract Background The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. Results We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. Conclusion The simulation of regulatory networks aims at predicting the behavior of a whole system when subject

  10. Monoamine transporters: Insights from molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Julie eGrouleff

    2015-10-01

    Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.

  11. Monoamine transporters: insights from molecular dynamics simulations

    Science.gov (United States)

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  12. Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

    Science.gov (United States)

    Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

    2016-09-21

    The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen

  13. Simulations of boundary migration during recrystallization using molecular dynamics

    DEFF Research Database (Denmark)

    Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.

    2007-01-01

    We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...

  14. A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3.

    Science.gov (United States)

    Nowroozi, Amin; Shahlaei, Mohsen

    2017-02-01

    In this study, a computational pipeline was therefore devised to overcome homology modeling (HM) bottlenecks. The coupling of HM with molecular dynamics (MD) simulation is useful in that it tackles the sampling deficiency of dynamics simulations by providing good-quality initial guesses for the native structure. Indeed, HM also relaxes the severe requirement of force fields to explore the huge conformational space of protein structures. In this study, the interaction between the human bombesin receptor subtype-3 and MK-5046 was investigated integrating HM, molecular docking, and MD simulations. To improve conformational sampling in typical MD simulations of GPCRs, as in other biomolecules, multiple trajectories with different initial conditions can be employed rather than a single long trajectory. Multiple MD simulations of human bombesin receptor subtype-3 with different initial atomic velocities are applied to sample conformations in the vicinity of the structure generated by HM. The backbone atom conformational space distribution of replicates is analyzed employing principal components analysis. As a result, the averages of structural and dynamic properties over the twenty-one trajectories differ significantly from those obtained from individual trajectories.

  15. Molecular Dynamics Simulations of Hypervelocity Impacts

    Science.gov (United States)

    Owens, Eli T.; Bachlechner, Martina E.

    2007-03-01

    Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.

  16. Sensitivity Analysis of Fire Dynamics Simulation

    DEFF Research Database (Denmark)

    Brohus, Henrik; Nielsen, Peter V.; Petersen, Arnkell J.

    2007-01-01

    equations require solution of the issues of combustion and gas radiation to mention a few. This paper performs a sensitivity analysis of a fire dynamics simulation on a benchmark case where measurement results are available for comparison. The analysis is performed using the method of Elementary Effects......In case of fire dynamics simulation requirements to reliable results are most often very high due to the severe consequences of erroneous results. At the same time it is a well known fact that fire dynamics simulation constitutes rather complex physical phenomena which apart from flow and energy...

  17. The numerical simulation study of the dynamic evolutionary processes in an earthquake cycle on the Longmen Shan Fault

    Science.gov (United States)

    Tao, Wei; Shen, Zheng-Kang; Zhang, Yong

    2016-04-01

    concentration areas in the model, one is located in the mid and upper crust on the hanging wall where the strain energy could be released by permanent deformation like folding, and the other lies in the deep part of the fault where the strain energy could be released by earthquakes. (5) The whole earthquake dynamic process could be clearly reflected by the evolutions of the strain energy increments on the stages of the earthquake cycle. In the inter-seismic period, the strain energy accumulates relatively slowly; prior to the earthquake, the fault is locking and the strain energy accumulates fast, and some of the strain energy is released on the upper crust on the hanging wall of the fault. In coseismic stage, the strain energy is released fast along the fault. In the poseismic stage, the slow accumulation process of strain recovers rapidly as that in the inerseismic period in around one hundred years. The simulation study in this thesis would help better understand the earthquake dynamic process.

  18. Thermodynamics and intrinsic structure of the Al-Pb liquid-liquid interface: a molecular dynamics simulation study.

    Science.gov (United States)

    Yang, Yang; Laird, Brian B

    2014-07-17

    We examine the thermodynamics and intrinsic structure of the Al-Pb liquid-liquid interface using molecular dynamics simulation and embedded atom method potentials. The instantaneous interfacial positions, from which the intrinsic structure and the capillary fluctuation spectrum are determined, are calculated using a grid-based method. The interfacial free energy extracted from the capillary fluctuation spectrum is shown to be in excellent agreement with that calculated mechanically by integrating the stress profile. The intrinsic liquid-liquid interfacial density profile shows structural oscillations in the liquid phases in the interfacial region that are shown to be quantitatively similar to the radial distribution functions of the bulk liquid, consistent with theoretical predictions from classical density functional theory and with earlier simulations on liquid-liquid and liquid-vapor interfaces. In addition, we show the mean interfacial density profile for this system is well described as a convolution of the intrinsic density profile and the probability distribution of interfacial position.

  19. Molecular dynamics simulation study on zwitterionic structure to maintain the natural behavior of polyalanine13 in aqueous environment

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transition from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."

  20. Molecular dynamics simulation study: The decryption of bi and tri aromatics behavior with NaX zeolite.

    Science.gov (United States)

    Asl, M Haghighi; Moosavi, F; Sargolzaei, J; Sharifi, Kh

    2016-09-01

    Molecular dynamics simulations have been carried out to provide an atomic description of the behavior of naphthalene and anthracene in NaX zeolite. The force field parameters, which were selected in this process, were chosen carefully to examine dependence of the self-diffusion coefficient of sorbates over a wide range of loading, temperature, and pressure. The simulated adsorption isotherm and calculated adsorption energies at low concentration were found to be in a reasonable qualitative and quantitative agreement with the corresponding scarce experimental data which can evaluate the effectiveness of proposed calculation method and force field parameters. The simulations provided new insights into the simulated concentration dependence of the atomic behavior of bi and tri aromatics inside NaXmicropores. Collective effects of the mutual interactions of sorbates molecules competing for the most preferable sites at the supercages (SCs) were found to be key factors responsible for the observed behavior of the adsorption isotherms, heat of adsorption, activation energy, and self-diffusivity. All involved calculations were performed in time period 6ns and repeated calculations have been done at least two times to confirm the results and use the average values, which made the results being reliable.

  1. Molecular dynamic simulation study of plasma etching L10 FePt media in embedded mask patterning (EMP process

    Directory of Open Access Journals (Sweden)

    Jianxin Zhu

    2017-05-01

    Full Text Available Plasma etching process of single-crystal L10-FePt media [H. Wang et al., Appl. Phys. Lett. 102(5 (2013] is studied using molecular dynamic simulation. Embedded-Atom Method [M. S. Daw and M. I. Baskes, Phy. Rev. B 29, 6443 (1984; X. W. Zhou, R. A. Johnson and H. N. G. Wadley, Phy. Rev. B 69, 144113 (2004] is used to calculate the interatomic potential within atoms in FePt alloy, and ZBL potential [J.F. Ziegler, J. P. Biersack and U. Littmark, “The Stopping and Range of Ions in Matter,” Volume 1, Pergamon,1985] in comparison with conventional Lennard-Jones “12-6” potential is applied to interactions between etching gas ions and metal atoms. It is shown the post-etch structure defects can include amorphized surface layer and lattice interstitial point defects that caused by etchant ions passed through the surface layer. We show that the amorphized or damaged FePt lattice surface layer (or “magnetic dead-layer” thickness after etching increases with ion energy for Ar ion impacts, but significantly small for He ions at up to 250eV ion energy. However, we showed that He sputtering creates more interstitial defects at lower energy levels and defects are deeper below the surface compared to Ar sputtering. We also calculate the interstitial defect level and depth as dependence on ion energy for both Ar and He ions. Media magnetic property loss due to these defects is also discussed.

  2. Material removal mechanism during porous silica cluster impact on crystal silicon substrate studied by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Chen Ruling, E-mail: chenrl04@mails.tsinghua.edu.cn [Research Center of Nano-science and Nano-technology, Shanghai University, Shanghai 200444 (China); Jiang Ranran; Lei Hong; Liang Min [Research Center of Nano-science and Nano-technology, Shanghai University, Shanghai 200444 (China)

    2013-01-01

    Highlights: Black-Right-Pointing-Pointer The impact of the porous silica clusters on a silicon substrate was studied by MD. Black-Right-Pointing-Pointer The porous cluster shows high MRR and low surface damage at an optimal pore size. Black-Right-Pointing-Pointer The high MRR is due to the combined effects of plough, adhesion and permeation. Black-Right-Pointing-Pointer The low surface damage is due to the decreasing of the penetration depth. Black-Right-Pointing-Pointer Enlarged contact area is more effective than increased penetration to enhance MRR. - Abstract: Molecular dynamics (MD) simulation is applied in analyzing the material removal mechanism of silicon substrate under the impact of large porous silica cluster with different pore diameters. With the increasing of the pore diameter of the porous cluster, the number of the atoms removed from the impact silicon surface will firstly increase and then decrease until the cluster is adhered to the substrate, which is due to the combinational effects of plough of the cluster, adhesion between the cluster and the substrate, and permeation of the substrate atoms through the pore of the cluster. And adhesion is the most significant one among these three effects. Meanwhile, the damage of the impact substrate will become weaker due to the decreasing of the penetration depth with the increasing of the pore diameter. In addition, it is found that the effect of an enlarged real contact area between the cluster and the substrate is more significant than that of deeper penetration of the cluster in order to enhance the material removal rate (MRR) during the impact process. These findings are instructive in optimizing the process parameters to obtain lower surface roughness and higher material removal rate during the chemical mechanical polishing process.

  3. Dynamic simulation of flywheel-type fuses

    Directory of Open Access Journals (Sweden)

    Editorial Office

    1996-07-01

    Full Text Available Rounds of ammunition are normally armed with a fuse. In this study, a fuse is developed which uses a flywheel-type mechanism controlled by time or distance. Due to its simplicity of operation and construction, the concept is expected to have high reliabil­ity. The dynamic response of all the components of this flywheel-type fuse is mathematically modelled. Simulation software was developed which connects the mathematical models of the various components. With the definition of boundary values, the response of the projectile, flywheel and other components can be determined continuously for firing and in-flight conditions.

  4. [Oligoglycine surface structures: molecular dynamics simulation].

    Science.gov (United States)

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  5. Molecular Dynamics Simulations of Interface Failure

    Science.gov (United States)

    Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.

    2007-03-01

    The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.

  6. Molecular Dynamics Simulations of Ligand-Induced Flap Conformational Changes in Cathepsin-D-A Comparative Study.

    Science.gov (United States)

    Arodola, Olayide A; Soliman, Mahmoud E S

    2016-11-01

    The flap region in aspartic proteases is a unique structural feature to this class of enzymes, and found to have a profound impact on protein overall structure, function, and dynamics. Understanding the structure and dynamic behavior of the flap regions is crucial in the design of selective inhibitors against aspartic proteases. Cathepsin-D, an aspartic protease enzyme, has been implicated in a long list of degenerative diseases as well as breast cancer progression. Presented herein, for the first time, is a comprehensive description of the conformational flap dynamics of cathepsin-D using a comparative 50 ns "multiple" molecular dynamics simulations. Diverse collective metrics were proposed to accurately define flap dynamics. These are distance d1 between the flap tips residues (Gly79 and Met301); dihedral angle ϕ; in addition to TriCα angles Gly79-Asp33-Asp223, θ1 , and Gly79-Asp223-Met301, θ2 . The maximum distance attained throughout the simulation was 17.42 and 11.47 Å for apo and bound cathepsin-D, respectively, while the minimum distance observed was 8.75 and 6.32 Å for apo and bound cathepsin-D, respectively. The movement of the flap as well as the twist of the active pocket can properly be explained by measuring the angle, θ1 , between Gly79-Asp33-Met301 and correlating it with the distance Cα of the flap tip residues. The asymmetrical opening of the binding cavity was best described by the large shift of -6.26° to +20.94° in the dihedral angle, ϕ, corresponding to the full opening of the flap at a range of 31-33 ns. A wide-range of post-dynamic analyses was also applied in this report to supplement our findings. We believe that this report would augment current efforts in designing potent structure-based inhibitors against cathepsin-D in the treatment of breast cancer and other degenerative diseases. J. Cell. Biochem. 117: 2643-2657, 2016. © 2016 Wiley Periodicals, Inc.

  7. On the importance of including vegetation dynamics in hydrological simulation under climate change: A case study in the Jing River Basin

    Science.gov (United States)

    Li, Q.; Li, Z.; Ishidaira, H.

    2012-04-01

    The role of catchment vegetation within the hydrological cycle and its impact on hydrological processes has long been a topic of research within hydrology. A key element in quantifying the hydrological impact of climate change is the relationship between catchment vegetation and runoff, which continues to be a productive area of research within hydrology. However, the parameterization of vegetation composition and distribution as a dynamic component is insufficient in stand-alone hydrological modeling studies. Dynamic global vegetation models (DGVMs) are able to simulate transient structural changes in major vegetation types but do not simulate runoff generation reliably. A biosphere hydrological model (LPJH) coupling a prominent DGVM (Lund-Postdam-Jena model referred to as LPJ) with a stand-alone hydrological model (HYMOD) may simulate both vegetation dynamics and runoff generation reasonably. This study applies the LPJH model to the Jing River basin, a tributary of the Yellow River, with the objective of analyzing the role of vegetation in the hydrological processes at this semi-arid basin and evaluating the impact of vegetation change on the hydrological processes under climate change. The results show that the LPJH model gives reasonable hydrological simulation in terms of runoff. It is shown that changing climate conditions in terms of co2, temperature, precipitation, and the combination changes of these variables would result in actual evapotranspiration and runoff changes. Theses changes are mainly attributable to changes in transpiration driven by vegetation dynamics, which are not simulated in stand-alone hydrological models. Therefore, the composition and distribution of vegetation are of fundamental importance for evapotranspiration and runoff generation, especially under climate change. The percent of impact from each climate variable is also explored by using the LPJH model, which gives an overall view of climate change impact on hydrological processes

  8. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    王慧; 胡元中; 邹鲲; 冷永胜

    2001-01-01

    The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.

  9. How does stress affect human being—a molecular dynamic simulation study on cortisol and its glucocorticoid receptor

    Directory of Open Access Journals (Sweden)

    Dan Zhang

    2017-03-01

    Full Text Available Stress can be either positive or negative to human beings. Under stressful conditions, the mental and physical conditions of human can be affected. There exists certain relation between stress and illness. The cortisol and other glucocorticoids bind to the same receptor, which is called glucocorticoid receptor. Some evidences indicated that cortisol molecule binding to its glucocorticoid receptor was necessary for the stress response. Up to now, the structure–function relationships between cortisol molecule and its glucocorticoid receptor have not been deliberated from the atomic-level. In order to get a detailed understanding of the structure–function relationships between the cortisol molecule and glucocorticoids receptor, we have carried out molecular dynamic (MD simulations on glucocorticoid receptor (Apo system and cortisol with its glucocorticoid receptor complex (HCY system. On the basis of molecular dynamic simulations, a couple of key residues were identified, which were crucial for the binding of cortisol molecule. The results of binding free energy calculations are in good agreement with the experiment data. Our research gives clear insights from atomic-level into the structural–functional aspects of cortisol molecule and its glucocorticoid receptor, and also provides valuable information for the design of drug which can treat stress related illnesses.

  10. How does stress affect human being-a molecular dynamic simulation study on cortisol and its glucocorticoid receptor.

    Science.gov (United States)

    Zhang, Dan; Tian, Geng

    2017-03-01

    Stress can be either positive or negative to human beings. Under stressful conditions, the mental and physical conditions of human can be affected. There exists certain relation between stress and illness. The cortisol and other glucocorticoids bind to the same receptor, which is called glucocorticoid receptor. Some evidences indicated that cortisol molecule binding to its glucocorticoid receptor was necessary for the stress response. Up to now, the structure-function relationships between cortisol molecule and its glucocorticoid receptor have not been deliberated from the atomic-level. In order to get a detailed understanding of the structure-function relationships between the cortisol molecule and glucocorticoids receptor, we have carried out molecular dynamic (MD) simulations on glucocorticoid receptor (Apo system) and cortisol with its glucocorticoid receptor complex (HCY system). On the basis of molecular dynamic simulations, a couple of key residues were identified, which were crucial for the binding of cortisol molecule. The results of binding free energy calculations are in good agreement with the experiment data. Our research gives clear insights from atomic-level into the structural-functional aspects of cortisol molecule and its glucocorticoid receptor, and also provides valuable information for the design of drug which can treat stress related illnesses.

  11. Simulating protein dynamics: Novel methods and applications

    Science.gov (United States)

    Vishal, V.

    This Ph.D dissertation describes several methodological advances in molecular dynamics (MD) simulations. Methods like Markov State Models can be used effectively in combination with distributed computing to obtain long time scale behavior from an ensemble of short simulations. Advanced computing architectures like Graphics Processors can be used to greatly extend the scope of MD. Applications of MD techniques to problems like Alzheimer's Disease and fundamental questions in protein dynamics are described.

  12. Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Bo; Zhang, Lian Dong; Yu, Jingjing [Parallel Robot and Mechatronic System Laboratory of Hebei Province, Yanshan University, Qinhuangdao, Hebei (China)

    2016-11-15

    A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed.

  13. Molecular Dynamics Simulations of Polyelectrolyte Solutions

    Science.gov (United States)

    Dobrynin, Andrey

    2014-03-01

    Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings

  14. Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations.

    Science.gov (United States)

    Patra, Swarna M; Baştug, Turgut; Kuyucak, Serdar

    2007-09-27

    The accurate description of protein-ligand binding energies and configurations is an important problem in molecular biology with many applications in medicine and pharmacology. Molecular dynamics (MD) simulations provide the required accuracy but they are too slow for searching binding positions. Conversely, docking methods are much faster but have limited accuracy. An appropriate combination of the two methods could avoid the shortcomings associated with each, thus offering a better approach to the protein-ligand binding problem. Here we investigate the feasibility of such a combined docking-MD approach in a well-defined system: binding of organic cations to the gramicidin A channel. We use the AutoDock program to generate a set of protein-ligand binding configurations, which are then refined in MD simulations. For each system, we examine the binding configuration in detail and calculate the binding free energy by constructing the potential of mean force for the ligand. Our results show that AutoDock provides suitable initial configurations, which can be used profitably in MD simulations to obtain an accurate description of protein-ligand binding with a reasonable computational effort.

  15. Visualizing Structure and Dynamics of Disaccharide Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.

    2012-01-01

    We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

  16. Simulating Flexible-Spacecraft Dynamics and Control

    Science.gov (United States)

    Fedor, Joseph

    1987-01-01

    Versatile program applies to many types of spacecraft and dynamical problems. Flexible Spacecraft Dynamics and Control program (FSD) developed to aid in simulation of large class of flexible and rigid spacecraft. Extremely versatile and used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. Applicable to inertially oriented spinning, Earth-oriented, or gravity-gradient-stabilized spacecraft. Written in FORTRAN 77.

  17. 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.)

  18. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  19. Object Oriented Modelling and Dynamical Simulation

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1998-01-01

    This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...... onduction simulation experiments....

  20. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  1. Multiscale Model Approach for Magnetization Dynamics Simulations

    CERN Document Server

    De Lucia, Andrea; Tretiakov, Oleg A; Kläui, Mathias

    2016-01-01

    Simulations of magnetization dynamics in a multiscale environment enable rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with f...

  2. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  3. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui(

    2001-01-01

    [1]Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.[2]Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.[3]Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.[4]Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.[5]Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.[6]Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.[7]Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.[8]Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.[9]Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.[10]Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.[11]Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.[12]Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.[13]Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.

  4. A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function

    Science.gov (United States)

    Cardamone, Francesca; Iacovelli, Federico; Chillemi, Giovanni; Falconi, Mattia; Desideri, Alessandro

    2017-03-01

    The human sterile alpha motif SAM and HD domain-containing protein 1 (SAMHD1) restricts in non-cycling cells type the infection of a large range of retroviruses including HIV-1, reducing the intracellular pool concentration of deoxynucleoside triphosphates (dNTPs) required for the reverse transcription of the viral genome. The enzyme is in equilibrium between different forms depending on bound cofactors and substrate. In this work, two SAMHD1 three-dimensional models have been investigated through classical molecular dynamics simulation, to define the role of cofactors and metal ions in the association of the tetrameric active form. A detailed analysis of the inter-subunit interactions, taking place at the level of helix 13, indicates that removal of metal ions and cofactors induces an asymmetric loosening of the monomer-monomer interface leading to the formation of a loose tetramer where the two dimeric interfaces are weakened in different way.

  5. Effect of twin boundary on nanoimprint process of bicrystal Al thin film studied by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    谢月红; 徐建刚; 宋海洋; 张云光

    2015-01-01

    The effects of twin boundary (TB) on the mechanical properties of two types of bicrystal Al thin films during the nanoimprint process are investigated by using molecular dynamics simulations. The results indicate that for the TB direction parallel to the imprinting direction, the yield stress reaches the maximum for the initial dislocation nucleation when the mould directly imprints to the TB, and the yield stress first decreases with the increase of the marker interval and then increases. However, for the TB direction perpendicular to the imprinting direction, the effect of the TB location to the imprinting forces is very small, and the yield stress is greater than that with the TB direction parallel to the imprinting direction. The results also demonstrate that the direction of the slip dislocations and the deformation of the thin film caused by spring-back are different due to various positions and directions of the TB.

  6. A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function

    Science.gov (United States)

    Cardamone, Francesca; Iacovelli, Federico; Chillemi, Giovanni; Falconi, Mattia; Desideri, Alessandro

    2017-05-01

    The human sterile alpha motif SAM and HD domain-containing protein 1 (SAMHD1) restricts in non-cycling cells type the infection of a large range of retroviruses including HIV-1, reducing the intracellular pool concentration of deoxynucleoside triphosphates (dNTPs) required for the reverse transcription of the viral genome. The enzyme is in equilibrium between different forms depending on bound cofactors and substrate. In this work, two SAMHD1 three-dimensional models have been investigated through classical molecular dynamics simulation, to define the role of cofactors and metal ions in the association of the tetrameric active form. A detailed analysis of the inter-subunit interactions, taking place at the level of helix 13, indicates that removal of metal ions and cofactors induces an asymmetric loosening of the monomer-monomer interface leading to the formation of a loose tetramer where the two dimeric interfaces are weakened in different way.

  7. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1

    Directory of Open Access Journals (Sweden)

    Ismaila Yada Sudi

    2012-11-01

    Full Text Available Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD simulation and docking of D-2-chloropropionate (D-2CP, D-2-bromopropionate (D-2BP, monochloroacetate (MCA, monobromoacetate (MBA, 2,2-dichloropropionate (2,2-DCP, d,l-2,3-dichloropropionate (d,l-2,3-DCP, and 3-chloropropionate (3-CP into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.

  8. Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations.

    Science.gov (United States)

    Li, Zhenlong; Gorfe, Alemayehu A

    2015-01-14

    Lipid-polymer hybrid (LPH) nanoparticles represent a novel class of targeted drug delivery platforms that combine the advantages of liposomes and biodegradable polymeric nanoparticles. However, the molecular details of the interaction between LPHs and their target cell membranes remain poorly understood. We have investigated the receptor-mediated membrane adhesion process of a ligand-tethered LPH nanoparticle using extensive dissipative particle dynamics (DPD) simulations. We found that the spontaneous adhesion process follows a first-order kinetics characterized by two distinct stages: a rapid nanoparticle-membrane engagement, followed by a slow growth in the number of ligand-receptor pairs coupled with structural re-organization of both the nanoparticle and the membrane. The number of ligand-receptor pairs increases with the dynamic segregation of ligands and receptors toward the adhesion zone causing an out-of-plane deformation of the membrane. Moreover, the fluidity of the lipid shell allows for strong nanoparticle-membrane interactions to occur even when the ligand density is low. The LPH-membrane avidity is enhanced by the increased stability of each receptor-ligand pair due to the geometric confinement and the cooperative effect arising from multiple binding events. Thus, our results reveal the unique advantages of LPH nanoparticles as active cell-targeting nanocarriers and provide some general principles governing nanoparticle-cell interactions that may aid future design of LPHs with improved affinity and specificity for a given target of interest.

  9. Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations

    Science.gov (United States)

    Li, Zhenlong; Gorfe, Alemayehu A.

    2014-12-01

    Lipid-polymer hybrid (LPH) nanoparticles represent a novel class of targeted drug delivery platforms that combine the advantages of liposomes and biodegradable polymeric nanoparticles. However, the molecular details of the interaction between LPHs and their target cell membranes remain poorly understood. We have investigated the receptor-mediated membrane adhesion process of a ligand-tethered LPH nanoparticle using extensive dissipative particle dynamics (DPD) simulations. We found that the spontaneous adhesion process follows a first-order kinetics characterized by two distinct stages: a rapid nanoparticle-membrane engagement, followed by a slow growth in the number of ligand-receptor pairs coupled with structural re-organization of both the nanoparticle and the membrane. The number of ligand-receptor pairs increases with the dynamic segregation of ligands and receptors toward the adhesion zone causing an out-of-plane deformation of the membrane. Moreover, the fluidity of the lipid shell allows for strong nanoparticle-membrane interactions to occur even when the ligand density is low. The LPH-membrane avidity is enhanced by the increased stability of each receptor-ligand pair due to the geometric confinement and the cooperative effect arising from multiple binding events. Thus, our results reveal the unique advantages of LPH nanoparticles as active cell-targeting nanocarriers and provide some general principles governing nanoparticle-cell interactions that may aid future design of LPHs with improved affinity and specificity for a given target of interest.

  10. Characteristics of Sucrose Transport through the Sucrose-Specific Porin ScrY Studied by Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Liping eSun

    2016-02-01

    Full Text Available Sucrose-specific porin (ScrY is a transmembrane protein that allows for the uptake of sucrose under growth-limiting conditions. The crystal structure of ScrY was resolved before by X-ray crystallography, both in its uncomplexed form and with bound sucrose. However, little is known about the molecular characteristics of the transport mechanism of ScrY. To date, there has not yet been any clear demonstration for sucrose transport through the ScrY.Here, the dynamics of the ScrY trimer embedded in a phospholipid bilayer as well as the characteristics of sucrose translocation were investigated by means of atomistic molecular dynamics (MD simulations. The potential of mean force (PMF for sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Energy decomposition allowed to pinpoint three aspartic acids as key residues opposing the passage of sucrose, all located within the L3 loop. Mutation of two aspartic acids to uncharged residues resulted in an accordingly modified electrostatics and decreased PMF barrier. The chosen methodology and results will aid in the design of porins with modified transport specificities.

  11. Study of 3-D Dynamic Roughness Effects on Flow Over a NACA 0012 Airfoil Using Large Eddy Simulations at Low Reynolds Numbers

    Science.gov (United States)

    Guda, Venkata Subba Sai Satish

    There have been several advancements in the aerospace industry in areas of design such as aerodynamics, designs, controls and propulsion; all aimed at one common goal i.e. increasing efficiency --range and scope of operation with lesser fuel consumption. Several methods of flow control have been tried. Some were successful, some failed and many were termed as impractical. The low Reynolds number regime of 104 - 105 is a very interesting range. Flow physics in this range are quite different than those of higher Reynolds number range. Mid and high altitude UAV's, MAV's, sailplanes, jet engine fan blades, inboard helicopter rotor blades and wind turbine rotors are some of the aerodynamic applications that fall in this range. The current study deals with using dynamic roughness as a means of flow control over a NACA 0012 airfoil at low Reynolds numbers. Dynamic 3-D surface roughness elements on an airfoil placed near the leading edge aim at increasing the efficiency by suppressing the effects of leading edge separation like leading edge stall by delaying or totally eliminating flow separation. A numerical study of the above method has been carried out by means of a Large Eddy Simulation, a mathematical model for turbulence in Computational Fluid Dynamics, owing to the highly unsteady nature of the flow. A user defined function has been developed for the 3-D dynamic roughness element motion. Results from simulations have been compared to those from experimental PIV data. Large eddy simulations have relatively well captured the leading edge stall. For the clean cases, i.e. with the DR not actuated, the LES was able to reproduce experimental results in a reasonable fashion. However DR simulation results show that it fails to reattach the flow and suppress flow separation compared to experiments. Several novel techniques of grid design and hump creation are introduced through this study.

  12. Heterogeneous growth of calcite at aragonite {001}- and vaterite {001}-melt interfaces: A molecular dynamics simulation study

    Science.gov (United States)

    Nada, Hiroki; Nishimura, Tatsuya; Sakamoto, Takeshi; Kato, Takashi

    2016-09-01

    Crystal growth at the interface between a calcium carbonate (CaCO3) crystal and its melt at a high temperature of 1500 K is investigated by means of a molecular dynamics simulation. The simulation is performed for the interfaces of a calcite {104} plane, aragonite {001}, {100}, and {010} planes, and vaterite {001}, {110}, and {100} planes. The growth from a pure melt and that from a melt containing Mg2+ are examined. Calcite growth occurs on the calcite {104} plane, aragonite growth occurs on the aragonite {100}, and {010} planes, and vaterite growth occurs on the vaterite {110} and {100} planes. However, the heterogeneous growth of calcite occurs on the {001} plane of aragonite and vaterite, irrespective of the presence of Mg2+. The results advance our understanding of geological processes that occur at high temperature, such as the formation of CaCO3 crystals from carbonatite magma and the formation of marble. Moreover, the results provide useful information for the control of CaCO3 crystal formation in material design.

  13. A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models.

    Directory of Open Access Journals (Sweden)

    David A Rolls

    Full Text Available We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR epidemic dynamics. The types of network models are exponential random graph models (ERGMs and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a "hidden population". In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure.

  14. Spin dynamics simulations at AGS

    Energy Technology Data Exchange (ETDEWEB)

    Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.

    2010-05-23

    To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.

  15. Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study.

    Science.gov (United States)

    Moeinpour, Farid; Mohseni-Shahri, Fatemeh S; Malaekeh-Nikouei, Bizhan; Nassirli, Hooriyeh

    2016-09-25

    The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results.

  16. Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Amit Kumar

    Full Text Available Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism.

  17. Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study

    Science.gov (United States)

    Kumar, Amit; Cocco, Eleonora; Atzori, Luigi; Marrosu, Maria Giovanna; Pieroni, Enrico

    2013-01-01

    Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC) class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism. PMID:23555757

  18. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  19. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  20. Rotational Brownian Dynamics simulations of clathrin cage formation

    NARCIS (Netherlands)

    Ilie, I.M.; Otter, den W.K.; Briels, W.J.

    2014-01-01

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assem

  1. Rotational Brownian Dynamics simulations of clathrin cage formation

    NARCIS (Netherlands)

    Ilie, Ioana Mariuca; den Otter, Wouter K.; Briels, Willem J.

    2014-01-01

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the

  2. Dynamic Procedure for Filtered Gyrokinetic Simulations

    CERN Document Server

    Morel, Pierre; Albrecht-Marc, Michel; Carati, Daniele; Merz, Florian; Görler, Tobias; Jenko, Frank

    2011-01-01

    Large Eddy Simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the GENE code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved Direct Numerical Simulations (DNS). Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in Ion Temperature Gradient (ITG) driven turbulence. Moreover, the degree of anisotropy of the problem, that can vary with parameters, can be adapted dynamically by the method that shows Gyrokinetic Large Eddy Simulation (GyroLES) to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

  3. Molecular modeling and molecular dynamics simulation study of the human Rab9 and RhoBTB3 C-terminus complex

    Science.gov (United States)

    Junaid, Muhammad; Muhseen, Ziyad Tariq; Ullah, Ata; Wadood, Abdul; Liu, Junjun; Zhang, Houjin

    2014-01-01

    Rab9 is required for the transport of mannose 6-phosphate receptors to the trans-Golgi network from late endosomes through the interaction with its effector: RhoBTB3. Earlier research indicates the C-terminus of RhoBTB3 (Rho_Cterm) is used for the interaction with Rab9. We used the homology modeling along with the molecular dynamics (MD) simulation to study the binding pattern of Rho_Cterm and Rab9 at atomic level. Both modeled structures, Rab9 and Rho_Cterm, are of high quality as suggested by the Ramachandran plot and ProCheck. The complex of Rab9-Rho_Cterm was generated by unrestrained pairwise docking using ZDOCK server. The interface of complex is consistent with the previous experimental data. The results of MD simulation indicate that the binding interface is stable along the simulation process. PMID:25670879

  4. Induction generator models in dynamic simulation tools

    DEFF Research Database (Denmark)

    Knudsen, Hans; Akhmatov, Vladislav

    1999-01-01

    For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained. It is fo......For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained....... It is found to be possible to include a transient model in dynamic stability tools and, then, obtain correct results also in dynamic tools. The representation of the rotating system influences on the voltage recovery shape which is an important observation in case of windmills, where a heavy mill is connected...

  5. Molecular Dynamics Simulation Study of Skin Lipids: Effects of the Molar Ratio of Individual Components over a Wide Temperature Range.

    Science.gov (United States)

    Gupta, Rakesh; Rai, Beena

    2015-09-03

    Atomistic molecular dynamics (MD) simulations were employed to systematically investigate the effects of the molar ratio of the individual components cholesterol (CHOL), free fatty acid (FFA), and ceramides (CER) on the properties of the skin lipid bilayer over a wide temperature range (300-400 K). Several independent simulations were performed for bilayers comprised of only CER, CHOL, or FFA molecules as well as those made up of a mixture of CER:CHOL:FFA molecules in different molar ratios. It was found that CHOL increases the stability of the bilayer, since the mixed (CER:CHOL:FFA) 1:1:0, 1:1:1, and 2:2:1 bilayers remained stable until 400 K while the pure ceramide bilayer disintegrated around ∼390 K. It was also observed that CHOL reduces the volume spanned by ceramide molecules, thereby leading to a higher area per CER and FFA molecule in the mixed bilayer system. The CHOL molecule provided more rigidity to the mixed bilayer and led to a more ordered phase at elevated temperatures. The CHOL molecule provided fluidity to the bilayer below the phase transition temperature of CER and kept the bilayer rigid above the phase transition temperature. The FFA interdigitizes with CER molecules and increases the thickness of the bilayer, while rigid CHOL decreases the bilayer thickness. The presence of CHOL increases the compressibility of the bilayer which is responsible for the high barrier function of skin. The CER molecule forms inter- and intramolecular hydrogen bonds, while CHOL only forms intermolecular hydrogen bonds.

  6. Kinetic Simulations of Plasmoid Chain Dynamics

    CERN Document Server

    Markidis, Stefano; Lapenta, Giovanni; Divin, Andrey; Goldman, Martin; Newman, David; Laure, Erwin

    2013-01-01

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids, that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid...

  7. A Dynamical Simulation Facility for Hybrid Systems

    CERN Document Server

    Back, A; Myers, M; Back, Allen; Guckenheimer, John; Myers, Mark

    1993-01-01

    Abstract: This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the dynamical system are crucial since they provide the link between a natural mathematical formulation of a problem and the correct application of standard numerical algorithms. We describe a partial implementation of the design methodology and use this simulation tool for a specific control problem in robotics as an illustration of the utility of the approach for practical applications.

  8. The Communication of Meaning in Anticipatory Systems: A Simulation Study of the Dynamics of Intentionality in Social Interactions

    CERN Document Server

    Leydesdorff, Loet

    2009-01-01

    Psychological and social systems provide us with a natural domain for the study of anticipations because these systems are based on and operate in terms of intentionality. Psychological systems can be expected to contain a model of themselves and their environments social systems can be strongly anticipatory and therefore co-construct their environments, for example, in techno-economic (co-)evolutions. Using Duboi's hyper-incursive and incursive formulations of the logistic equation, these two types of systems and their couplings can be simulated. In addition to their structural coupling, psychological and social systems are also coupled by providing meaning reflexively to each other's meaning-processing. Luhmann's distinctions among (1) interactions between intentions at the micro-level, (2) organization at the meso-level, and (3) self-organization of the fluxes of meaningful communication at the global level can be modeled and simulated using three hyper-incursive equations. The global level of self-organiz...

  9. Testing dynamic stabilisation in complex Langevin simulations

    CERN Document Server

    Attanasio, Felipe

    2016-01-01

    Complex Langevin methods have been successfully applied in theories that suffer from a sign problem such as QCD with a chemical potential. We present and illustrate a novel method (dynamic stabilisation) that ensures that Complex Langevin simulations stay close to the SU(3) manifold, which lead to correct and improved results in the framework of pure Yang-Mills simulations and QCD in the limit of heavy quarks.

  10. Coarse-grained protein molecular dynamics simulations

    Science.gov (United States)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  11. Is bursting more effective than spiking in evoking pituitary hormone secretion? A spatiotemporal simulation study of calcium and granule dynamics.

    Science.gov (United States)

    Tagliavini, Alessia; Tabak, Joël; Bertram, Richard; Pedersen, Morten Gram

    2016-04-01

    Endocrine cells of the pituitary gland secrete a number of hormones, and the amount of hormone released by a cell is controlled in large part by the cell's electrical activity and subsequent Ca(2+) influx. Typical electrical behaviors of pituitary cells include continuous spiking and so-called pseudo-plateau bursting. It has been shown that the amplitude of Ca(2+) fluctuations is greater in bursting cells, leading to the hypothesis that bursting cells release more hormone than spiking cells. In this work, we apply computer simulations to test this hypothesis. We use experimental recordings of electrical activity as input to mathematical models of Ca(2+) channel activity, buffered Ca(2+) diffusion, and Ca(2+)-driven exocytosis. To compare the efficacy of spiking and bursting on the same cell, we pharmacologically block the large-conductance potassium (BK) current from a bursting cell or add a BK current to a spiking cell via dynamic clamp. We find that bursting is generally at least as effective as spiking at evoking hormone release and is often considerably more effective, even when normalizing to Ca(2+) influx. Our hybrid experimental/modeling approach confirms that adding a BK-type K(+) current, which is typically associated with decreased cell activity and reduced secretion, can actually produce an increase in hormone secretion, as suggested earlier.

  12. High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    Seshasayee Aswin Sai Narain

    2005-03-01

    Full Text Available Abstract Background Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. Results High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg and Root Mean Square Deviation (RMSD have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. Conclusion Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE, shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.

  13. Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations.

    Science.gov (United States)

    Olson, Mark A; Lee, Michael S; Yeh, In-Chul

    2017-01-28

    This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale. We found the GBSW implicit membrane model to produce results of limited accuracy in conformational properties of the peptide when compared to the NMR structure, yet the model resolution is sufficient to determine the effect of sequence differentiation on peptide-membrane integration. © 2016 Wiley Periodicals, Inc.

  14. Thermodynamic Studies of Decane on Boron Nitride and Graphite Substrates Using Synchrotron Radiation and Molecular Dynamics Simulations

    Science.gov (United States)

    Strange, Nicholas; Arnold, Thomas; Forster, Matthew; Parker, Julia; Larese, J. Z.; Diamond Light Source Collaboration; University of Tennessee Team

    2014-03-01

    Hexagonal boron nitride (hBN) has a lattice structure similar to that of graphite with a slightly larger lattice parameter in the basal plane. This, among other properties, makes it an excellent substrate in place of graphite, eliciting some important differences. This work is part of a larger effort to examine the interaction of alkanes with magnesium oxide, graphite, and boron nitride surfaces. In our current presentation, we will discuss the interaction of decane with these surfaces. Decane exhibits a fully commensurate structure on graphite and hBN at monolayer coverages. In this particular experiment, we have examined the monolayer structure of decane adsorbed on the basal plane of hBN using synchrotron x-ray radiation at Diamond Light Source. Additionally, we have examined the system experimentally with volumetric isotherms as well as computationally using molecular dynamics simulations. The volumetric isotherms allow us to calculate properties which provide important information about the adsorbate's interaction with not only neighboring molecules, but also the interaction with the adsorbent boron nitride.

  15. A study on phase transformation of monocrystalline silicon due to ultra-precision polishing by molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Lin Zhang

    2012-12-01

    Full Text Available A three-dimensional molecular dynamics (MD simulation is conducted to investigate the material removal mechanism of monocrystalline silicon by mechanical polishing at atomistic scale with diamond abrasives. By monitoring relative positions of atoms in the monocrystalline silicon specimen, the microstructure transformation of monocrystalline silicon is clearly identified and analyzed. The phase transformation is accomplished under extreme conditions with high temperature and huge hydrostatic pressure, and as a result the silicon microstructure transforms from the four-coordinated diamond cubic structure (Si-I to the six-coordinated body-centered tetragonal structure (β-silicon. The values of local pressure and temperature are consistent with previous experimental results. In addition, the force between the diamond abrasive and specimen indicates the occurrence of phase transformation in the specimen. The potential energy of each atom is also calculated, which provides us an effective approach to analyze the energy variation of atoms in the mechanism of material deformation and the formation of machined surface after ultra-precision polishing.

  16. Study on Exploration of Azeotropic Point of Pb-Sb Alloys by Vacuum Distillation and Ab Initio Molecular Dynamic Simulation

    Science.gov (United States)

    Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian

    2016-10-01

    The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.

  17. The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

    Science.gov (United States)

    Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Xu, Jian; Huai, Ping; Deng, Huiqiu; Hu, Wangyu

    2016-02-01

    Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the HeN and HeNV1SIA1 clusters, the average length of He-He bonds shortens, but it elongates for the HeNV1 clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of HeNVM cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

  18. Micromechanism of oxygen transport during initial stage oxidation in Si(100) surface: A ReaxFF molecular dynamics simulation study

    Science.gov (United States)

    Sun, Yu; Liu, Yilun; Chen, Xuefeng; Zhai, Zhi; Xu, Fei; Liu, Yijun

    2017-06-01

    The early stage oxidation in Si(100) surface has been investigated in this work by a reactive force field molecular dynamics (ReaxFF MD) simulation, manifesting that the oxygen transport acted as a dominant issue for initial oxidation process. Due to the oxidation, a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Si(100) surface and further prevented oxidation in the deeper layer. In contrast, thermal actuation was beneficial to the oxygen transport into deeper layer as temperature increases. Therefore, a competition mechanism was found for the oxygen transport during early stage oxidation in Si(100) surface. At room temperature, the oxygen transport was governed by the blocking effect of compressive stress, so a better quality oxide film with more uniform interface and more stoichiometric oxide structure was obtained. Indeed, the mechanism presented in this work is also applicable for other self-limiting oxidation (e.g. metal oxidation) and is helpful for the design of high-performance electronic devices.

  19. Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Xiaolei Wang

    2013-12-01

    Full Text Available We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.

  20. Quantum Simulation for Open-System Dynamics

    Science.gov (United States)

    Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry

    2013-03-01

    Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.

  1. Simulating food web dynamics along a gradient: quantifying human influence.

    Directory of Open Access Journals (Sweden)

    Ferenc Jordán

    Full Text Available Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo. The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1, when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling

  2. Simulating food web dynamics along a gradient: quantifying human influence.

    Science.gov (United States)

    Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M

    2012-01-01

    Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics

  3. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    Energy Technology Data Exchange (ETDEWEB)

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  4. Induction generator models in dynamic simulation tools

    DEFF Research Database (Denmark)

    Knudsen, Hans; Akhmatov, Vladislav

    1999-01-01

    . It is found to be possible to include a transient model in dynamic stability tools and, then, obtain correct results also in dynamic tools. The representation of the rotating system influences on the voltage recovery shape which is an important observation in case of windmills, where a heavy mill is connected......For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained...

  5. Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations.

    Science.gov (United States)

    Reshetnikov, Roman; Golovin, Andrey; Spiridonova, Vera; Kopylov, Alexei; Šponer, Jiří

    2010-10-12

    The thrombin-binding aptamer (15-TBA) is a 15-mer DNA oligonucleotide with sequence d(GGTTGGTGTGGTTGG). 15-TBA folds into a quadruplex DNA (G-DNA) structure with two planar G-quartets connected by three single-stranded loops. The arrangement of the 15-TBA-thrombin complex is unclear, particularly with respect to the precise 15-TBA residues that interact with the thrombin structure. Our present understanding suggests either the 15-TBA single stranded loops containing sequential thymidines (TT) or alternatively a single-stranded loop, containing a guanine flanked by 2 thymidines (TGT), physically associates with thrombin protein. In the present study, the explicit solvent molecular dynamics (MD) simulation method was utilized to further analyze the 15-TBA-thrombin three-dimensional structure. Functional annotation of the loop residues was made with long simulations in the parmbsc0 force field. In total, the elapsed time of simulations carried out in this study exceeds 12 microseconds, substantially surpassing previous G-DNA simulation reports. Our simulations suggest that the TGT-loop function is to stabilize the structure of the aptamer, while the TT-loops participate in direct binding to thrombin. The findings of the present report advance our understanding of the molecular structure of the 15-TBA-thrombin structure further enabling the construction of biosensors for aptamer bases and the development of anticoagulant agents.

  6. Experimental and molecular dynamics simulation study of structure of liquid and amorphous Ni 62 Nb 38 alloy

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y.; Ashcraft, R.; Mendelev, M. I.; Wang, C. Z.; Kelton, K. F.

    2016-11-28

    The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate the AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni–Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. The analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to Tg and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni62Nb38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.

  7. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2001-01-01

    Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...

  8. Fluid Dynamics Theory, Computation, and Numerical Simulation

    CERN Document Server

    Pozrikidis, Constantine

    2009-01-01

    Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...

  9. Monte carlo simulation for soot dynamics

    KAUST Repository

    Zhou, Kun

    2012-01-01

    A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.

  10. Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study

    Indian Academy of Sciences (India)

    SANDIPA INDRA; RANJIT BISWAS BISWAS

    2016-12-01

    Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been investigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutionshave been thoroughly examined for the search of slow dynamics. Note, TMAO possesses zwitterionic structure and is a protein stabilizer whereas TMU is a neutral dipolar molecule and a strong denaturant. Results suggest that water-TMAO solutions possess stronger DH than water-TMU solutions with the solute concentration dependence being stronger for TMAO than for TMU. Diffusive dynamics slows down near the solute surface for both the solutes. Solvation structure shows TMAO-water interaction is stronger than TMU-waterinteraction, producing longer H-bond fluctuation timescale in TMAO solutions. In short, this paper presents, for the first time, a systematic and comparative study of motional features and inter-species interactions between aqueous solutions containing solutes that differ in their individual impacts on protein stability.

  11. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  12. Multiscale mathematical modeling and simulation of cellular dynamical process.

    Science.gov (United States)

    Nakaoka, Shinji

    2014-01-01

    Epidermal homeostasis is maintained by dynamic interactions among molecules and cells at different spatiotemporal scales. Mathematical modeling and simulation is expected to provide clear understanding and precise description of multiscaleness in tissue homeostasis under systems perspective. We introduce a stochastic process-based description of multiscale dynamics. Agent-based modeling as a framework of multiscale modeling to achieve consistent integration of definitive subsystems is proposed. A newly developed algorithm that particularly aims to perform stochastic simulations of cellular dynamical process is introduced. Finally we review applications of multiscale modeling and quantitative study to important aspects of epidermal and epithelial homeostasis.

  13. Dynamical simulation of tether in orbit deployment

    Science.gov (United States)

    Smirnov, N. N.; Demyanov, Yu. A.; Zvyaguin, A. V.; Malashin, A. A.; Luzhin, A. A.

    2010-08-01

    The paper is aimed at studying the peculiarities of dynamical behavior of tether in its deployment in low Earth orbit during YES2 experiment in Foton-M3 mission, and performing flight data analysis with account of these effects. The analysis in the first part of the paper uses as input a pre-provided tension profile for the mission (resulting from a simulation to be independently validated). With this input it then performs an open-loop simulation which explains the sensitivity to the initial parameters. For the actual flight design a feedback mechanism and algorithm was used in order to control the deployment speed along a nominal profile, minimizing sensitivity to conditions such as initial velocity and endmass value. The paper provides solutions accounting for final velocities of wave propagation in tether, which is especially important for such stages of the deployment as sharp changing of the velocity direction and intensive braking. Moreover the YES2 data is used to validate the theoretical derivations.

  14. Object Oriented Modelling and Dynamical Simulation

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1998-01-01

    This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...

  15. Molecular dynamics simulations of magnetized dusty plasmas

    Science.gov (United States)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

    The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)

  16. Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine (DPPC) membrane: A Molecular Dynamics Simulations Study

    Energy Technology Data Exchange (ETDEWEB)

    Cournia, Zoe [Yale University; Ullmann, G. Matthias [University of Bayreuth; Smith, Jeremy C [ORNL

    2007-02-01

    Lipid raft/domain formation may arise as a result of the effects of specific sterols on the physical properties of membranes. Here, using molecular dynamics simulation, we examine the effects of three closely-related sterols, ergosterol, cholesterol, and lanosterol, at a biologically relevant concentration (40 mol %) on the structural properties of a model dipalmitoyl phosphatidylcholine (DPPC) membrane at 309 and 323 K. All three sterols are found to order the DPPC acyl tails and condense the membrane relative to the DPPC liquid-phase membrane, but each one does this to a significantly different degree. The smooth {alpha}-face of ergosterol, together with the presence of tail unsaturation in this sterol, leads to closer interaction of ergosterol with the lipids and closer packing of the lipids with each other, so ergosterol has a higher condensing effect on the membrane, as reflected by the area per lipid. Moreover, ergosterol induces a higher proportion of trans lipid conformers, a thicker membrane, and higher lipid order parameters and is aligned more closely with the membrane normal. Ergosterol also positions itself closer to the bilayer/water interface. In contrast, the rough {alpha}-face of lanosterol leads to a less close interaction of the steroid ring system with the phospholipid acyl chains, and so lanosterol orders, straightens, and packs the lipid acyl chains less well and is less closely aligned with the membrane normal. Furthermore, lanosterol lies closer to the relatively disordered membrane center than do the other sterols. The behavior of cholesterol in all the above respects is intermediate between that of lanosterol and ergosterol. The findings here may explain why ergosterol is the most efficient of the three sterols at promoting the liquid-ordered phase and lipid domain formation and may also furnish part of the explanation as to why cholesterol is evolutionarily preferred over lanosterol in higher-vertebrate plasma membranes.

  17. Speciation and Structural Properties of Hydrothermal Solutions of Sodium and Potassium Sulfate Studied by Molecular Dynamics Simulations.

    Science.gov (United States)

    Reimer, Joachim; Vogel, Frédéric; Steele-MacInnis, Matthew

    2016-05-18

    Aqueous solutions of salts at elevated pressures and temperatures play a key role in geochemical processes and in applications of supercritical water in waste and biomass treatment, for which salt management is crucial for performance. A major question in predicting salt behavior in such processes is how different salts affect the phase equilibria. Herein, molecular dynamics (MD) simulations are used to investigate molecular-scale structures of solutions of sodium and/or potassium sulfate, which show contrasting macroscopic behavior. Solutions of Na-SO4 exhibit a tendency towards forming large ionic clusters with increasing temperature, whereas solutions of K-SO4 show significantly less clustering under equivalent conditions. In mixed systems (Nax K2-x SO4 ), cluster formation is dramatically reduced with decreasing Na/(K+Na) ratio; this indicates a structure-breaking role of K. MD results allow these phenomena to be related to the characteristics of electrostatic interactions between K(+) and SO4 (2-) , compared with the analogous Na(+) -SO4 (2-) interactions. The results suggest a mechanism underlying the experimentally observed increasing solubility in ternary mixtures of solutions of Na-K-SO4 . Specifically, the propensity of sodium to associate with sulfate, versus that of potassium to break up the sodium-sulfate clusters, may affect the contrasting behavior of these salts. Thus, mutual salting-in in ternary hydrothermal solutions of Na-K-SO4 reflects the opposing, but complementary, natures of Na-SO4 versus K-SO4 interactions. The results also provide clues towards the reported liquid immiscibility in this ternary system.

  18. Exploring molecular insights into aggregation of hydrotrope sodium cumene sulfonate in aqueous solution: a molecular dynamics simulation study.

    Science.gov (United States)

    Das, Shubhadip; Paul, Sandip

    2015-02-19

    Hydrotropes are an important class of molecules that enhance the solubility of an otherwise insoluble or sparingly soluble solute in water. Besides this, hydrotropes are also known to self-assemble in aqueous solution and form aggregates. It is the hydrotrope aggregate that helps in solubilizing a solute molecule in water. In view of this, we try to understand the underlying mechanism of self-aggregation of hydrotrope sodium cumene sulfonate (SCS) in water. We have carried out classical molecular dynamics simulations of aqueous SCS solutions with a regime of concentrations. Moreover, to examine the effect of temperature change on SCS aggregation, if any, we consider four different temperatures ranging from 298 to 358 K. From the estimation of densities of different solutions we calculate apparent and partial molal volumes of the hydrotrope. The changes in these quantities increase sharply at a characteristic minimum hydrotrope concentration. The determination of molal expansibility at infinite dilution for different temperatures indicates the water structure breaking by SCS molecules, which is further confirmed by the calculations of water-water pair correlation functions. In comparison with typical surfactants in micelles, a slightly lower value of volumetric change upon aggregation per carbon atom suggests the formation of a more closely packed structure of hydrotrope aggregates. A close examination of different structural properties of hydrotrope solutions reveals that the hydrophobic interactions through their hydrophobic tails significantly contribute in hydrotrope aggregation,and the dehydration of hydrophobic tail at elevated temperatures is also visible. Remarkably, the aggregates have little or no impact on the average number of water-SCS hydrogen bonds.

  19. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

  20. Probing Cellular Dynamics with Mesoscopic Simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    Cellular processes span a huge range of length and time scales from the molecular to the near-macroscopic. Understanding how effects on one scale influence, and are themselves influenced by, those on lower and higher scales is a critical issue for the construction of models in Systems Biology....... Advances in computing hardware and software now allow explicit simulation of some aspects of cellular dynamics close to the molecular scale. Vesicle fusion is one example of such a process. Experiments, however, typically probe cellular behavior from the molecular scale up to microns. Standard particle...... soon be coupled to Mass Action models allowing the parameters in such models to be continuously tuned according to the finer resolution simulation. This will help realize the goal of a computational cellular simulation that is able to capture the dynamics of membrane-associated processes...

  1. Computer simulation of confined liquid crystal dynamics

    CERN Document Server

    Webster, R E

    2001-01-01

    are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results...

  2. In silico FRET from simulated dye dynamics

    Science.gov (United States)

    Hoefling, Martin; Grubmüller, Helmut

    2013-03-01

    Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language

  3. Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

    Science.gov (United States)

    Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

    2011-01-01

    The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

  4. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  5. The Communication of Meaning in Anticipatory Systems: A Simulation Study of the Dynamics of Intentionality in Social Interactions

    Science.gov (United States)

    Leydesdorff, Loet

    2008-10-01

    Psychological and social systems provide us with a natural domain for the study of anticipations because these systems are based on and operate in terms of intentionality. Psychological systems can be expected to contain a model of themselves and their environments; social systems can be strongly anticipatory and therefore co-construct their environments, for example, in techno-economic (co-)evolutions. Using Dubois' hyper-incursive and incursive formulations of the logistic equation, these two types of systems and their couplings can be simulated. In addition to their structural coupling, psychological and social systems are also coupled by providing meaning reflexively to each other's meaning-processing. Luhmann's distinctions among (1) interactions between intentions at the micro-level, (2) organization at the meso-level, and (3) self-organization of the fluxes of meaningful communication at the global level can be modeled and simulated using three hyper-incursive equations. The global level of self-organizing interactions among fluxes of communication is retained at the meso-level of organization. In a knowledge-based economy, these two levels of anticipatory structuration can be expected to propel each other at the supra-individual level.

  6. Nanoscale deicing by molecular dynamics simulation

    Science.gov (United States)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice

  7. Dynamic Simulation of the Harvester Boom Cylinder

    Directory of Open Access Journals (Sweden)

    Rongfeng Shen

    2017-04-01

    Full Text Available Based on the complete dynamic calculation method, the layout, force, and strength of harvester boom cylinders were designed and calculated. Closed simulations for the determination of the dynamic responses of the harvester boom during luffing motion considering the cylinder drive system and luffing angle position control have been realized. Using the ADAMS mechanical system dynamics analysis software, six different arm poses were selected and simulated based on the cylinder as the analysis object. A flexible model of the harvester boom luffing motion has been established. The movement of the oil cylinder under different conditions were analyzed, and the main operation dimensions of the harvester boom and the force condition of the oil cylinder were obtained. The calculation results show that the dynamic responses of the boom are more sensitive to the luffing acceleration, in comparison with the luffing velocity. It is seen that this method is very effective and convenient for boom luffing simulation. It is also reasonable to see that the extension of the distance of the bottom of the boom is shortened by adjusting the initial state of the boom in the working process, which can also effectively reduce the workload of the boom—thus improving the mechanical efficiency.

  8. Activated carbon immersed in water-the origin of linear correlation between enthalpy of immersion and oxygen content studied by molecular dynamics simulation.

    Science.gov (United States)

    Terzyk, Artur P; Gauden, Piotr A; Furmaniak, Sylwester; Wesołowski, Radosław P; Kowalczyk, Piotr

    2010-09-28

    First Molecular Dynamics simulation results of activated carbon immersion in water are reported. Using a Virtual Porous Carbon Model of "soft" carbon the influence of surface oxygen content, distribution of groups and micropore diameter on the enthalpy of immersion is studied. The empirical relation between enthalpy and concentration of surface groups (as well as polar surface area) is reproduced by molecular simulation results. It is shown that for strongly hydrophobic carbons immersed in water, the water-vapour interface inside pores appears. This interface vanishes with the rise in content of surface oxygen. We discuss some nuances of the interfacial region using proximal distribution functions and hydrogen bonds statistics. Finally we conclude that the mechanism of immersion process is in accordance with Pratt-Chandler theory of hydrophobic interactions.

  9. Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r)

    Science.gov (United States)

    Boek, E. S.; Briels, W. J.

    1993-01-01

    Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)].

  10. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Xiaokun; Han, Min; Ming, Dengming, E-mail: dming@fudan.edu.cn [Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai (China)

    2015-10-07

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  11. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations.

    Science.gov (United States)

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-01

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  12. Acyclic forms of aldohexoses and ketohexoses in aqueous and DMSO solutions: conformational features studied using molecular dynamics simulations.

    Science.gov (United States)

    Plazinski, Wojciech; Plazinska, Anita; Drach, Mateusz

    2016-04-14

    The molecular properties of aldohexoses and ketohexoses are usually studied in the context of their cyclic, furanose or pyranose structures which is due to the abundance of related tautomeric forms in aqueous solution. We studied the conformational features of a complete series of D-aldohexoses (D-allose, D-altrose, D-glucose, D-mannose, D-gulose, d-idose, D-galactose and D-talose) and D-ketohexoses (D-psicose, D-fructose, D-sorbose and D-tagatose) as well as of L-psicose by using microsecond-timescale molecular dynamics in explicit water and DMSO with the use of enhanced sampling methods. In each of the studied cases the preferred conformation corresponded to an extended chain structure; the less populated conformers included the quasi-cyclic structures, close to furanose rings and common for both aldo- and ketohexoses. The orientational preferences of the aldehyde or ketone groups are correlated with the relative populations of anomers characteristic of cyclic aldo- and ketohexoses, respectively, thus indicating that basic features of anomeric equilibria are preserved even if hexose molecules are not in their cyclic forms. No analogous relationship is observed in the case of other structural characteristics, such as the preferences of acyclic molecules to form either the furanose-or pyranose-like structures or maintaining the chair-like geometry of pseudo-pyranose rings.

  13. Fast simulation of Brownian dynamics in a crowded environment

    CERN Document Server

    Smith, Stephen

    2016-01-01

    Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large spee...

  14. Strong Analog Classical Simulation of Coherent Quantum Dynamics

    Science.gov (United States)

    Wang, Dong-Sheng

    2017-02-01

    A strong analog classical simulation of general quantum evolution is proposed, which serves as a novel scheme in quantum computation and simulation. The scheme employs the approach of geometric quantum mechanics and quantum informational technique of quantum tomography, which applies broadly to cases of mixed states, nonunitary evolution, and infinite dimensional systems. The simulation provides an intriguing classical picture to probe quantum phenomena, namely, a coherent quantum dynamics can be viewed as a globally constrained classical Hamiltonian dynamics of a collection of coupled particles or strings. Efficiency analysis reveals a fundamental difference between the locality in real space and locality in Hilbert space, the latter enables efficient strong analog classical simulations. Examples are also studied to highlight the differences and gaps among various simulation methods. Funding support from NSERC of Canada and a research fellowship at Department of Physics and Astronomy, University of British Columbia are acknowledged

  15. Molecular Dynamics Simulation of Glass Transition Behavior of Polyimide Ensemble

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The effect of chromophores to the glass transition temperature of polyimide ensemble has been investigated by means of molecular dynamics simulation in conjunction with barrier analysis. Simulated Tg results indicated a good agreement with experimental value. This study showed the MD simulation could estimate the effect of chromophores to the Tg of polyimide ensemble conveniently and an estimation approach method had a surprising deviation of Tg from experiment. At the same time, a polyimide structure with higher barrier energy was designed and validated by MD simulation.

  16. Classical trajectory simulations of post-transition state dynamics

    Science.gov (United States)

    Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.

    Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.

  17. Microscopic Dynamics and Topology of Polymer Rings Immersed in a Host Matrix of Longer Linear Polymers: Results from a Detailed Molecular Dynamics Simulation Study and Comparison with Experimental Data

    Directory of Open Access Journals (Sweden)

    George D. Papadopoulos

    2016-08-01

    Full Text Available We have performed molecular dynamics (MD simulations of melt systems consisting of a small number of long ring poly(ethylene oxide (PEO probes immersed in a host matrix of linear PEO chains and have studied their microscopic dynamics and topology as a function of the molecular length of the host linear chains. Consistent with a recent neutron spin echo spectroscopy study (Goossen et al., Phys. Rev. Lett. 2015, 115, 148302, we have observed that the segmental dynamics of the probe ring molecules is controlled by the length of the host linear chains. In matrices of short, unentangled linear chains, the ring probes exhibit a Rouse-like dynamics, and the spectra of their dynamic structure factor resemble those in their own melt. In striking contrast, in matrices of long, entangled linear chains, their dynamics is drastically altered. The corresponding dynamic structure factor spectra exhibit a steep initial decay up to times on the order of the entanglement time τe of linear PEO at the same temperature but then they become practically time-independent approaching plateau values. The plateau values are different for different wavevectors; they also depend on the length of the host linear chains. Our results are supported by a geometric analysis of topological interactions, which reveals significant threading of all ring molecules by the linear chains. In most cases, each ring is simultaneously threaded by several linear chains. As a result, its dynamics at times longer than a few τe should be completely dictated by the release of the topological restrictions imposed by these threadings (interpenetrations. Our topological analysis did not indicate any effect of the few ring probes on the statistical properties of the network of primitive paths of the host linear chains.

  18. Evaluation of the effect of the chiral centers of Taxol on binding to β-tubulin: A docking and molecular dynamics simulation study.

    Science.gov (United States)

    Ghadari, Rahim; Alavi, Fatemeh S; Zahedi, Mansour

    2015-06-01

    Taxol is one of the most important anti-cancer drugs. The interaction between different variants of Taxol, by altering one of its chiral centers at a time, with β-tubulin protein has been investigated. To achieve such goal, docking and molecular dynamics (MD) simulation studies have been performed. In docking studies, the preferred conformers have been selected to further study by MD method based on the binding energies reported by the AutoDock program. The best result of docking study which shows the highest affinity between ligand and protein has been used as the starting point of the MD simulations. All of the complexes have shown acceptable stability during the simulation process, based on the RMSDs of the backbone of the protein structure. Finally, MM-GBSA calculations have been carried out to select the best ligand, considering the binding energy criteria. The results predict that two of the structures have better affinity toward the mentioned protein, in comparison with Taxol. Three of the structures have affinity similar to that of the Taxol toward the β-tubulin.

  19. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Nanoscale deicing by molecular dynamics simulation.

    Science.gov (United States)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.

  1. Molecular dynamics simulations of vibrated granular gases.

    Science.gov (United States)

    Barrat, Alain; Trizac, Emmanuel

    2002-11-01

    We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.

  2. Simulation of Gas-Surface Dynamical Interactions

    Science.gov (United States)

    2007-07-01

    Brenig, Z. Phys. B 36, 81 (1979). [39] J. Böheim and W. Brenig, Z. Phys. B 41, 243 (1981). [40] G. B. Arfken and H. J. Weber, Mathematical Methods for...excitation of the substrate have to be taken into account. In this lecture, the quantum and classical methods required for the simulation of gas-surface...well-defined conditions [2]. In this chapter, I will briefly review the theoretical methods necessary to determine the dynamics of processes at surfaces

  3. Dynamics modeling and simulation of mechanism with joint clearance

    Institute of Scientific and Technical Information of China (English)

    BAI Zheng-feng; TIAN Hao; ZHAO Yang

    2010-01-01

    The existence of clearance in the joints of mechanisms system is inevitable.The movements of the real mechanism are deftection from the ideal mechanism due to the clearances and the motion accuracv is decreased.The effects of the hinge clearance on the crank and rocker mechanism system are studied.The svstem dynamics equation with clearance is presented.The contact dynamics model is established using the nonlinear equivalent spring-damp model and the friction effect is considered by using Coulomb friction model.Then the models are incorporated into ADAMS,and based on the model,large numbers numeric simulations are made.The regularity of contact forces in clearance are studied in detail.And the effects of clearance size.clearance friction on the mechanism dynamics characteristic are analyzed.The simulation resuhs Can predict the effects of clearance on the mechanism dynamics characteristic preferably.

  4. IGCC Dynamic Simulator and Training Center

    Energy Technology Data Exchange (ETDEWEB)

    Zitney, S.E.; Erbes, M.R. (Enginomix, LLC)

    2006-10-01

    Integrated Gasification Combined Cycle (IGCC) is emerging as the technology of choice for providing clean, low-cost electricity for the next generation of coal-fired power plants and will play a central role in the development of high-efficiency, zero-emissions power plants such as FutureGen. Several major utilities and developers recently announced plans to build IGCC plants and other major utilities are evaluating IGCC’s suitability for base-load capacity additions. This recent surge of attention to IGCC power generation is creating a growing demand for experience with the analysis, operation, and control of commercial-scale IGCC plants. To meet this need, the National Energy Technology Laboratory (NETL) has launched a project to develop a generic, full-scope, IGCC dynamic plant simulator for use in establishing a state-of-the-art simulator training center at West Virginia University’s (WVU) National Research Center for Coal and Energy (NRCCE). The IGCC Dynamic Simulator & Training (DS&T) Center will be established under the auspices of the Collaboratory for Process & Dynamic Systems Modeling (“Collaboratory”) organized between NETL, WVU, the University of Pittsburgh, and Carnegie Mellon University.

  5. Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation.

    Directory of Open Access Journals (Sweden)

    Changsun Eun

    Full Text Available Transcription factor IIS (TFIIS is a protein known for catalyzing the cleavage reaction of the 3'-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS.

  6. SIMULATION OF INTERLINE DYNAMIC VOLTAGE RESTORER

    Directory of Open Access Journals (Sweden)

    J.Singaravelan

    2011-08-01

    Full Text Available This paper presents a new approach for the dynamic control of a current source inverter (CSI using Super Conductive Magnetic energy storage (SMES based Interline DVR. The dynamic voltage restorer (DVR provides a technically advanced and economical solution to voltage-sag problem. As the voltage-restoration process involves the real-power injection into the distribution system, the capability ofa DVR, especially for compensating long-duration voltage sags, it depends on the energy storage capacity of the DVR. The interline DVR proposed in this paper provides a way to replenish Dc-link energy storage dynamically. The IDVR consists of several DVRs connected to different distribution feeders in the power system. The DVRs in the IDVR system shares the common energy storage. When one of the DVRcompensates for voltage sag appearing in that feeder, the other DVRs replenish the energy in the common dc-link dynamically. Thus, one DVR in the IDVR system works in voltage-sag compensation mode whilethe other DVRs in the IDVR system operate in power-flow control mode. The proposed topology is simulated using Matlab/Simulink and total IDVR system is simulated using Matlab/Simulink.

  7. Molecular Dynamics Simulations of Network Glasses

    Science.gov (United States)

    Drabold, David A.

    The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References

  8. Solubilization of menthol by platycodin D in aqueous solution: an integrated study of classical experiments and dissipative particle dynamics simulation.

    Science.gov (United States)

    Ding, Haiou; Yin, Qianqian; Wan, Guang; Dai, Xingxing; Shi, Xinyuan; Qiao, Yanjiang

    2015-03-01

    Menthol (M) and platycodin D (PD) are the main active ingredients in Mentha haplocalyx and Platycodon grandiflorum A. DC., respectively. They are commonly used in combination in traditional Chinese medicine. In this study, laboratory experiments and computer simulations were used to investigate the solubilization of M by PD, which was believed to be one of the main causes of the synergistic effect of M. haplocalyx and P. grandiflorum A. DC. Results showed that both the method by which M was added and the concentration of PD had significant effects on the solubilization efficiency of M, and these influences were closely associated with each other. Temperature, an important environmental condition, was also found to have a significant effect on the solubilization effect of PD. These findings not only clarify the molecular basis of the solubilization effect, including amount solubilized at the macroscale and the structures of the micelles, and the drug loading mechanisms and processing at the mesoscale. This work may provide some guidance for the further development of saponins and fundamental research in the drug delivery system.

  9. Molecular Dynamics Simulation and Experimental Studies on the Visual Pigment Rhodopsin: Multiple Conformational States and Structural Changes

    CERN Document Server

    Kholmurodov, Kh T; Ostrovsky, M A; Biochemical Physics Institute, Russian Academy of Sciences, Moscow, Russia

    2005-01-01

    Based on the MD simulations with a supercomputer and the special-purposes MDGRAPE-2 machine we have performed 3-ns MD calculations on the rhodopsin molecule and presented the structure analysis data for its dark-adapted state. We have fulfilled the RMSD (root-mean-square deviation) and structural analysis for the rhodopsin (with 11-\\textit{cis} retinal), generated the pictures of the atomic-scale processes for the binding pocket, surrounding the chromophore retinal, and compared the helical deviations for the beta-ionone ring and Schiff base linkage regions of the protein. The most remarkable point of our observations is that the rhodopsin helical distortions in the dark state are accompanied with the transformation of the retinal chromophore, viz. with the rotation of the beta-ionone ring inside the protein binding pocket. The low-temperature absorption spectroscopy technique has been used to study the primary stages of rhodopsin photolysis. The structural transformation properties of rhodopsin were discusse...

  10. Molecular Dynamics Simulation on thermodynamic Properties and Transport Coefficients

    Institute of Scientific and Technical Information of China (English)

    D.X.Xiong

    1996-01-01

    Moecular dynamics simulation (MDS) is used to study the thermodynamic properties and transport coefficients of an argon system with Lennend-Jones potential.The results on the velocity distribution,mean free path,mean collison time,specific heat and self0diffusion coefficient agree well with the existing theoretical /experimental data,It shows that molecular dynamics method is another bridge to connect microworld and macreoworld.

  11. Nanodrop contact angles from molecular dynamics simulations

    Science.gov (United States)

    Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim

    2016-11-01

    The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.

  12. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations.

    Science.gov (United States)

    Gao, Xiaodong; Han, Liping; Ren, Yujie

    2016-05-05

    Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q² values (0.531, 0.726), fitted correlation r² coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.

  13. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    Science.gov (United States)

    Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen

    2017-02-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  14. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

    Science.gov (United States)

    Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J Valentine, Stephen

    2017-05-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.

  15. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    Science.gov (United States)

    Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen

    2017-05-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  16. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

    KAUST Repository

    Adhikari, Aniruddha

    2016-10-10

    Lipid/water interaction is essential for many biological processes. The water structure at the nonionic lipid interface remains little known, and there is no scope of a priori prediction of water orientation at nonionic interfaces, either. Here, we report our study combining advanced nonlinear spectroscopy and molecular dynamics simulation on the water orientation at the ceramide/water interface. We measured χ spectrum in the OH stretch region of ceramide/isotopically diluted water interface using heterodyne-detected vibrational sum-frequency generation spectroscopy and found that the interfacial water prefers an overall hydrogen-up orientation. Molecular dynamics simulation indicates that this preferred hydrogen-up orientation of water is determined by a delicate balance between hydrogen-up and hydrogen-down orientation induced by lipid-water and intralipid hydrogen bonds. This mechanism also suggests that water orientation at neutral lipid interfaces depends highly on the chemical structure of the lipid headgroup, in contrast to the charged lipid interfaces where the net water orientation is determined solely by the charge of the lipid headgroup.

  17. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Xiaodong Gao

    2016-05-01

    Full Text Available Checkpoint kinase 1 (Chk1 is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q2 values (0.531, 0.726, fitted correlation r2 coefficients (higher than 0.90, and standard error of prediction (less than 0.250. These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.

  18. Density functional theory and molecular dynamics simulation study on corrosion inhibition performance of mild steel by mercapto-quinoline Schiff base corrosion inhibitor

    Science.gov (United States)

    Saha, Sourav Kr.; Ghosh, Pritam; Hens, Abhiram; Murmu, Naresh Chandra; Banerjee, Priyabrata

    2015-02-01

    Corrosion inhibition mechanism of two mercapto-quinoline Schiff bases, eg., 3-((phenylimino)methyl)quinoline-2-thiol (PMQ) and 3-((5-methylthiazol-2-ylimino)methyl) quinoline-2-thiol (MMQT) on mild steel surface is investigated by quantum chemical calculation and molecular dynamics simulation. Quantum chemical parameters such as EHOMO, ELUMO, energy gap (ΔE), dipolemoment (μ), electronegativity (χ), global hardness (η) and fraction of electron transfers from the inhibitor molecule to the metallic atom surface (ΔN) have been studied to investigate their relative corrosion inhibition performance. Parameters like local reactive sites of the present molecule have been analyzed through Fukui indices. Moreover, adsorption behavior of the inhibitor molecules on Fe (1 1 0) surface have been analyzed using molecular dynamics simulation. The binding strength of the concerned inhibitor molecules on mild steel surface follows the order MMQT>PMQ, which is in good agreement with the experimentally determined inhibition efficiencies. In view of the above, our approach will be helpful for quick prediction of a potential inhibitor from a lot of similar inhibitors and subsequently in their rational designed synthesis for corrosion inhibition application following a wet chemical synthetic route.

  19. Modeling of the hEP1 receptor based on the crystallographic structure of β2-adrenergic receptor and its assessment with docking studies and molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    B Zare

    2009-12-01

    Full Text Available "nIntroduction: The human EP1 (hEP1 prostanoid receptor is a G-Protein Coupled Receptor (GPCR which plays important physiological roles in some systems in the body like cardiovascular and immune systems and could be a very important target for drug design. "nMaterials and methods: To understand the molecular structure of hEP1 receptor, a homology model of the receptor was constructed from the 2.4 Å resolution crystal structure of human β2-adrenergic receptor (PDB code: 2RH1, using three different sequence alignments. The model including PGE2 inside the active site was subjected to molecular dynamics simulation. Docking studies were performed for PGE2 and 10 prostanoid analogs in the active site of the modeled receptor. Results and Discussion: The structure of modeled receptor remained stable during the 10 nanosecond(ns simulation. In the docking simulations a correlation of r2=0.74 was observed between the Ki values and the docking scores of the prostanoid compounds. The structure which was modeled in the present study can be used in the structure-based drug design, helping the rational design of novel ligands for the hEP1 receptor. "n "n 

  20. Molecular Dynamics Simulations of DNA Translocation through a biological Nanopore

    OpenAIRE

    Barder, Simen Eidsmo

    2012-01-01

    Experimental and simulation studies of nucleic acid transport through nanosized channels, both biological and synthetic, has become a rapidly growing research area over the last decade. While the utilization of the alpha-hemolysin channel as a sequencing device is soon to be realized, other biological nanochannels may hold advantages that are yet unknown. Motivated by this, the first reported molecular dynamics simulations of DNA translocation through a connexon 26 channel were accomplished, ...

  1. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    OpenAIRE

    Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...

  2. Prototyping Bio-Nanorobots using Molecular Dynamics Simulation

    OpenAIRE

    Hamdi, Mustapha; Sharma, Gaurav; Ferreira, A.; Mavroidis, Constantinos

    2005-01-01

    Submitted on behalf of EDA Publishing Association (http://irevues.inist.fr/handle/2042/5920); International audience; This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The mai...

  3. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

    Science.gov (United States)

    Krepl, Miroslav; Réblová, Kamila; Koča, Jaroslav; Sponer, Jiří

    2013-05-09

    The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 μs of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction. Alternatively, the anti conformation may be a real substate whose population could be pH-dependent, since the guanine syn orientation requires protonation of cytosine in the tertiary contact. In absence of structural data, we use molecular modeling to explore the GCCA tetraloop that is dominant in bacteria and suggest that the GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate that the long bulge is a stalk-specific eight-nucleotide insertion into consensual kink-turn only subtly modifying its structural dynamics. We discuss a possible evolutionary role of helix H78 and a mechanism of L1 stalk interaction with tRNA. We also assess the simulation methodology. The simulations provide a good description of the studied systems with the latest bsc0χOL3 force field showing improved performance. Still, even bsc0χOL3 is unable to fully stabilize an essential

  4. Study on a Dynamic Vegetation Model for Simulating Land Surface Flux Exchanges at Lien-Hua-Chih Flux Observation Site in Taiwan

    Science.gov (United States)

    Yeh, T. Y.; Li, M. H.; Chen, Y. Y.; Ryder, J.; McGrath, M.; Otto, J.; Naudts, K.; Luyssaert, S.; MacBean, N.; Bastrikov, V.

    2016-12-01

    Dynamic vegetation model ORCHIDEE (Organizing Carbon and Hydrology In Dynamic EcosystEms) is a state of art land surface component of the IPSL (Institute Pierre Simon Laplace) Earth System Model. It has been used world-wide to investigate variations of water, carbon, and energy exchanges between the land surface and the atmosphere. In this study we assessed the applicability of using ORCHIDEE-CAN, a new feature with 3-D CANopy structure (Naudts et al., 2015; Ryder et al., 2016), to simulate surface fluxes measured at tower-based eddy covariance fluxes at the Lien-Hua-Chih experimental watershed in Taiwan. The atmospheric forcing including radiation, air temperature, wind speed, and the dynamics of vertical canopy structure for driving the model were obtained from the observations site. Suitable combinations of default plant function types were examined to meet in-situ observations of soil moisture and leaf area index from 2009 to 2013. The simulated top layer soil moisture was ranging from 0.1 to 0.4 and total leaf area was ranging from 2.2 to 4.4, respectively. A sensitivity analysis was performed to investigate the sensitive of model parameters and model skills of ORCHIDEE-CAN on capturing seasonal variations of surface fluxes. The most sensitive parameters were suggested and calibrated by an automatic data assimilation tool ORCHDAS (ORCHIDEE Data Assimilation Systems; http://orchidas.lsce.ipsl.fr/). Latent heat, sensible heat, and carbon fluxes simulated by the model were compared with long-term observations at the site. ORCHIDEE-CAN by making use of calibrated surface parameters was used to study variations of land-atmosphere interactions on a variety of temporal scale in associations with changes in both land and atmospheric conditions. Ref: Naudts, K., et al.,: A vertically discretised canopy description for ORCHIDEE (SVN r2290) and the modifications to the energy, water and carbon fluxes, Geoscientific Model Development, 8, 2035-2065, doi:10.5194/gmd-8

  5. Dynamical simulation of non-abelian cosmic strings

    CERN Document Server

    McGraw, P

    1996-01-01

    We describe a method for simulating the dynamics of an S_3 cosmic string network. We use a lattice Monte Carlo to generate initial conditions for the network, which subsequently is allowed to relax continuously according to a simplified model of string dynamics. The dynamics incorporates some novel features which, to our knowledge, have not been studied in previous numerical simulations: The existence of two types of string which may have different tensions, and the possibility that two non-commuting strings may intersect. Simulation of the non-commuting fluxes presents a computational challenge as it requires a rather complex gauge-fixing procedure. The flux definitions change as strings change their positions and orientations relative to each other and must be carefully updated as the network evolves. The method is described here in some detail, with results to be presented elsewhere.

  6. A dynamic simulation model of desertification in Egypt

    Directory of Open Access Journals (Sweden)

    M. Rasmy

    2010-12-01

    Full Text Available This paper presents the development of a system dynamic model to simulate and analyze potential future state of desertification in Egypt. The presented model enhances the MEDALUS methodology developed by European Commission. It illustrates the concept of desertification through different equations and simulation output graphs. It is supplemented with a causal loop diagram showing the feedback between different variables. For the purpose of testing and measuring the effect of different policy scenarios on desertification in Egypt, a simulation model using stock and flow diagram was designed. Multi-temporal data were used to figure out the dynamic changes in desertification sensitivity related to the dynamic nature of desert environment. The model was applied to Al Bihira governorate in western Nile Delta, Egypt, as the study area, and the results showed that the urban expansion, salinization, and not applying the policy enforcement are considered the most variables provoking the desertification.

  7. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    Energy Technology Data Exchange (ETDEWEB)

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  8. Simulation of Naval Guns' Breechblock System Dynamics Based on ADAMS

    Science.gov (United States)

    Tan, Bo; Liu, Hui-Min; Liu, Kai

    In order to study the dynamical characteristics of the breechblock system during gun firing, a virtual prototype model was established based on ADAMS, in which motion and force transmission among mechanisms are realized by collision. By simulation, kinematics and dynamics properties of main components are obtained, and the relationships between the motion of breechblock and the position of breechblock opening plate are analyzed. According to the simulation results, the collision among the breechblock opening plate and the roller is discontinuous, which may make the breechblock system fail to hitch the breechblock reliably. And within allowable scope of the structure, the breechblock opening template should be installed near the upside as much as possible.

  9. Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis

    Science.gov (United States)

    Alakent, Burak; Doruker, Pemra; Camurdan, Mehmet C.

    2004-09-01

    Time series analysis is applied on the collective coordinates obtained from principal component analysis of independent molecular dynamics simulations of α-amylase inhibitor tendamistat and immunity protein of colicin E7 based on the Cα coordinates history. Even though the principal component directions obtained for each run are considerably different, the dynamics information obtained from these runs are surprisingly similar in terms of time series models and parameters. There are two main differences in the dynamics of the two proteins: the higher density of low frequencies and the larger step sizes for the interminima motions of colicin E7 than those of α-amylase inhibitor, which may be attributed to the higher number of residues of colicin E7 and/or the structural differences of the two proteins. The cumulative density function of the low frequencies in each run conforms to the expectations from the normal mode analysis. When different runs of α-amylase inhibitor are projected on the same set of eigenvectors, it is found that principal components obtained from a certain conformational region of a protein has a moderate explanation power in other conformational regions and the local minima are similar to a certain extent, while the height of the energy barriers in between the minima significantly change. As a final remark, time series analysis tools are further exploited in this study with the motive of explaining the equilibrium fluctuations of proteins.

  10. A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors.

    Science.gov (United States)

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-11-01

    Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.

  11. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    Full Text Available Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III Hexamine ions or Mg(2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III Hexamine ions were found to bind stronger with the loop than Mg(2+ ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III Hexamine ions on CorA ions transportation.

  12. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  13. In Silico and In Vitro Investigation of the Piperine's Male Contraceptive Effect: Docking and Molecular Dynamics Simulation Studies in Androgen-Binding Protein and Androgen Receptor.

    Science.gov (United States)

    Chinta, Gopichand; Ramya Chandar Charles, Mariasoosai; Klopčič, Ivana; Sollner Dolenc, Marija; Periyasamy, Latha; Selvaraj Coumar, Mohane

    2015-07-01

    Understanding the molecular mechanism of action of traditional medicines is an important step towards developing marketable drugs from them. Piperine, an active constituent present in the Piper species, is used extensively in Ayurvedic medicines (practiced on the Indian subcontinent). Among others, piperine is known to possess a male contraceptive effect; however, the molecular mechanism of action for this effect is not very clear. In this regard, detailed docking and molecular dynamics simulation studies of piperine with the androgen-binding protein and androgen receptors were carried out. Androgen receptors control male sexual behavior and fertility, while the androgen-binding protein binds testosterone and maintains its concentration at optimal levels to stimulate spermatogenesis in the testis. It was found that piperine docks to the androgen-binding protein, similar to dihydrotestosterone, and to androgen receptors, similar to cyproterone acetate (antagonist). Also, the piperine-androgen-binding protein and piperine-androgen receptors interactions were found to be stable throughout 30 ns of molecular dynamics simulation. Further, two independent simulations for 10 ns each also confirmed the stability of these interactions. Detailed analysis of the piperine-androgen-binding protein interactions shows that piperine interacts with Ser42 of the androgen-binding protein and could block the binding with its natural ligands dihydrotestosterone/testosterone. Moreover, piperine interacts with Thr577 of the androgen receptors in a manner similar to the antagonist cyproterone acetate. Based on the in silico results, piperine was tested in the MDA-kb2 cell line using the luciferase reporter gene assay and was found to antagonize the effect of dihydrotestosterone at nanomolar concentrations. Further detailed biochemical experiments could help to develop piperine as an effective male contraceptive agent in the future.

  14. Insights into the structure and dynamics of a room-temperature ionic liquid: ab initio molecular dynamics simulation studies of 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]-CO2 mixture.

    Science.gov (United States)

    Bhargava, B L; Balasubramanian, S

    2007-05-03

    Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.

  15. Numerical simulation of the dynamic flow behavior in a bubble column: a study of closures for turbulence and interface forces

    NARCIS (Netherlands)

    Zhang, D.; Deen, N.G.; Kuipers, J.A.M.

    2006-01-01

    Numerical simulations of the bubbly flow in two square cross-sectioned bubble columns were conducted with the commercial CFD package CFX-4.4. The effect of the model constant used in the sub-grid scale (SGS) model, CS, as well as the interfacial closures for the drag, lift and virtual mass forces

  16. Simulation study of the effect of wall roughness on the dynamics of granular flows in rotating semicylindrical chutes

    NARCIS (Netherlands)

    Shirsath, Sushil S.; Padding, Johan T.; Kuipers, J.A.M. (Hans); Clercx, Herman J.H.

    2015-01-01

    A discrete element model (DEM) is used to investigate the behavior of spherical particles flowing down a semicylindrical rotating chute. The DEM simulations are validated by comparing with particle tracking velocimetry results of spherical glass particles flowing through a smooth semicylindrical chu

  17. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  18. Using Simulation to Assess the Opportunities of Dynamic Waste Collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.

    In this paper, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  19. Using simulation to assess the opportunities of dynamic waste collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.; Bangsow, S.

    2012-01-01

    In this chapter, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  20. Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

    Science.gov (United States)

    Sakhteman, Amirhossein; Khoddami, Minasadat; Negahdaripour, Manica; Mehdizadeh, Arash; Tatar, Mohsen; Ghasemi, Younes

    2016-09-01

    Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to homology modeling studies and molecular dynamic simulation within a DPPC lipid bilayer for 100 ns. Several frames were thereafter extracted from simulation trajectories representing the receptor at different states. In order to find a proper model of the receptor at the antagonist state, all frames were subjected to cross-docking studies of some antagonists with known experimental values (Ki). Frame 194 revealed a reasonable correlation between docking calculated energy scores and experimental activity values (|r| = 0.91). The obtained correlation was validated by means of SSLR and showed the presence of no chance correlation for the obtained model. Different structural features reported for the receptor, such as two disulfide bridges and ionic lock between GLU90 and LYS 121 were also investigated in the final model.

  1. Dynamical simulations of strongly correlated electron materials

    Science.gov (United States)

    Kress, Joel; Barros, Kipton; Batista, Cristian; Chern, Gia-Wei; Kotliar, Gabriel

    We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

  2. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    Science.gov (United States)

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences.

  3. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    Science.gov (United States)

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  4. Prediction of new Hsp90 inhibitors based on 3,4-isoxazolediamide scaffold using QSAR study, molecular docking and molecular dynamic simulation.

    Science.gov (United States)

    Abbasi, Maryam; Sadeghi-Aliabadi, Hojjat; Amanlou, Massoud

    2017-06-30

    Heat shock protein90 (Hsp90) are overexpressed in tumor cells, so the inhibition of the Hsp90 ATPase activity would be a significantly effective strategy in cancer therapy. In the current study, 3,4-isoxazolediamide derivatives were suggested as an Hsp90 inhibitor for anti-cancer therapy. Multiple linear regression (MLR) and genetic algorithm of partial least square (GA-PLS) methods were performed to build models to predict the inhibitory activity of Hsp90. The leave-one out (LOO) cross-validation and Y-randomization tests were performed to models' validation. The new ligands were monitored by applicability domain. Molecular docking studies were also conducted to evaluate the mode of interaction of these compounds with Hsp90. Identification of the likely pathways into the active site pocket and the involved residues were performed by CAVAER 3.0.1 software. According to QSAR models and docking analysis, three new compounds were predicted. 50 ns molecular dynamic simulation was performed for the strongest synthesized compound and the best predicted compound in terms of binding energy and interactions between ligand and protein. The made models showed the significance of size, shape, symmetry, and branching of molecules in inhibitory activities of Hsp90. Docking studies indicated that two hydroxyl groups in the resorcinol ring were important in interacting with Asp93 and the orientation of these groups was related to substitution of different R1 groups. Comparing of molecular dynamic simulation (MDs) results shows that new compound perched in active site with lower binding energy than the best synthesized compound. The QSAR and docking analyses shown to be beneficial tools in the proposal of anti-cancer activities and a leader to the synthesis of new Hsp90 inhibitors based 3,4-isoxazolediamide. The MDs confirmed that predicted ligand is steady in the Hsp90 active sites.

  5. Study of temperature dependence of thermal conductivity in cross-linked epoxies using molecular dynamics simulations with long range interactions

    Science.gov (United States)

    Kumar, A.; Sundararaghavan, V.; Browning, A. R.

    2014-03-01

    In this work, we demonstrate the use of the Green-Kubo integral of the heat flux autocorrelation function, incorporating long-range corrections to model the thermal conductivity versus temperature relationship of cross-linked polymers. The simulations were performed on a cross-linked epoxy made from DGEBA and a curing agent (diamino diphenyl sulfone) using a consistent valence force field (CVFF). A dendrimeric approach was utilized for building equilibrated cross-linked structures that allowed replication of the experimental dilatometric curve for the epoxy system. We demonstrate that the inclusion of a long-range correction within the Ewald/PPPM approach brings the results close to experimentally measured conductivity within an error of 10% while providing a good prediction of the relationship of thermal conductivity versus temperature. This method shows significant promise towards the computation of thermal conductivity from simulations even before synthesis of the polymer for purposes of materials by design.

  6. Study of Sediment Transportation in the Gulf of Kachchh, using 3D Hydro-dynamic Model Simulation and Satellite Data

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    . Modeling is, therefore, the integrated development of mathematical equations, logical rules and constraints and a computer program embodying the equations, the logical rules and the solutions to them. Simulation on the other hand, is the experimental... in the Gulf of Kachchh without considering influence of other factors except M2 tide components. It seems that surface current velocity in the Gulf is mainly controlled by the tide system. The COSMOS numerical modeling results also confirmed this conclusion...

  7. Traffic flow dynamics data, models and simulation

    CERN Document Server

    Treiber, Martin

    2013-01-01

    This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on ...

  8. Molecular dynamics simulations of classical stopping power.

    Science.gov (United States)

    Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S

    2013-11-22

    Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.

  9. Molecular Dynamics Simulations for Predicting Surface Wetting

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-06-01

    Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.

  10. Schwinger model simulations with dynamical overlap fermions

    CERN Document Server

    Bietenholz, W; Volkholz, J

    2007-01-01

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate Sigma vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain -- for the very light fermion masses -- values for $\\Sigma$ that follow closely the analytical predictions in the continuum.

  11. Schwinger model simulations with dynamical overlap fermions

    Energy Technology Data Exchange (ETDEWEB)

    Bietenholz, W. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Shcheredin, S. [Bielefeld Univ. (Germany). Fakultaet fuer Physik; Volkholz, J. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik

    2007-11-15

    We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate {sigma} vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain - for the very light fermion masses - values for {sigma} that follow closely the analytical predictions in the continuum. (orig.)

  12. GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential.

    Directory of Open Access Journals (Sweden)

    Wenduo Chen

    Full Text Available Gay-Berne (GB potential is regarded as an accurate model in the simulation of anisotropic particles, especially for liquid crystal (LC mesogens. However, its computational complexity leads to an extremely time-consuming process for large systems. Here, we developed a GPU-accelerated molecular dynamics (MD simulation with coarse-grained GB potential implemented in GALAMOST package to investigate the LC phase transitions for mesogens in small molecules, main-chain or side-chain polymers. For identical mesogens in three different molecules, on cooling from fully isotropic melts, the small molecules form a single-domain smectic-B phase, while the main-chain LC polymers prefer a single-domain nematic phase as a result of connective restraints in neighboring mesogens. The phase transition of side-chain LC polymers undergoes a two-step process: nucleation of nematic islands and formation of multi-domain nematic texture. The particular behavior originates in the fact that the rotational orientation of the mesogenes is hindered by the polymer backbones. Both the global distribution and the local orientation of mesogens are critical for the phase transition of anisotropic particles. Furthermore, compared with the MD simulation in LAMMPS, our GPU-accelerated code is about 4 times faster than the GPU version of LAMMPS and at least 200 times faster than the CPU version of LAMMPS. This study clearly shows that GPU-accelerated MD simulation with GB potential in GALAMOST can efficiently handle systems with anisotropic particles and interactions, and accurately explore phase differences originated from molecular structures.

  13. Parallel Monte Carlo Simulation of Aerosol Dynamics

    Directory of Open Access Journals (Sweden)

    Kun Zhou

    2014-02-01

    Full Text Available A highly efficient Monte Carlo (MC algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process. Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallel