WorldWideScience

Sample records for atom molecular dynamics

  1. Dynamical processes in atomic and molecular physics

    CERN Document Server

    Ogurtsov, Gennadi

    2012-01-01

    Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

  2. Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong

    2004-01-01

    Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.

  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. Probing atomic and molecular dynamics from within

    Energy Technology Data Exchange (ETDEWEB)

    Berrah, N. E-mail: berrah@wmich.edu; Bilodeau, R.C.; Ackerman, G.; Bozek, J.D.; Turri, G.; Kukk, E.; Cheng, W.T.; Snell, G

    2004-08-01

    We have investigated with unprecedented levels of detail photodetachment of negative ions and photoionization of molecules using the brightness, spectral resolution, and tunability of the Advanced Light Source at Lawrence Berkeley National Laboratory. In particular, we report here on investigations carried out in K-shell photodetachment of atomic Li{sup -} and He{sup -}. We also report on angular distribution of core-level iodine 4d photoelectrons from the HI molecule. In both cases comparison with calculations is discussed.

  5. Thermodynamics of small clusters of atoms: A molecular dynamics simulation

    DEFF Research Database (Denmark)

    Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J

    1974-01-01

    The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...

  6. Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides

    Science.gov (United States)

    Held, Marie; Nicolau, Dan V.

    2007-12-01

    The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA) and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity. Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues. The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an expected biomolecular activity from the immobilized biomolecules.

  7. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    Science.gov (United States)

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  8. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  9. 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

  10. Imaging Multi-Particle Atomic and Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Landers, Allen [Auburn Univ., AL (United States)

    2016-02-12

    Final Report for Grant Number: DE- FG02-10ER16146 This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms and molecules with photons and electrons. The duration of the grant was the 5 year period from 4/1/2010 – 10/31/2015. All of the support from the grant was used to pay salaries of the PI, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 20 peer reviewed publications over these 5 years with 2 of the publications in Physical Review Letters and 1 in Nature; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B ...).

  11. Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R

    2005-02-02

    Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.

  12. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  13. Molecular Dynamics Simulations of Atomic H Etching SiC Surface

    NARCIS (Netherlands)

    Sun, W.; Liu, H.; Lin, L.; Zhao, C. L.; Lu, X. D.; He, P. N.; Gou, F.

    2012-01-01

    In this paper, molecular dynamics simulations were performed to study interactions between atomic H and SiC, silicon carbon surfaces were continuously bombarded by atomic H with different energies. The Tersoff-Brenner potentials were implemented. The simulation results show that with increasing

  14. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    Science.gov (United States)

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.

  15. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model

  16. 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.

  17. Molecular dynamics simulations of the atom packing characteristics of three deformed silver nanoparticles at room temperature.

    Science.gov (United States)

    Zhang, Lin

    2016-03-14

    Deformation is of significance in controlling the shape of materials, but the key structural information of metal nanoparticles is still limited. Molecular dynamics simulations are performed to explore the microscopic details of atom packing differences in three deformed silver nanoparticles with one atom difference. Analytical tools are used to demonstrate the effects of external load and surface atoms of particles on the packing patterns in these deformed nanoparticles including internal energy per atom, pair numbers, and pair distribution functions as well as cross-sectional images. The simulation results show that under small compression, the particles present elastic behaviors. The increasing compression results in the sliding of the atoms in different parts of these particles, and some interfaces are formed between these parts. As the external load becomes large, these deformed particles are compressed into the thickness of several atomic layers. The unloaded particles present different behaviors.

  18. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si3N4(0001) nanopixels

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 μm silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si3N4(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3 GPa and the stress is tensile, -1 GPa, in silicon below the interface.

  19. Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates

    OpenAIRE

    Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)

    2005-01-01

    We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.

  20. Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets.

    Science.gov (United States)

    Bünermann, Oliver; Kornilov, Oleg; Haxton, Daniel J; Leone, Stephen R; Neumark, Daniel M; Gessner, Oliver

    2012-12-07

    The ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets are studied with time-resolved extreme ultraviolet ion imaging spectroscopy. At excitation energies of 23.6 ± 0.2 eV, Rydberg atoms in n = 3 and n = 4 states are ejected on different time scales and with significantly different kinetic energy distributions. Specifically, n = 3 Rydberg atoms are ejected with kinetic energies as high as 0.85 eV, but their appearance is delayed by approximately 200 fs. In contrast, n = 4 Rydberg atoms appear within the time resolution of the experiment with considerably lower kinetic energies. Major features in the Rydberg atom kinetic energy distributions for both principal quantum numbers can be described within a simple elastic scattering model of localized perturbed atomic Rydberg atoms that are expelled from the droplet due to their repulsive interaction with the surrounding helium bath. Time-dependent kinetic energy distributions of He(2) (+) and He(3) (+) ions are presented that support the formation of molecular ions in an indirect droplet ionization process and the ejection of neutral Rydberg dimers on a similar time scale as the n = 3 Rydberg atoms.

  1. Process of Energetic Carbon Atom Deposition on Si (001) Substrate by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    于威; 滕晓云; 李晓苇; 傅广生

    2002-01-01

    The process of energetic C atom deposition on Si (001)-(2×1) is studied by the molecular dynamics method using the semi-empirical many-bond Tersoff potential. It is found that the incident energy of the carbon atom has an important effect on the collision process and its diffusion process on the substrate. Most of the incident energy of the carbon atom is transferred to the substrate atoms within the initial two vibration periods of substrate atoms and its value increases with the incident energy. The spreading distance and penetration depth of the incident atom increasing with the incident energy are also identified. The simulated results imply that an important effect of energy of incident carbon on the film growth at Iow substrate temperature provides activation energy for silicon carbide formation through the vibration enhancement of local substrate atoms. In addition, suppressing carbon atom inhomogeneous collection and dispensing with the silicon diffusion process may be effectively promoted by the spreading and penetration of the energetic carbon atom in the silicon substrate.

  2. Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

    Science.gov (United States)

    Kukol, Andreas

    2009-03-10

    United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.

  3. Modified morphology of graphene sheets by Argon-atom bombardment: molecular dynamics simulations.

    Science.gov (United States)

    Wei, Xiao-Lin; Zhang, Kai-Wang; Wang, Ru-Zhi; Liu, Wen-Liang; Zhong, Jian-Xin

    2011-12-01

    By a molecular dynamics method, we simulated the process of Argon-atom bombardment on a graphene sheet with 2720 carbon atoms. The results show that, the damage of the bombardment on the graphene sheet depends not only on the incident energy but also on the particle flux density of Argon atoms. To compare and analyze the effect of the incident energy and the particle flux density in the Argon-atom bombardment, we defined the impact factor on graphene sheet by calculating the broken-hole area. The results indicate that, there is an exponential accumulated-damage for the impact of both the incident energy and the particle flux density and there is a critical incident energy ranging from 20-30 eV/atom in Argon-atom bombardment. Different configurations, such as sieve-like and circle-like graphene can be formed by controlling of different particle flux density as the incident energy is more than the critical value. Our results supply a feasible method on fabrication of porous graphene-based materials for gas-storages and molecular sieves, and it also helps to understand the damage mechanism of graphene-based electronic devices under high particle radiation.

  4. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  5. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  6. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  7. High-throughput all-atom molecular dynamics simulations using distributed computing.

    Science.gov (United States)

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

  8. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob;

    2002-01-01

    , the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations...

  9. Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.

    Science.gov (United States)

    Klocke, Michael; Wolf, Dietrich E

    2016-01-01

    A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.

  10. Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Michael Klocke

    2016-05-01

    Full Text Available A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.

  11. mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.

    Science.gov (United States)

    Kasahara, Kota; Mohan, Neetha; Fukuda, Ikuo; Nakamura, Haruki

    2016-08-15

    We previously reported the multi-modal Dynamic Cross Correlation (mDCC) method for analyzing molecular dynamics trajectories. This method quantifies the correlation coefficients of atomic motions with complex multi-modal behaviors by using a Bayesian-based pattern recognition technique that can effectively capture transiently formed, unstable interactions. Here, we present an open source toolkit for performing the mDCC analysis, including pattern recognitions, complex network analyses and visualizations. We include a tutorial document that thoroughly explains how to apply this toolkit for an analysis, using the example trajectory of the 100 ns simulation of an engineered endothelin-1 peptide dimer. The source code is available for free at http://www.protein.osaka-u.ac.jp/rcsfp/pi/mdcctools/, implemented in C ++ and Python, and supported on Linux. kota.kasahara@protein.osaka-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  12. Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of Muonic Molecular Complex

    CERN Document Server

    Fujiwara, M C; Bailey, J M; Beer, G A; Beveridge, J L; Faifman, M P; Huber, T M; Kammel, P; Kim, S K; Knowles, P E; Kunselman, A R; Maier, M; Markushin, V E; Marshall, G M; Martoff, C J; Mason, G R; Mulhauser, F; Olin, A; Petitjean, C; Porcelli, T A; Wozniak, J; Zmeskal, J

    2001-01-01

    Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.

  13. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Samuel Hertig

    2016-06-01

    Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  14. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Science.gov (United States)

    Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

    2016-06-01

    Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  15. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yu Sun; Yi-Zhou Qi; Wengen Ouyang; Xi-Qiao Feng; Qunyang Li

    2016-01-01

    Although atomic stick–slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competi-tion of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves nor-mally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effec-tively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  16. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Science.gov (United States)

    Sun, Xiao-Yu; Qi, Yi-Zhou; Ouyang, Wengen; Feng, Xi-Qiao; Li, Qunyang

    2016-08-01

    Although atomic stick-slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competition of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves normally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effectively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  17. Deformation behavior of metallic glasses with shear band like atomic structure: a molecular dynamics study.

    Science.gov (United States)

    Zhong, C; Zhang, H; Cao, Q P; Wang, X D; Zhang, D X; Ramamurty, U; Jiang, J Z

    2016-08-02

    Molecular dynamics simulations were employed to investigate the plastic deformation within the shear bands in three different metallic glasses (MGs). To mimic shear bands, MG specimens were first deformed until flow localization occurs, and then the volume of the material within the localized regions was extracted and replicated. Homogeneous deformation that is independent of the size of the specimen was observed in specimens with shear band like structure, even at a temperature that is far below the glass transition temperature. Structural relaxation and rapid cooling were employed to examine the effect of free volume content on the deformation behavior. This was followed by detailed atomic structure analyses, employing the concepts of Voronoi polyhedra and "liquid-like" regions that contain high fraction of sub-atomic size open volumes. Results suggest that the total fraction of atoms in liquid-like regions is a key parameter that controls the plastic deformation in MGs. These are discussed in the context of reported experimental results and possible strategies for synthesizing monolithic amorphous materials that can accommodate large tensile plasticity are suggested.

  18. 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.

  19. Mechanical Properties of Boehmite Evaluated by Atomic Force Microscopy Experiments and Molecular Dynamic Finite Element Simulations

    Directory of Open Access Journals (Sweden)

    J. Fankhänel

    2016-01-01

    Full Text Available Boehmite nanoparticles show great potential in improving mechanical properties of fiber reinforced polymers. In order to predict the properties of nanocomposites, knowledge about the material parameters of the constituent phases, including the boehmite particles, is crucial. In this study, the mechanical behavior of boehmite is investigated using Atomic Force Microscopy (AFM experiments and Molecular Dynamic Finite Element Method (MDFEM simulations. Young’s modulus of the perfect crystalline boehmite nanoparticles is derived from numerical AFM simulations. Results of AFM experiments on boehmite nanoparticles deviate significantly. Possible causes are identified by experiments on complementary types of boehmite, that is, geological and hydrothermally synthesized samples, and further simulations of imperfect crystals and combined boehmite/epoxy models. Under certain circumstances, the mechanical behavior of boehmite was found to be dominated by inelastic effects that are discussed in detail in the present work. The studies are substantiated with accompanying X-ray diffraction and Raman experiments.

  20. All-atom molecular dynamics simulation of a photosystem I/detergent complex

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Bradley J. [Univ. of Tennessee, Knoxville, TN (United States); Cheng, Xiaolin [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Frymier, Paul [Univ. of Tennessee, Knoxville, TN (United States)

    2014-09-18

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  1. Atomic and molecular supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.

    1997-12-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  2. Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces.

    Science.gov (United States)

    Kim, Hyun-Joon; Kim, Dae-Eun

    2012-07-01

    Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than that of a smooth surface under specific contact conditions. The effect of applied load on the friction coefficient was dependent on the size of the corrugation. Furthermore, stiffness of the nano-structure was identified to be an important variable in dictating the frictional behavior.

  3. Quantum molecular dynamics study of expanded beryllium: evolution from warm dense matter to atomic fluid.

    Science.gov (United States)

    Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun

    2014-07-31

    By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.

  4. Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation.

    Science.gov (United States)

    Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

    2015-08-27

    Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of "melting pots in a supercomputer" is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments.

  5. Atomic and molecular manipulation

    CERN Document Server

    Mayne, Andrew J

    2011-01-01

    Work with individual atoms and molecules aims to demonstrate that miniaturized electronic, optical, magnetic, and mechanical devices can operate ultimately even at the level of a single atom or molecule. As such, atomic and molecular manipulation has played an emblematic role in the development of the field of nanoscience. New methods based on the use of the scanning tunnelling microscope (STM) have been developed to characterize and manipulate all the degrees of freedom of individual atoms and molecules with an unprecedented precision. In the meantime, new concepts have emerged to design molecules and substrates having specific optical, mechanical and electronic functions, thus opening the way to the fabrication of real nano-machines. Manipulation of individual atoms and molecules has also opened up completely new areas of research and knowledge, raising fundamental questions of "Optics at the atomic scale", "Mechanics at the atomic scale", Electronics at the atomic scale", "Quantum physics at the atomic sca...

  6. Analysis of Adhesive Characteristics of Asphalt Based on Atomic Force Microscopy and Molecular Dynamics Simulation.

    Science.gov (United States)

    Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng

    2016-05-18

    Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt.

  7. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    Science.gov (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  8. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  9. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Science.gov (United States)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  10. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Energy Technology Data Exchange (ETDEWEB)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  11. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke;

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured usi...

  12. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulation...

  13. Embedded atom approach for gold–silicon system from ab initio molecular dynamics simulations using the force matching method

    Indian Academy of Sciences (India)

    A NASSOUR

    2016-09-01

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.

  14. Molecular Dynamics Study of the Motion of Atomic Components of the DNA Molecule and its Environment.

    Science.gov (United States)

    Perez, Patricio

    It is of great interest for us to come to a better understanding of some biological processes through a study of the behavior of the atomic entities involved in them. One of the most important biological molecules in DNA. In the outer part of its helical structure, phosphate groups are known to be present. The natural environment of this molecule is liquid water. Some cations like Na('+) and Mg('2+) are often found in its surroundings. In this work we show results of applying a polarizable water model (the PE model) to the molecular dynamics simulation of hydrated sodium ion microclusters. We found that the PE model with just two adjustable parameters reproduces the experimental enthalpies of formation of the ion-water microclusters better than a number of other methods. We also found that for the case of six water molecules at O K, they do not form a regular octahedron around the sodium ion as predicted by other models. The predicted change in structure appears to be in agreement with experimental observations. We introduced later a phosphate group and performed a molecular dynamics simulation of its interaction with water and a sodium cation. We use polarizable models for both water and the phosphate group. According to our calculation, a potential fitted to quantum mechanical results produces a strong binding between the sodium and the phosphate group. This binding is such that hydration of the sodium is not clearly observed. Regardless of this we can conclude that the effect of assuming the phosphate group polarizable is not significant.

  15. Atomic & Molecular Interactions

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  16. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    Science.gov (United States)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  17. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    Science.gov (United States)

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  18. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

    KAUST Repository

    Di Marino, Daniele

    2015-08-06

    © 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  19. Molecular dynamics study of the interactions of incident N or Ti atoms with the TiN(001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhenhai [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Zeng, Quanren [Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Yuan, Lin [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Qin, Yi [Centre for Precision Manufacturing, Department of Design, Manufacture and Engineering Management, The University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Chen, Mingjun [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Shan, Debin, E-mail: d.b.shan@gmail.com [National Key Laboratory for Precision Hot Processing of Metals & School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China)

    2016-01-01

    Graphical abstract: - Highlights: • Interactions of incident N or Ti atoms with TiN(001) surface are studied by CMD. • The impact position of incident N on the surface determines the interaction modes. • Adsorption could occur due to the atomic exchange process. • Resputtering and reflection may simultaneously occur. • The initial sticking coefficient of N on TiN(001) is much smaller than that of Ti. - Abstract: The interaction processes between incident N or Ti atoms and the TiN(001) surface are simulated by classical molecular dynamics based on the second nearest-neighbor modified embedded-atom method potentials. The simulations are carried out for substrate temperatures between 300 and 700 K and kinetic energies of the incident atoms within the range of 0.5–10 eV. When N atoms impact against the surface, adsorption, resputtering and reflection of particles are observed; several unique atomic mechanisms are identified to account for these interactions, in which the adsorption could occur due to the atomic exchange process while the resputtering and reflection may simultaneously occur. The impact position of incident N atoms on the surface plays an important role in determining the interaction modes. Their occurrence probabilities are dependent on the kinetic energy of incident N atoms but independent on the substrate temperature. When Ti atoms are the incident particles, adsorption is the predominant interaction mode between particles and the surface. This results in the much smaller initial sticking coefficient of N atoms on the TiN(001) surface compared with that of Ti atoms. Stoichiometric TiN is promoted by N/Ti flux ratios larger than one.

  20. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Energy Technology Data Exchange (ETDEWEB)

    Pabst, Stefan Ulf

    2013-04-15

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO{sub 2} is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  1. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si{sub 3}N{sub 4}(0001) nanopixels

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, M.E.; Omeltchenko, A.; Nakano, A.; Kalia, R.K.; Vashishta, P. [Concurrent Computing Laboratory for Materials Simulations, Department of Physics Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana70803-4001 (United States); Ebbsjoe, I. [Studsvik Neutron Research Laboratory, University of Uppsala, S-611 82Nykoeping (Sweden); Madhukar, A. [Department of Materials Science and Engineering, University of Southern California, Los Angeles, California90089-0241 (United States); Messina, P. [Center for Advanced Computing Research, California Institute of Technology, Pasadena, California91125 (United States)

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 {mu}m silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si{sub 3}N{sub 4}(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3GPa and the stress is tensile, {minus}1GPa, in silicon below the interface. {copyright} {ital 1998 American Institute of Physics.}

  2. Analytic solutions and their dynamics of atomic-molecular Bose-Einstein condensates with time- and space-modulated nonlinearities

    Science.gov (United States)

    Wu, Huilan; Yao, Yuqin

    2017-01-01

    The time- and space-modulated nonlinearity is the important character of the Bose-Einstein condensates (BECs). Many works have been done on atomic BECs with spatially modulated nonlinearity, but there is little work on atomic-molecular BECs. In this paper, we construct one family of explicitly exact solutions of the atomic-molecular BECs with time- and space-modulated nonlinearities and trapping potential by similarity transformations. We discuss the dynamics of matter waves including breathing solitons, quasi-breathing solitons, resonant solitons and moving solitons. We analyze the linear stability of the solutions by adding various initial stochastic noise. We also provide the experimental parameters to produce these phenomena in future experiments.

  3. Molecular-dynamics simulation of lateral friction in contact-mode atomic force microscopy of alkane films: The role of molecular flexibility

    DEFF Research Database (Denmark)

    Soza, P.; Hansen, Flemming Yssing; Taub, H.

    2011-01-01

    Molecular-dynamics simulations are used to investigate lateral friction in contact-mode atomic force microscopy of tetracosane (n-C24H50) films. We find larger friction coefficients on the surface of monolayer and bilayer films in which the long axis of the molecules is parallel to the interface ...

  4. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  5. Reaction of Np atom with H₂O in the gas phase: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-01

    The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.

  6. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets

    CERN Document Server

    Miceli, Giacomo; Pasquarello, Alfredo

    2016-01-01

    We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.

  7. All-atom molecular dynamics studies of the full-length {beta}-amyloid peptides

    Energy Technology Data Exchange (ETDEWEB)

    Luttmann, Edgar [Department of Chemistry, Faculty of Science, University of Paderborn, Warburgerstr. 100, 33098 Paderborn (Germany); Fels, Gregor [Department of Chemistry, Faculty of Science, University of Paderborn, Warburgerstr. 100, 33098 Paderborn (Germany)], E-mail: fels@uni-paderborn.de

    2006-03-31

    {beta}-Amyloid peptides are believed to play an essential role in Alzheimer's disease (AD), due to their sedimentation in the form of {beta}-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39-43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an A{beta}-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research. In this paper, we report results from all-atom molecular dynamics simulations based on experimental data from four different peptides of 40 amino acids and two peptides consisting of 42 amino acids. The simulations allow for the analysis of intramolecular interactions and the role of structural features. In particular, they show the appearance of {beta}-turn in the region between amino acid 21 and 33, forming a hook-like shape as it is known to exist in the fibrillar A{beta}-structures. This folding does not depend on the formation of a salt bridge between Asp-23 and Lys-28 but requires the A{beta}(1-42) as such structure was not observed in the shorter system A{beta}(1-40)

  8. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    Science.gov (United States)

    Seppä, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti

    2017-03-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20-60 %rh. Force-distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.

  9. Molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  10. Nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  11. A molecular dynamics simulation of hydrogen atoms collisions on an H-preadsorbed silica surface

    Science.gov (United States)

    Rutigliano, M.; Gamallo, P.; Sayós, R.; Orlandini, S.; Cacciatore, M.

    2014-08-01

    The interaction of hydrogen atoms and molecules with a silica surface is relevant for many research and technological areas. Here, the dynamics of hydrogen atoms colliding with an H-preadsorbed β-cristobalite (0 0 1) surface has been studied using a semiclassical collisional method in conjunction with a recently developed analytical potential energy surface based on density functional theory (DFT) calculations. The atomic recombination probability via an Eley-Rideal (E-R) mechanism, as well as the probabilities for other competitive surface processes, have been determined in a broad range of collision energies (0.04-3.0 eV) for off-normal (θv = 45°) and normal (θv = 0°) incidence and for two different surface temperatures (TS = 300 and 1000 K). H2,gas molecules form in roto-vibrational excited levels while the energy transferred to the solid surface is below 10% for all simulated conditions. Finally, the global atomic recombination coefficient (γE-R) and vibrational state resolved recombination coefficients (γ(v)) were calculated and compared with the available experimental values. The calculated collisional data are of interest in chemical kinetics studies and fluid dynamics simulations of silica surface processes in H-based low-temperature, low-pressure plasmas.

  12. Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Dan Wang; Wen-juan Wu

    2013-01-01

    All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution.Intramolecular distances,root-mean-square deviation,radius of gyration,and solvent-accessible surface are used to characterize the properties of the carnosine.Carnosine can shift between extended and folded states,but exists mostly in extended state in water.Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment.The NMR experimental results are consistent with the molecular dynamics simulations.

  13. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    Science.gov (United States)

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  14. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam

    2000-01-01

    Mechanical behavior of the Si\\(111\\)/Si3N4\\(0001\\) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the \\(1¯ 1¯1\\) plane of the silicon substrate with a speed of 500 \\(+/-100\\) m/s. Time evolution of the dislocation emission and nature of defects is studied.

  15. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam

    2000-01-10

    Mechanical behavior of the Si(111)/Si{sub 3}N{sub 4} (0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1 11) plane of the silicon substrate with a speed of 500 ({+-}100) m/s . Time evolution of the dislocation emission and nature of defects is studied. (c) 2000 The American Physical Society.

  16. First-Principles Molecular Dynamics Investigation of the Atomic-Scale Energy Transport: From Heat Conduction to Thermal Radiation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing thermostats to keep constant temperatures of the nanoscale thin layers, initial thermal non-equilibrium between the neighboring layers is established under the vacuum condition. Models with variable gap distances with an interval of lattice constant increment of the simulated materials are set up and statistical comparisons of temperature evolution curves are made. Moreover, the equilibration time from non-equilibrium state to thermal equilibrium state of different silicon or/and germanium layers combinations are calculated. The results show significant distinctions of heat transfer under different materials and temperatures combinations. Further discussions on the equilibrium time are made to explain the simulation results. As the first work of the atomic scale energy tra...

  17. Molecular Dynamics Study on Interfacial Energy and Atomic Structure of Ag/Ni and Cu/Ni Heterophase System

    Institute of Scientific and Technical Information of China (English)

    Haijiang LIU; Shaoqing WANG; An DU; Caibei ZHANG

    2004-01-01

    The results of molecular dynamics calculations on the interfacial energies and atomic structures of Ag/Ni and Cu/Ni interaces are presented. Calculation on Ag/Ni interfaces with low-index planes shows that those containing the (111) plane have the lowest energies, which is in agreement with the experiments. Comparing surface energy with interracial energy, it is found the order of the interfacial energies of Ag/Ni and Cu/Ni containing the planes fall in the same order as solid-vapor surface energies of Ag, Cu and Ni. In this MD simulation, the relaxed atomic structure and dislocation network of (110)Ag||(110)Ni interface are coincident to HREM observations.

  18. Electron Impact Ionization and Fragmentation Dynamics of Small Atomic and Molecular Clusters

    Science.gov (United States)

    Dorn, Alexander

    2016-09-01

    New ionization and fragmentation reactions emerge if target atoms or molecules are embedded in an environment as it is the case in small clusters or in the condensed phase. These can be intermolecular energy and charge transfer processes or a completely modified fragmentation behavior of the molecular ions. Here we study low energy electron impact induced ionization with a multi-electron and ion imaging spectrometer (reaction microscope) and a supersonic gas jet target which can produce small clusters of various target species. Interatomic reactions are studied for the model system of weakly bound Ar2 dimers. Here, the coincident detection of three electrons and two ions gives detailed insight in interatomic Coulombic decay and radiative charge transfer processes. Such processes were also found in bio-relevant systems like water clusters. We studied pure and water-mixed clusters of tetrahydrofuran (C4H8O, THF) which is the simplest analog of deoxyribose in the DNA backbone. One observation is that ionization of the outermost valence orbital for the monomer leads to stable THF ions. In contrast if THF is bound to another THF or a water molecule the molecular ring breaks. In addition we identify intermolecular Coulombic decay induced by energy transfer from a water molecule ionized in the inner valence shell to the neighboring THF molecule.

  19. Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

    Science.gov (United States)

    Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J

    2014-08-07

    Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the

  20. On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters

    Science.gov (United States)

    Andricioaei, Ioan; Straub, John E.

    1997-12-01

    Generalized Monte Carlo and molecular dynamics algorithms which provide enhanced sampling of the phase space in the calculation of equilibrium thermodynamic properties is presented. The algorithm samples trial moves from a generalized statistical distribution derived from a modification of the Gibbs-Shannon entropy proposed by Tsallis. Results for a one-dimensional model potential demonstrate that the algorithm leads to a greatly enhanced rate of barrier crossing and convergence in the calculation of equilibrium averages. Comparison is made with standard Metropolis Monte Carlo and the J-walking algorithm of Franz, Freeman and Doll. Application to a 13-atom Lennard-Jones cluster demonstrates the ease with which the algorithm may be applied to complex molecular systems.

  1. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  2. All-atom molecular dynamics insights on preQ1 riboswitch aptamer

    Science.gov (United States)

    Gong, Zhou; Zhao, Yunjie; Chen, Changjun; Xiao, Yi

    2012-02-01

    Recently, a series of experiments have focused on two types of preQ1 riboswitch with known smallest aptamer. One of them is from Bacillus subtilis, which have been discussed before. The other one comes from T. tengcongensis, and Jenkins et al recently release its crystal structure in both ligand-bound and free state. These two types of riboswitch aptamer have similar structures but totally different functions. Consequently, contrast studies of these two preQ1 riboswitches will help us to understand the regulation function of riboswitch better. Here, we study the dynamical properties of two types of preQ1 riboswitches using molecular dynamics simulation. We find that the unfolding pathway of the two preQ1 aptamer domains in bound state are both hierarchical and have an intermediate state. We believe that such conformation would be a good candidate structure for ligand binding. On the other hand, in the absent of ligand, the preQ1 riboswitch from Bacillus subtilis can only form the stable state with P1-L3 triplex, while the preQ1 riboswitch from T. tengcongensis can form the conformation with pseudoknot shape. We suggest that such intermediate structures may perform regulation functions in the absent of ligand.

  3. Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5' nucleotidase.

    Science.gov (United States)

    Arafat, A Syed Yasir; Arun, A; Ilamathi, M; Asha, J; Sivashankari, P R; D'Souza, Cletus J M; Sivaramakrishnan, V; Dhananjaya, B L

    2014-03-01

    5' Nucleotidase (5' NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5' nucleotidase (SV-5' NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5' NUC structure were validated using several computational approaches. Key interactions of SV-5' NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5' NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor-(SV-5' NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5' NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5' NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5' NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management.

  4. Car-Parrinello molecular dynamics study of the melting behaviors of n-atom (n = 6, 10) graphene quantum dots

    Science.gov (United States)

    Shekaari, Ashkan; Abolhassani, Mohammad Reza

    2017-06-01

    First-principles molecular dynamics has been applied to inquire into the melting behaviors of n-atom (n = 6, 10) graphene quantum dots (GQD6 and zigzag GQD10) within the temperature range of T = 0-500 K. The temperature dependence of the geometry of each quantum dot is thoroughly evaluated via calculating the related shape deformation parameters and the eigenvalues of the quadrupole tensors. Examining the variations of some phase-transition indicators such as root-mean-square bond length fluctuations and mean square displacements broadly proposes the value of Tm = 70 K for the melting point of GQD6 while a continuous, two-stage phase transition has been concluded for zigzag GQD10.

  5. Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

    Science.gov (United States)

    Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

    2017-09-01

    Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

  6. Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

    Science.gov (United States)

    Kobayashi, Kazuya; Liang, Yunfeng; Amano, Ken-ichi; Murata, Sumihiko; Matsuoka, Toshifumi; Takahashi, Satoru; Nishi, Naoya; Sakka, Tetsuo

    2016-04-19

    With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

  7. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    Science.gov (United States)

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

  8. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    Science.gov (United States)

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  9. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale.

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-19

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  10. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  11. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  12. ADATOM, VACANCY AND SPUTTERING YIELDS OF ENERGETIC Pt ATOMS IMPACTING ON Pt(100) BY MOLECULAR DYNAMICS SIMULATION

    Institute of Scientific and Technical Information of China (English)

    YE ZI-YAN; ZHANG QING-YU

    2001-01-01

    We have studied the influence of incident atoms with low energy on the Pt(100) surface by molecular dynamics simulation. The interaction potential obtained by the embedded atom method (EAM) was used in the simulation. The incident energy changes from 0.leV to 200eV, and the target temperature ranges from 100 to 500 K. The target scales are 6×6×4 and 8×8×4 fcc cells for lower and higher incident energies, respectively. The adatom, sputtering, vacancy and backscattering yields are calculated. It was found that there is a sputtering threshold for the incident energy. When the incident energy is higher than the sputtering threshold, the sputtering yield increases with the increase of incident energy, and the sputtering shows a symmetrical pattern. We found that the adatom and vacancy yields increase as the incident energy increases. The vacancy yields are much higher than those obtained by Monte Carlo simulation. The dependence of the adatom and sputtering yields on the incident energy and the relative atomistic mechanisms are discussed.

  13. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    Science.gov (United States)

    Perilla, Juan R.; Schulten, Klaus

    2017-07-01

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

  14. Differential dynamics of the serotonin1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation.

    Science.gov (United States)

    Patra, Swarna M; Chakraborty, Sudip; Shahane, Ganesh; Prasanna, Xavier; Sengupta, Durba; Maiti, Prabal K; Chattopadhyay, Amitabha

    2015-01-01

    The serotonin1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

  15. Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics.

    Science.gov (United States)

    Nash, Jessica A; Singh, Abhishek; Li, Nan K; Yingling, Yaroslava G

    2015-12-22

    The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

  16. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-11-01

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

  17. Molecules Near Absolute Zero and External Field Control of Atomic and Molecular Dynamics

    CERN Document Server

    Krems, R V

    2005-01-01

    This article reviews the current state of the art in the field of cold and ultracold molecules and demonstrates that chemical reactions, inelastic collisions and dissociation of molecules at subKelvin temperatures can be manipulated with external electric or magnetic fields. The creation of ultracold molecules may allow for spectroscopy measurements with extremely high precision and tests of fundamental symmetries of nature, quantum computation with molecules as qubits, and controlled chemistry. The probability of chemical reactions and collisional energy transfer can be very large at temperatures near zero Kelvin. The collision energy of ultracold atoms and molecules is much smaller than perturbations due to interactions with external electric or magnetic fields available in the laboratory. External fields may therefore be used to induce dissociation of weakly bound molecules, stimulate forbidden electronic transitions, suppress the effect of centrifugal barriers in outgoing reaction channels or tune Feshbac...

  18. Time-Resolved Diffraction Profiles and Atomic Dynamics in Short-Pulse Laser-Induced Structural Transformations: Molecular Dynamics Study

    Science.gov (United States)

    2006-05-16

    clearly reflected in the evolution of the structure function. In just 3–4 ps the peaks characteristic of the fcc structure dis- appear and the structure...apparent in the figure. The diffraction peaks from 111 and 311 atomic planes, present in the original fcc structure , shift in the direction of smaller Q...the fcc crystalline structure. Each peak in Gr corresponds to a specific interatomic distance between a pair of atoms in a perfect fcc structure . For

  19. The stereo-dynamics of collisional autoionization of ammonia by helium and neon metastable excited atoms through molecular beam experiments

    Energy Technology Data Exchange (ETDEWEB)

    Falcinelli, Stefano, E-mail: stefano.falcinelli@unipg.it; Vecchiocattivi, Franco [Department of Civil and Environmental Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia (Italy); Bartocci, Alessio; Cavalli, Simonetta; Pirani, Fernando [Department of Chemistry, Biology, and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123 Perugia (Italy)

    2015-10-28

    A combined analysis of both new (energy spectra of emitted electrons) and previously published (ionization cross sections) experimental data, measured under the same conditions and concerning electronically excited lighter noble gas –NH{sub 3} collisional autoionization processes, is carried out. Such an analysis, performed by exploiting a formulation of the full potential energy surface both in the real and imaginary parts, provides direct information on energetics, structure, and lifetime of the intermediate collision complex over all the configuration space. The marked anisotropy in the attraction of the real part, driving the approach of reagents, and the selective role of the imaginary component, associated to the charge transfer coupling between entrance and exit channels, suggests that reactive events occur almost exclusively in the molecular hemisphere containing the nitrogen lone pair. Crucial details on the stereo-dynamics of elementary collisional autoionization processes are then obtained, in which the open shell nature of the disclosed ionic core of metastable atom plays a crucial role. The same analysis also suggests that the strength of the attraction and the anisotropy of the interaction increases regularly along the series Ne{sup *}({sup 3}P), He{sup *}({sup 3}S), He{sup *}({sup 1}S)–NH{sub 3}. These findings can be ascribed to the strong rise of the metastable atom electronic polarizability (deformability) along the series. The obtained results can stimulate state of the art ab initio calculations focused on specific features of the transition state (energetics, structure, lifetime, etc.) which can be crucial for a further improvement of the adopted treatment and to better understand the nature of the leading interaction components which are the same responsible for the formation of the intermolecular halogen and hydrogen bond.

  20. The stereo-dynamics of collisional autoionization of ammonia by helium and neon metastable excited atoms through molecular beam experiments.

    Science.gov (United States)

    Falcinelli, Stefano; Bartocci, Alessio; Cavalli, Simonetta; Pirani, Fernando; Vecchiocattivi, Franco

    2015-10-28

    A combined analysis of both new (energy spectra of emitted electrons) and previously published (ionization cross sections) experimental data, measured under the same conditions and concerning electronically excited lighter noble gas -NH3 collisional autoionization processes, is carried out. Such an analysis, performed by exploiting a formulation of the full potential energy surface both in the real and imaginary parts, provides direct information on energetics, structure, and lifetime of the intermediate collision complex over all the configuration space. The marked anisotropy in the attraction of the real part, driving the approach of reagents, and the selective role of the imaginary component, associated to the charge transfer coupling between entrance and exit channels, suggests that reactive events occur almost exclusively in the molecular hemisphere containing the nitrogen lone pair. Crucial details on the stereo-dynamics of elementary collisional autoionization processes are then obtained, in which the open shell nature of the disclosed ionic core of metastable atom plays a crucial role. The same analysis also suggests that the strength of the attraction and the anisotropy of the interaction increases regularly along the series Ne*((3)P), He*((3)S), He*((1)S)-NH3. These findings can be ascribed to the strong rise of the metastable atom electronic polarizability (deformability) along the series. The obtained results can stimulate state of the art ab initio calculations focused on specific features of the transition state (energetics, structure, lifetime, etc.) which can be crucial for a further improvement of the adopted treatment and to better understand the nature of the leading interaction components which are the same responsible for the formation of the intermolecular halogen and hydrogen bond.

  1. Atomic and Molecular Processes

    Science.gov (United States)

    1980-06-25

    The topics investigated experimentally and theoretically by the Pittsburgh Atomic Sciences Institute with applications to high power laser development and atmospheric IR backgrounds are enumerated. Reports containing the detailed scientific progress in these studies are cited. Finally, a list of the journal articles describing the results of the programs, with full references, is given.

  2. Nonlinear dynamics in atom optics

    Energy Technology Data Exchange (ETDEWEB)

    Chen Wenyu; Dyrting, S.; Milburn, G.J. [Queensland Univ., St. Lucia, QLD (Australia). Dept. of Physics

    1996-12-31

    In this paper theoretical work on classical and quantum nonlinear dynamics of cold atoms is reported. The basic concepts in nonlinear dynamics are reviewed and then applied to the motion of atoms in time-dependent standing waves and to the atomic bouncer. The quantum dynamics for the cases of regular and chaotic classical dynamics is described. The effect of spontaneous emission and external noise is also discussed. 104 refs., 1 tab., 21 figs.

  3. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

    Science.gov (United States)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H

    2016-11-07

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  4. Adsorption of Synthetic Cationic Polymers on Model Phospholipid Membranes: Insight from Atomic-Scale Molecular Dynamics Simulations.

    Science.gov (United States)

    Kostritskii, Andrei Yu; Kondinskaia, Diana A; Nesterenko, Alexey M; Gurtovenko, Andrey A

    2016-10-11

    Although synthetic cationic polymers represent a promising class of effective antibacterial agents, the molecular mechanisms behind their antimicrobial activity remain poorly understood. To this end, we employ atomic-scale molecular dynamics simulations to explore adsorption of several linear cationic polymers of different chemical structure and protonation (polyallylamine (PAA), polyethylenimine (PEI), polyvinylamine (PVA), and poly-l-lysine (PLL)) on model bacterial membranes (4:1 mixture of zwitterionic phosphatidylethanolamine (PE) and anionic phosphatidylglycerol (PG) lipids). Overall, our findings show that binding of polycations to the anionic membrane surface effectively neutralizes its charge, leading to the reorientation of water molecules close to the lipid/water interface and to the partial release of counterions to the water phase. In certain cases, one has even an overcharging of the membrane, which was shown to be a cooperative effect of polymer charges and lipid counterions. Protonated amine groups of polycations are found to interact preferably with head groups of anionic lipids, giving rise to formation of hydrogen bonds and to a noticeable lateral immobilization of the lipids. While all the above findings are mostly defined by the overall charge of a polymer, we found that the polymer architecture also matters. In particular, PVA and PEI are able to accumulate anionic PG lipids on the membrane surface, leading to lipid segregation. In turn, PLL whose charge twice exceeds charges of PVA/PEI does not induce such lipid segregation due to its considerably less compact architecture and relatively long side chains. We also show that partitioning of a polycation into the lipid/water interface is an interplay between its protonation level (the overall charge) and hydrophobicity of the backbone. Therefore, a possible strategy in creating highly efficient antimicrobial polymeric agents could be in tuning these polycation's properties through proper

  5. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carles Calero

    2016-04-01

    Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  6. 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.

  7. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    Science.gov (United States)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  8. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  9. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Science.gov (United States)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  10. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

    Science.gov (United States)

    Wallace, Jason A; Shen, Jana K

    2012-11-14

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  11. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    Science.gov (United States)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  12. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-06

    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  13. Atomic motions in poly(vinyl methyl ether): A combined study by quasielastic neutron scattering and molecular dynamics simulations in the light of the mode coupling theory.

    Science.gov (United States)

    Capponi, S; Arbe, A; Alvarez, F; Colmenero, J; Frick, B; Embs, J P

    2009-11-28

    Quasielastic neutron scattering experiments (time-of-flight, neutron spin echo, and backscattering) on protonated poly(vinyl methyl ether) (PVME) have revealed the hydrogen dynamics above the glass-transition temperature. Fully atomistic molecular dynamics simulations properly validated with the neutron scattering results have allowed further characterization of the atomic motions accessing the correlation functions directly in real space. Deviations from Gaussian behavior are found in the high-momentum transfer range, which are compatible with the predictions of mode coupling theory (MCT). We have applied the MCT phenomenological version to the self-correlation functions of PVME atoms calculated from our simulation data, obtaining consistent results. The unusually large value found for the lambda-exponent parameter is close to that recently reported for polybutadiene and simple polymer models with intramolecular barriers.

  14. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

    Science.gov (United States)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-07

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  15. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N

    2014-05-16

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1-120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm-3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. © 2014 IOP Publishing Ltd.

  16. Interactive molecular dynamics

    CERN Document Server

    Schroeder, Daniel V

    2015-01-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.

  17. Interactive molecular dynamics

    Science.gov (United States)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  18. Stress Domains in Si\\(111\\)/a-Si3N4 Nanopixel: Ten-Million-Atom Molecular Dynamics Simulations on Parallel Computers

    Science.gov (United States)

    Omeltchenko, Andrey; Bachlechner, Martina E.; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul

    2000-01-01

    Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si\\(111\\)/Si3N4\\(0001\\) and Si\\(111\\)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nm×33 nm, mesa tensile stress domains \\(~300 Å\\) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.

  19. Stress domains in Si(111)/a-Si3N4 nanopixel: ten-million-atom molecular dynamics simulations on parallel computers

    Science.gov (United States)

    Omeltchenko; Bachlechner; Nakano; Kalia; Vashishta; Ebbsjo; Madhukar; Messina

    2000-01-10

    Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si(111)/Si(3)N4(0001) and Si(111)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nmx33 nm, mesa tensile stress domains ( approximately 300 A) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.

  20. Non-adiabatic dynamics of reactions of O(1D) with Xe, CO, NO2, and CO2 from crossed atomic and molecular beam experiments

    Science.gov (United States)

    Boering, Kristie

    2015-03-01

    Reactions of the first excited state of atomic oxygen, O(1D), with small molecules such as CO, NO2, and CO2 continue to be of interest in aeronomy and atmospheric chemistry, thus providing additional motivation to understand the dynamics of these reactions and how well they are predicted by theory. In collaboration with Prof. Jim Lin of the Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan, we have studied the dynamics of quenching and non-quenching reactions between O(1D) and various small molecules using a universal crossed atomic and molecular beam apparatus. New experimental results for the dynamics of quenching of O(1D) by Xe and CO will be presented and compared with previous results for NO2 (K.A. Mar, A.L. Van Wyngarden, C.-W. Liang, Y.T. Lee, J.J. Lin, K.A. Boering, J. Chem. Phys., 137, 044302, doi: 10.1063/1.4736567, 2012) and CO2 (M.J. Perri, A.L. Van Wyngarden, K.A. Boering, J.J. Lin, and Y.T. Lee, J. Chem. Phys., 119(16), 8213-8216, 2003; M.J. Perri, A.L. Van Wyngarden, J.J. Lin, Y.T. Lee, and K.A. Boering, J. Phys. Chem. A, 108(39), 7995-8001, doi: 10.1021/jp0485845, 2004). Among the most intriguing of the new results are for quenching of O(1D) by Xe, for which marked oscillations in the differential cross sections were observed for the O(3P) and Xe products. The shape and relative phase of the oscillatory structure depended strongly on collision energy. This behavior is likely due to the quantum nature of the collision dynamics, caused by interferences among multiple curve crossing pathways accessible during electronic quenching, known as Stueckelberg oscillations.

  1. Surface chemistry of copper metal and copper oxide atomic layer deposition from copper(ii) acetylacetonate: a combined first-principles and reactive molecular dynamics study.

    Science.gov (United States)

    Hu, Xiao; Schuster, Jörg; Schulz, Stefan E; Gessner, Thomas

    2015-10-28

    Atomistic mechanisms for the atomic layer deposition using the Cu(acac)2 (acac = acetylacetonate) precursor are studied using first-principles calculations and reactive molecular dynamics simulations. The results show that Cu(acac)2 chemisorbs on the hollow site of the Cu(110) surface and decomposes easily into a Cu atom and the acac-ligands. A sequential dissociation and reduction of the Cu precursor [Cu(acac)2 → Cu(acac) → Cu] are observed. Further decomposition of the acac-ligand is unfavorable on the Cu surface. Thus additional adsorption of the precursors may be blocked by adsorbed ligands. Molecular hydrogen is found to be nonreactive towards Cu(acac)2 on Cu(110), whereas individual H atoms easily lead to bond breaking in the Cu precursor upon impact, and thus release the surface ligands into the gas-phase. On the other hand, water reacts with Cu(acac)2 on a Cu2O substrate through a ligand-exchange reaction, which produces gaseous H(acac) and surface OH species. Combustion reactions with the main by-products CO2 and H2O are observed during the reaction between Cu(acac)2 and ozone on the CuO surface. The reactivity of different co-reactants toward Cu(acac)2 follows the order H > O3 > H2O.

  2. Available Instruments for Analyzing Molecular Dynamics Trajectories.

    Science.gov (United States)

    Likhachev, I V; Balabaev, N K; Galzitskaya, O V

    2016-01-01

    Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.

  3. Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

    Science.gov (United States)

    Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

    2017-10-01

    Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

  4. 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.

  5. 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.

  6. Physics through the 1990s: Atomic, molecular and optical physics

    Science.gov (United States)

    1986-01-01

    The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

  7. Dynamic molecular graphs: "hopping" structures.

    Science.gov (United States)

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, West Bengal 700098 (India)

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  9. A Molecular Dynamics of Cold Neutral Atoms Captured by Carbon Nanotube Under Electric Field and Thermal Effect as a Selective Atoms Sensor.

    Science.gov (United States)

    Santos, Elson C; Neto, Abel F G; Maneschy, Carlos E; Chen, James; Ramalho, Teodorico C; Neto, A M J C

    2015-05-01

    Here we analyzed several physical behaviors through computational simulation of systems consisting of a zig-zag type carbon nanotube and relaxed cold atoms (Rb, Au, Si and Ar). These atoms were chosen due to their different chemical properties. The atoms individually were relaxed on the outside of the nanotube during the simulations. Each system was found under the influence of a uniform electric field parallel to the carbon nanotube and under the thermal effect of the initial temperature at the simulations. Because of the electric field, the cold atoms orbited the carbon nanotube while increasing the initial temperature allowed the variation of the radius of the orbiting atoms. We calculated the following quantities: kinetic energy, potential energy and total energy and in situ temperature, molar entropy variation and average radius of the orbit of the atoms. Our data suggest that only the action of electric field is enough to generate the attractive potential and this system could be used as a selected atoms sensor.

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

    Directory of Open Access Journals (Sweden)

    Toofanny Rudesh D

    2011-08-01

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

  11. Dependence of the atomic level Green-Kubo stress correlation function on wavevector and frequency: molecular dynamics results from a model liquid.

    Science.gov (United States)

    Levashov, V A

    2014-09-28

    We report on a further investigation of a new method that can be used to address vibrational dynamics and propagation of stress waves in liquids. The method is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the atomic level stress correlation functions. This decomposition, as was demonstrated previously for a model liquid studied in molecular dynamics simulations, reveals the presence of stress waves propagating over large distances and a structure that resembles the pair density function. In this paper, by performing the Fourier transforms of the atomic level stress correlation functions, we elucidate how the lifetimes of the stress waves and the ranges of their propagation depend on their frequency, wavevector, and temperature. These results relate frequency and wavevector dependence of the generalized viscosity to the character of propagation of the shear stress waves. In particular, the results suggest that an increase in the value of the frequency dependent viscosity at low frequencies with decrease of temperature is related to the increase in the ranges of propagation of the stress waves of the corresponding low frequencies. We found that the ranges of propagation of the shear stress waves of frequencies less than half of the Einstein frequency extend well beyond the nearest neighbor shell even above the melting temperature. The results also show that the crossover from quasilocalized to propagating behavior occurs at frequencies usually associated with the Boson peak.

  12. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

    Science.gov (United States)

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  13. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics.

    Science.gov (United States)

    Huang, Yu-Ming M; Chang, Chia-En A

    2011-05-25

    Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer. Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.

  14. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Huang Yu-ming M

    2011-05-01

    Full Text Available Abstract Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA domain. The first two recognize both phosphothreonine (pThr and phosphoserine (pSer residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Results Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA or in combination with α-helix (BRCT repeats or β-sheet (WW domain fail to differentiate pThr/pSer. Conclusions Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.

  15. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Bederson, Benjamin

    1993-01-01

    Advances in Atomic, Molecular, and Optical Physics, established in 1965, continues its tradition of excellence with Volume 32, published in honor of Founding Editor Sir David Bates upon his retirement as editorof the series. This volume presents reviews of topics related to the applications of atomic and molecular physics to atmospheric physics and astrophysics.

  16. 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.

  17. Stress Domains in Si(111)/a-Si{sub 3}N{sub 4} Nanopixel: Ten-Million-Atom Molecular Dynamics Simulations on Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Omeltchenko, Andrey; Bachlechner, Martina E.; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam; Messina, Paul

    2000-01-10

    Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si(111)/Si {sub 3}N{sub 4}(0001) and Si(111)/a-Si {sub 3}N{sub 4} nanopixels. Compared to the crystalline case, the stresses in amorphous Si{sub 3}N {sub 4} are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nmx33 nm , mesa tensile stress domains ({approx}300 Angstrom) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa , respectively. (c) 2000 The American Physical Society.

  18. Molecular Dynamics and Picosecond Vibrational Spectra.

    Science.gov (United States)

    1980-07-01

    and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute

  19. Dynamics in atomic signaling games

    KAUST Repository

    Fox, Michael J.

    2015-04-08

    We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.

  20. Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

    Science.gov (United States)

    Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-02-09

    A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

  1. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes.

    Science.gov (United States)

    Kokhan, Oleksandr; Shinkarev, Vladimir P

    2011-02-02

    Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

  2. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  3. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    Science.gov (United States)

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-03-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to  ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning’s theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1{{k}\\text{B}}T . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  4. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  5. Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics.

    Science.gov (United States)

    Marin-Gonzalez, Alberto; Vilhena, J G; Perez, Ruben; Moreno-Herrero, Fernando

    2017-07-03

    Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.

  6. 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

  7. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2016-01-01

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).

  8. 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.

  9. Molecular Dynamics Calculations

    Science.gov (United States)

    1996-01-01

    The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two

  10. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    Science.gov (United States)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

  11. Shock-induced poration, cholesterol flip-flop and small interfering RNA transfection in a phospholipid membrane: Multimillion atom, microsecond molecular dynamics simulations

    Science.gov (United States)

    Choubey, Amit

    Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long-time and large-scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. We investigate shock-induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip-flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip-flop rates by

  12. Atomic and molecular processes in fusion plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Janev, R.K. [International Atomic Energy Agency, Vienna (Austria)

    1997-01-01

    The role of atomic and molecular processes in achieving and maintaining the conditions for thermonuclear burn in a magnetically confined fusion plasma is described. Emphasis is given to the energy balance and power and particle exhaust issues. The most important atomic and molecular processes which affect the radiation losses and impurity transport in the core plasma, the neutral particle transport in the plasma edge and the radiative cooling of divertor plasmas are discussed in greater detail. (author)

  13. 1985 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  14. 1984 Bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howard, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1985-04-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  15. Bibliography of atomic and molecular processes, 1983

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  16. 1982 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  17. 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 ...

  18. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Berman, Paul R; Arimondo, Ennio

    2006-01-01

    Volume 54 of the Advances Series contains ten contributions, covering a diversity of subject areas in atomic, molecular and optical physics. The article by Regal and Jin reviews the properties of a Fermi degenerate gas of cold potassium atoms in the crossover regime between the Bose-Einstein condensation of molecules and the condensation of fermionic atom pairs. The transition between the two regions can be probed by varying an external magnetic field. Sherson, Julsgaard and Polzik explore the manner in which light and atoms can be entangled, with applications to quantum information processing

  19. The atomic and molecular reaction statics

    Institute of Scientific and Technical Information of China (English)

    ZHU; ZhengHe

    2007-01-01

    This work presents a new science called atomic and molecular reaction statics (AMRS). There are four parts for AMRS, i.e. the group theoretical derivation of molecular electronic states, the principle of microscopic reversibility, the principle of microscopic transitivity and the optimum energy process rule. AMRS has been developed for about twenty years.

  20. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

    Science.gov (United States)

    De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-12-09

    A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

  1. Intense Atomic and Molecular Beams via Neon Buffer Gas Cooling

    CERN Document Server

    Patterson, David; Doyle, John M

    2008-01-01

    We realize a continuous guided beam of cold deuterated ammonia with a flux of 3e11 ND3 molecules/s and a continuous free-space beam of cold potassium with a flux of 1e16 K atoms/s. A novel feature of the buffer gas source used to produce these beams is cold neon, which, due to intermediate Knudsen number beam dynamics, produces a forward velocity and low-energy tail that is comparable to much colder helium-based sources. We expect this source to be trivially generalizable to a very wide range of atomic and molecular species with significant vapor pressure below 1000 K. This source has properties that make it a good starting point for laser cooling of molecules or atoms, cold collision studies, trapping, or nonlinear optics in buffer-gas-cooled atomic or molecular gases.

  2. Committee on Atomic, Molecular and Optical Sciences

    Energy Technology Data Exchange (ETDEWEB)

    Lancaster, James [National Academy of Sciences, Washington, DC (United States)

    2015-06-30

    The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

  3. Tunneling Dynamics of Two-Species Molecular Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong; GAO Ke-Lin

    2004-01-01

    We study tunneling dynamics of atomic group in two-species molecular Bose-Einstein condensates. It is shown that the tunneling of the atom group depends on not only the tunneling coupling constant between the atomic pair molecular condensate and the three-atomic group molecular condensate, but also the inter-molecular nonlinear interactions and the initial number of atoms in these condensates. It is discovered that besides oscillating tunneling current between the atomic pair molecular condensate and the three-atomic group molecular condensate, the nonlinear atomic group tunneling dynamics sustains a self-maintained population imbalance: a macroscopic quantum self-trapping effect.

  4. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    Science.gov (United States)

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  5. Atomic and molecular adsorption on Rh(111)

    DEFF Research Database (Denmark)

    Mavrikakis, Manos; Rempel, J.; Greeley, Jeffrey Philip

    2002-01-01

    A systematic study of the chemisorption of both atomic (H, O, N, S, C), molecular (N-2, CO, NO), and radical (CH3, OH) species on Rh(111) has been performed. Self-consistent, periodic, density functional theory (DFT-GGA) calculations, using both PW91 and RPBE functionals, have been employed to de...

  6. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    1999-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics.

  7. Molecular photons interfaced with alkali atoms.

    Science.gov (United States)

    Siyushev, Petr; Stein, Guilherme; Wrachtrup, Jörg; Gerhardt, Ilja

    2014-05-01

    Future quantum communication will rely on the integration of single-photon sources, quantum memories and systems with strong single-photon nonlinearities. Two key parameters are crucial for the single-photon source: a high photon flux with a very small bandwidth, and a spectral match to other components of the system. Atoms or ions may act as single-photon sources--owing to their narrowband emission and their intrinsic spectral match to other atomic systems--and can serve as quantum nonlinear elements. Unfortunately, their emission rates are still limited, even for highly efficient cavity designs. Single solid-state emitters such as single organic dye molecules are significantly brighter and allow for narrowband photons; they have shown potential in a variety of quantum optical experiments but have yet to be interfaced with other components such as stationary memory qubits. Here we describe the optical interaction between Fourier-limited photons from a single organic molecule and atomic alkali vapours, which can constitute an efficient quantum memory. Single-photon emission rates reach up to several hundred thousand counts per second and show a high spectral brightness of 30,000 detectable photons per second per megahertz of bandwidth. The molecular emission is robust and we demonstrate perfect tuning to the spectral transitions of the sodium D line and efficient filtering, even for emitters at ambient conditions. In addition, we achieve storage of molecular photons originating from a single dibenzanthanthrene molecule in atomic sodium vapour. Given the large set of molecular emission lines matching to atomic transitions, our results enable the combination of almost ideal single-photon sources with various atomic vapours, such that experiments with giant single-photon nonlinearities, mediated, for example, by Rydberg atoms, become feasible.

  8. Stout: Cloudy's Atomic and Molecular Database

    CERN Document Server

    Lykins, M L; Kisielius, R; Chatzikos, M; Porter, R L; van Hoof, P A M; Williams, R J R; Keenan, F P; Stancil, P C

    2015-01-01

    We describe a new atomic and molecular database we developed for use in the spectral synthesis code Cloudy. The design of Stout is driven by the data needs of Cloudy, which simulates molecular, atomic, and ionized gas with kinetic temperatures 2.8 K < T < 1e10 K and densities spanning the low to high-density limits. The radiation field between photon energies $10^{-8}$ Ry and 100 MeV is considered, along with all atoms and ions of the lightest 30 elements, and ~100 molecules. For ease of maintenance, the data are stored in a format as close as possible to the original data sources. Few data sources include the full range of data we need. We describe how we fill in the gaps in the data or extrapolate rates beyond their tabulated range. We tabulate data sources both for the atomic spectroscopic parameters and for collision data for the next release of Cloudy. This is not intended as a review of the current status of atomic data, but rather a description of the features of the database which we will build ...

  9. Dynamics Resonances in Atomic States of Astrophysical Relevance

    Indian Academy of Sciences (India)

    K. N. Arefieff; K. Miculis; N. N. Bezuglov; M. S. Dimitrijević; A. N. Klyucharev; A. A. Mihajlov; V. A. Srećković

    2015-12-01

    Ionized geocosmic media parameters in a thermal and a subthermal range of energy have a number of unique features. The photoresonance plasma that is formed by optical excitation of the lowest excited (resonance) atomic states is one example of conversion of radiation energy into electrical one. Since spontaneous fluorescence of excited atoms is probabilistic, the description of the radiating quantized system evolution along with photon energy transfer in a cold atom medium, should include elements of stochastic dynamics. Finally, the chaotic dynamics of a weakly bound Rydberg electron over a grid of the energy level diagram of a quasi-molecular Rydberg complex provides an excitation migration of the electron forward to the ionization continuum. This work aims at discussing the specific features of the dynamic resonances formalism in the description of processes involving Rydberg states of an excited atom, including features in the fluorescence spectrum partially caused by the quantum defect control due to the presence of statistic electromagnetic fields.

  10. Dynamics Resonances in Atomic States of Astrophysical Relevance

    CERN Document Server

    Arefieff, K N; Bezuglov, N N; Dimitrijevic, M S; Klyucharev, A N; Mihajlov, A A; Sreckovic, V A

    2016-01-01

    Ionized geocosmic media parameters in a thermal and a subthermal range of energy have a number of unique features. The photoresonance plasma that is formed by optical excitation of the lowest excited (resonance) atomic states is one example of conversion of radiation energy into electrical one. Since spontaneous fluorescence of excited atoms is probabilistic, the description of the radiating quantized system evolution along with photons energy transfer in a cold atoms medium, should include elements of stochastic dynamics. Finally, the chaotic dynamics of a weakly bound Rydberg electron over a grid of the energy levels diagram of a quasi-molecular Rydberg complex provides an excitation migration of the electron forward to the ionization continuum. This work aims at discussing the specific features of the dynamic resonances formalism in the description of processes involving Rydberg states of an excited atom, including features in the fluorescence spectrum partially caused by the quantum defect control due to ...

  11. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  12. The structures and dynamics of atomic and molecular adsorbates on metal surfaces by scanning tunneling microscopy and low energy electron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hyungsuk Alexander [Univ. of California, Berkeley, CA (United States)

    1996-12-01

    Studies of surface structure and dynamics of atoms and molecules on metal surfaces are presented. My research has focused on understanding the nature of adsorbate-adsorbate and adsorbate-substrate interactions through surface studies of coverage dependency and coadsorption using both scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). The effect of adsorbate coverage on the surface structures of sulfur on Pt(111) and Rh(111) was examined. On Pt(111), sulfur forms p(2x2) at 0.25 ML of sulfur, which transforms into a more compressed (√3x√3)R30° at 0.33 ML. On both structures, it was found that sulfur adsorbs only in fcc sites. When the coverage of sulfur exceeds 0.33 ML, it formed more complex c(√3x7)rect structure with 3 sulfur atoms per unit cell. In this structure, two different adsorption sites for sulfur atoms were observed - two on fcc sites and one on hcp site within the unit cell.

  13. Atomic, molecular, and optical physics charged particles

    CERN Document Server

    Dunning, F B

    1995-01-01

    With this volume, Methods of Experimental Physics becomes Experimental Methods in the Physical Sciences, a name change which reflects the evolution of todays science. This volume is the first of three which will provide a comprehensive treatment of the key experimental methods of atomic, molecular, and optical physics; the three volumes as a set will form an excellent experimental handbook for the field. The wide availability of tunable lasers in the pastseveral years has revolutionized the field and lead to the introduction of many new experimental methods that are covered in these volumes. Traditional methods are also included to ensure that the volumes will be a complete reference source for the field.

  14. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2002-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered include related applied areas, such as atmospheric science, astrophysics, surface physics and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  15. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2000-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  16. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2001-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  17. Theory of atomic additivity in molecular hyperpolizabilities

    Science.gov (United States)

    Baird, James K.

    1987-01-01

    Hyperpolarizability is a function of frequency. This is called dispersion. Because of the Kramers-Kronig relations, researchers expect that a material that is dispersing light is also absorbing it. Where there is both dispersion and absorption, the molecular polarizabilities are complex functions of the frequency. This led researchers to consider atomic additivity in both the real and imaginary parts of the ordinary and hyperpolarizabilities. This effort is desirable not only from a theoretical point of view, but also because of the existence of a large body of complex refractive index data, which may be used to test the additivity principle with the complex valued ordinary dipole polarizability.

  18. Atomic, molecular, and optical physics electromagnetic radiation

    CERN Document Server

    Dunning, F B; Lucatorto, Thomas

    1997-01-01

    Combined with Volumes 29A and 29B, this volume is a comprehensive treatment of the key experimental methods of atomic, molecular, and optical physics, as well as an excellent experimental handbook for the field. Thewide availability of tunable lasers in the past several years has revolutionized the field and lead to the introduction of many new experimental methods that are covered in these volumes. Traditional methods are also included to ensure that the volumes will be a complete reference source for the field.

  19. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    1998-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material as well as detailed descriptions of important recent developments.

  20. All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC.

    Science.gov (United States)

    Xu, Wu; Amire-Brahimi, Benjamin; Xie, Xiao-Jun; Huang, Liying; Ji, Jun-Yuan

    2014-08-01

    The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable 'CDK8 submodule' consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop, as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate

  1. Atomic positional disorder, phonon spectrum, and molecular-dynamics simulation of Tl2CaBa2Cu2O8 and Tl2Ca2Ba2Cu3O10

    Science.gov (United States)

    Chaplot, S. L.

    1992-03-01

    The nature of the atomic positional disorder in the high-temperature superconducting ceramic oxides Tl2CaBa2Cu2O8 (Tl 2:1:2:2) and Tl2Ca2Ba2Cu3O10 (Tl 2:2:2:3) is studied with the help of an ionic-type interatomic potential and molecular-dynamics computer simulations. The pair distribution function and the phonon spectrum are calculated using this model and compared with results of neutron-scattering experiments on Tl 2:1:2:2. Calculated results on the partial pair distribution function, partial phonon density of states, mean square atomic vibrational amplitudes, and lattice specific heat are also presented.

  2. Molecular Dynamics and Protein Function

    National Research Council Canada - National Science Library

    M. Karplus; J. Kuriyan; Bruce J. Berne

    2005-01-01

    .... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...

  3. The Si/Si_3N4 Interface and Si/Si_3N4 Submicron Mesa: A Multi-million Atom Molecular Dynamics Study

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam

    1998-03-01

    Using molecular dynamics simulations on parallel computers, the interface structure, stress distribution, crack propagation and fracture in a Si_3N4 film on Si substrate are studied. Bulk Si is described by Stillinger-Weber potential and Si_3N4 is represented by a combination of two- and three-body covalent interactions. At the interface, the charge transfer is taken from LCAO electronic structure calculations (G.-L. Zhao and M.E. Bachlechner, Europhys. Lett. 36, 287 (1997)). Results for structural correlations at the interface and 3D stress distribution for the submicron mesa are presented.

  4. Chemical reaction dynamics of Rydberg atoms with neutral molecules: a comparison of molecular-beam and classical trajectory results for the H(n)+D2-->HD+D(n') reaction.

    Science.gov (United States)

    Song, Hui; Dai, Dongxu; Wu, Guorong; Wang, Chia Chen; Harich, Steven A; Hayes, Michael Y; Wang, Xiuyan; Gerlich, Dieter; Yang, Xueming; Skodje, Rex T

    2005-08-15

    Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D2-->HD+D(n) at low collision energies. It was discovered that the rotationally resolved product distribution was remarkably similar to a much more limited data set obtained at a single scattering angle for the ion-molecule reaction H++D2-->D++HD. The equivalence of these two problems would be consistent with the Fermi-independent-collider model (electron acting as a spectator) and would provide an important new avenue for the study of ion-molecule reactions. In this work, we employ a classical trajectory calculation on the ion-molecule reaction to facilitate a more extensive comparison between the two systems. The trajectory simulations tend to confirm the equivalence of the ion+molecule dynamics to that for the Rydberg-atom+molecule system. The theory reproduces the close relationship of the two experimental observations made previously. However, some differences between the Rydberg-atom experiments and the trajectory simulations are seen when comparisons are made to a broader data set. In particular, the angular distribution of the differential cross section exhibits more asymmetry in the experiment than in the theory. The potential breakdown of the classical model is discussed. The role of the "spectator" Rydberg electron is addressed and several crucial issues for future theoretical work are brought out.

  5. DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

    NARCIS (Netherlands)

    JUFFER, AH; BERENDSEN, HJC

    1993-01-01

    A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the surfa

  6. Molecular Dynamics of Lipid Bilayers

    Science.gov (United States)

    1989-08-09

    The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.

  7. [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.

  8. Molecular dynamics model of dimethyl ether

    Energy Technology Data Exchange (ETDEWEB)

    Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)

    1995-11-02

    We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.

  9. Molecular Dynamics Simulations of helium Behaviour in Copper Crystals

    Institute of Scientific and Technical Information of China (English)

    王玲; 宁西京

    2003-01-01

    Molecular dynamics simulations are performed to investigate the behaviour of helium atoms generated from tritium decay in perfect Cu crystals at 300K. At the early stage just after a 3He atom generation, the lattice structure is badly deformed and the local temperature rises considerably above 300 K. Single 3He atom diffuses by interstitial paths, whereas two 3He atoms attract each other and can form a stable dimer, which pushes a Cu atom out of its original lattice site and occupies the vacancy. This dimer can catch another 3He atom and form a trimer with an equilateral triangular structure.

  10. MDplot: Visualise Molecular Dynamics.

    Science.gov (United States)

    Margreitter, Christian; Oostenbrink, Chris

    2017-05-10

    The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

  11. Enhancing coherence in molecular spin qubits via atomic clock transitions

    Science.gov (United States)

    Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

    2016-03-01

    Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a ‘bottom-up’ approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits.

  12. Computational challenges in atomic, molecular and optical physics.

    Science.gov (United States)

    Taylor, Kenneth T

    2002-06-15

    Six challenges are discussed. These are the laser-driven helium atom; the laser-driven hydrogen molecule and hydrogen molecular ion; electron scattering (with ionization) from one-electron atoms; the vibrational and rotational structure of molecules such as H(3)(+) and water at their dissociation limits; laser-heated clusters; and quantum degeneracy and Bose-Einstein condensation. The first four concern fundamental few-body systems where use of high-performance computing (HPC) is currently making possible accurate modelling from first principles. This leads to reliable predictions and support for laboratory experiment as well as true understanding of the dynamics. Important aspects of these challenges addressable only via a terascale facility are set out. Such a facility makes the last two challenges in the above list meaningfully accessible for the first time, and the scientific interest together with the prospective role for HPC in these is emphasized.

  13. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  14. Atom laser dynamics in a tight waveguide

    Energy Technology Data Exchange (ETDEWEB)

    Campo, A del; Lizuain, I; Muga, J G [Departamento de Quimica-Fisica, UPV-EHU, Apartado. 644, Bilbao (Spain); Pons, M [Departamento de Fisica Aplicada I, E.U.I.T. de Minas y Obras Publicas, UPV-EHU, 48901 Barakaldo (Spain); Moshinsky, M [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 20-364, 01000 Mexico D.F. (Mexico)], E-mail: adolfo.delcampo@ehu.es

    2008-02-15

    We study the transient dynamics that arise during the formation of an atom laser beam in a tight waveguide. The time dependent density profile develops a series of wiggles which are related to the diffraction in time phenomenon. The apodization of matter waves, which relies on the use of smooth aperture functions, allows to suppress such oscillations in a time interval, after which there is a revival of the diffraction in time. The revival time scale is directly related to the inverse of the harmonic trap frequency for the atom reservoir.

  15. High-order-harmonic generation in atomic and molecular systems

    Science.gov (United States)

    Suárez, Noslen; Chacón, Alexis; Pérez-Hernández, Jose A.; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.

    2017-03-01

    High-order-harmonic generation (HHG) results from the interaction of ultrashort laser pulses with matter. It configures an invaluable tool to produce attosecond pulses, moreover, to extract electron structural and dynamical information of the target, i.e., atoms, molecules, and solids. In this contribution, we introduce an analytical description of atomic and molecular HHG, that extends the well-established theoretical strong-field approximation (SFA). Our approach involves two innovative aspects: (i) First, the bound-continuum and rescattering matrix elements can be analytically computed for both atomic and multicenter molecular systems, using a nonlocal short range model, but separable, potential. When compared with the standard models, these analytical derivations make possible to directly examine how the HHG spectra depend on the driven media and laser-pulse features. Furthermore, we can turn on and off contributions having distinct physical origins or corresponding to different mechanisms. This allows us to quantify their importance in the various regions of the HHG spectra. (ii) Second, as reported recently [N. Suárez et al., Phys. Rev. A 94, 043423 (2016), 10.1103/PhysRevA.94.043423], the multicenter matrix elements in our theory are free from nonphysical gauge- and coordinate-system-dependent terms; this is accomplished by adapting the coordinate system to the center from which the corresponding time-dependent wave function originates. Our SFA results are contrasted, when possible, with the direct numerical integration of the time-dependent Schrödinger equation in reduced and full dimensionality. Very good agreement is found for single and multielectronic atomic systems, modeled under the single active electron approximation, and for simple diatomic molecular systems. Interference features, ubiquitously present in every strong-field phenomenon involving a multicenter target, are also captured by our model.

  16. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Science.gov (United States)

    Li, Junchao; Zhu, Mengze; Abernathy, Douglas L.; Ke, Xianglin; Morelli, Donald T.; Lai, Wei

    2016-10-01

    Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS) experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous "phonon softening upon cooling" behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic "rattling" of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  17. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Directory of Open Access Journals (Sweden)

    Junchao Li

    2016-10-01

    Full Text Available Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (<1 W m−1 K−1 at 300 K remains limited. This work applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous “phonon softening upon cooling” behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic “rattling” of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  18. Atomic and Molecular Aspects of Astronomical Spectra

    Science.gov (United States)

    Sochi, Taha

    2012-11-01

    In the first section we present the atomic part where a C2+ atomic target was prepared and used to generate theoretical data to investigate recombination lines arising from electron-ion collisions in thin plasma. R-matrix method was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation. The data were used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, emissivities and dielectronic recombination coefficients. The data were cast in a line list containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature. The electron temperature investigation was also extended to include free electron energy analysis to investigate the long-standing problem of discrepancy between the results of recombination and forbidden lines analysis and its possible connection to the electron distribution. In the second section we present the results of our molecular investigation; the generation of a comprehensive, calculated line list of frequencies and transition probabilities for H2D+. The line list contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels and covers frequencies up to 18500 cm-1. About 15% of these levels are fully assigned with approximate rotational and vibrational quantum numbers. A temperature-dependent partition function and cooling function are presented. Temperature-dependent synthetic spectra for the temperatures T=100, 500, 1000 and 2000 K in the frequency range 0-10000 cm-1 were also generated and presented graphically.

  19. Evolution of the atomic and molecular gas content of galaxies

    NARCIS (Netherlands)

    Popping, Gergö; Somerville, Rachel S.; Trager, Scott C.

    2014-01-01

    We study the evolution of atomic and molecular gas in galaxies in semi-analytic models of galaxy formation that include new modelling of the partitioning of cold gas in galactic discs into atomic, molecular, and ionized phases. We adopt two scenarios for the formation of molecules: one pressure base

  20. Uncertainty Estimates for Theoretical Atomic and Molecular Data

    CERN Document Server

    Chung, H -K; Bartschat, K; Csaszar, A G; Drake, G W F; Kirchner, T; Kokoouline, V; Tennyson, J

    2016-01-01

    Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structure and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering.

  1. Molecular dynamics of silicon indentation

    Energy Technology Data Exchange (ETDEWEB)

    Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))

    1993-04-01

    We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.

  2. 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...

  3. Molecular modelling and molecular dynamics of CFTR.

    Science.gov (United States)

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  4. Current-induced dynamics in carbon atomic contacts

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Gunst, Tue; Brandbyge, Mads

    2011-01-01

    voltage, which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed...... of molecular-scale contacts. Systems based on molecules bridging electrically gated graphene electrodes may offer an interesting test-bed for these effects. Results: We employ a semi-classical Langevin approach in combination with DFT calculations to study the current-induced vibrational dynamics of an atomic...... carbon chain connecting electrically gated graphene electrodes. This illustrates how the device stability can be predicted solely from the modes obtained from the Langevin equation, including the current-induced forces. We point out that the gate offers control of the current, independent of the bias...

  5. Multiscale coupling of molecular dynamics and peridynamics

    Science.gov (United States)

    Tong, Qi; Li, Shaofan

    2016-10-01

    We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.

  6. Weak links between fast mobility and local structure in molecular and atomic liquids

    CERN Document Server

    Bernini, S; Leporini, D

    2016-01-01

    We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is characteristic of small $n$-alkanes and $n$-alcohols. Possible links between the fast mobility and ...

  7. Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics

    OpenAIRE

    Vila Verde, A.; Beltramo, Peter J.; Maranas, Janna K.

    2011-01-01

    We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala 10 , Ser 10 , Thr 10 , Arg 10 , Lys 10 , and Gln 10 ], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movemen...

  8. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  9. Multiscale Reactive Molecular Dynamics

    Science.gov (United States)

    2012-08-15

    as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP

  10. State-Dependent Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Ciann-Dong Yang

    2014-10-01

    Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.

  11. Entanglement dynamics between an isolated atom and a moving atom in the cavity

    Institute of Scientific and Technical Information of China (English)

    Deng Xiao-Juan; Fang Mao-Fa; Kang Guo-Dong

    2009-01-01

    The entanglement dynamics between an isolated atom and a moving atom interacting with a cavity field is investigated. The results show that there appears sudden death of entanglement between the isolated atom and the moving atom and that the time of entanglement sudden death (ESD) is independent of the initial state of the system. It is interesting that the isolated atom can also entangle with a cavity field, though they do not interact with each other originally, which stems from the fact that the entanglement between the isolated atom and the moving atom may turn into the entanglement between the isolated atom and the cavity.

  12. Atomic, Molecular, and Optical Physics Workshop Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Jr., Lloyd [University of Southern California

    1997-09-21

    This document contains the final reports from the five panels that comprised a Workshop held to explore future directions, scientific impacts and technological connections of research in Atomic, Molecular and Optical Physics. This workshop was sponsored by the Department of Energy, Office of Basic Energy Sciences, Chemical Sciences Division and was held at the Westfields International Conference Center in Chantilly, Virginia on September 21-24, 1997. The workshop was chaired by Lloyd Armstrong, Jr., University of Southern California and the five panels focused on the following topics: Panel A: Interactions of Atoms and Molecules with Photons - Low Field Daniel Kleppner (Massachusetts Institute of Technology), chair Panel B: Interactions of Atoms and Molecules with Photons - High Field Phil Bucksbaum (University of Michigan), chair Panel C: Surface Interactions with Photons, Electrons, Ions, Atoms and Molecules J. Wayne Rabalais (University of Houston), chair Panel D: Theory of Structure and Dynamics Chris Greene (University of Colorado), chair Panel E: Nano- and Mesocopic Structures Paul Alivisatos (Lawrence Berkeley National Laboratory), chair The choice of focus areas reflects areas of significant interest to DOE/BES but is clearly not intended to span all fields encompassed by the designation of atomic, molecular and optical physics, nor even all areas that would be considered for review and funding under DOE’s AMOP program. In a similar vein, not all research that might be suggested under these topics in this report would be appropriate for consideration by DOE’s AMOP program. The workshop format included overview presentations from each of the panel chairs, followed by an intensive series of panel discussion sessions held over a two-day period. The panels were comprised of scientists from the U. S. and abroad, many of whom are not supported by DOE’s AMOP Program. This workshop was held in lieu of the customary “Contractors Meeting” held annually for

  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. Dislocation glide in Ni-Al solid solutions from the atomic scale up: a molecular dynamics study; Etude du glissement des dislocations dans la solution solide Ni-Al par simulation a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Rodary, E

    2003-01-01

    The glide of an edge dislocation in solid solutions is studied by molecular dynamics, at fixed temperature and imposed external stress. We have optimized an EAM potential for Ni(1 a 8% A1): it well reproduces the lattice expansion, local atomic order, stacking fault energy as a function of composition, as well as the elastic properties of the {gamma}' phase with L1{sub 2} structure. On increasing the stress, the dislocation is first immobile, then glides with a velocity proportional to the stress and the velocity saturates on reaching the transverse sound velocity. However, only beyond a static threshold stress, {sigma}{sub s}, does the dislocation glide a distance large enough to allow macroscopic shear; the linear part of the velocity-stress curve extrapolates to zero at a dynamical threshold stress, {sigma}{sub d}, The friction coefficient, and the threshold stresses ({sigma}{sub s} and {sigma}{sub d}), increase with the A1 concentration and decrease with temperature (300 and 500 K). Close to the critical shear stress, {sigma}{sub s}, the dislocation glide is analysed with a 'stop and go' model. The latter yields the flight velocity between obstacles, the mean obstacle density and the distribution of the waiting time on each obstacle as a function of stress, composition and temperature. The obstacle to the glide is proposed to be the strong repulsion between Al atoms brought into nearest neighbour position by the glide process, and not the dislocation-solute interaction. The microscopic parameters so defined are introduced into a micro-mechanical model, which well reproduces the known behaviour of nickel base solid solutions. (author)

  15. R-matrix theory of atomic collisions. Application to atomic, molecular and optical processes

    Energy Technology Data Exchange (ETDEWEB)

    Burke, Philip G. [Queen' s Univ., Belfast (United Kingdom). School of Mathematics and Physics

    2011-07-01

    Commencing with a self-contained overview of atomic collision theory, this monograph presents recent developments of R-matrix theory and its applications to a wide-range of atomic molecular and optical processes. These developments include electron and photon collisions with atoms, ions and molecules required in the analysis of laboratory and astrophysical plasmas, multiphoton processes required in the analysis of superintense laser interactions with atoms and molecules and positron collisions with atoms and molecules required in antimatter studies of scientific and technological importance. Basic mathematical results and general and widely used R-matrix computer programs are summarized in the appendices. (orig.)

  16. R-Matrix Theory of Atomic Collisions Application to Atomic, Molecular and Optical Processes

    CERN Document Server

    Burke, Philip George

    2011-01-01

    Commencing with a self-contained overview of atomic collision theory, this monograph presents recent developments of R-matrix theory and its applications to a wide-range of atomic molecular and optical processes. These developments include electron and photon collisions with atoms, ions and molecules required in the analysis of laboratory and astrophysical plasmas, multiphoton processes required in the analysis of superintense laser interactions with atoms and molecules and positron collisions with atoms and molecules required in antimatter studies of scientific and technologial importance. Basic mathematical results and general and widely used R-matrix computer programs are summarized in the appendices.

  17. Current-induced dynamics in carbon atomic contacts

    Directory of Open Access Journals (Sweden)

    Jing-Tao Lü

    2011-12-01

    Full Text Available Background: The effect of electric current on the motion of atoms still poses many questions, and several mechanisms are at play. Recently there has been focus on the importance of the current-induced nonconservative forces (NC and Berry-phase derived forces (BP with respect to the stability of molecular-scale contacts. Systems based on molecules bridging electrically gated graphene electrodes may offer an interesting test-bed for these effects.Results: We employ a semi-classical Langevin approach in combination with DFT calculations to study the current-induced vibrational dynamics of an atomic carbon chain connecting electrically gated graphene electrodes. This illustrates how the device stability can be predicted solely from the modes obtained from the Langevin equation, including the current-induced forces. We point out that the gate offers control of the current, independent of the bias voltage, which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed. Molecular dynamics including current-induced forces enables an energy redistribution mechanism among the modes, mediated by anharmonic interactions, which is found to be vital in the description of the electrical heating.Conclusion: We have developed a semiclassical Langevin equation approach that can be used to explore current-induced dynamics and instabilities. We find instabilities at experimentally relevant bias and gate voltages for the carbon-chain system.

  18. Atomic and molecular manipulation with the scanning tunneling microscope.

    Science.gov (United States)

    Stroscio, J A; Eigler, D M

    1991-11-29

    The prospect of manipulating matter on the atomic scale has fascinated scientists for decades. This fascination may be motivated by scientific and technological opportunities, or from a curiosity about the consequences of being able to place atoms in a particular location. Advances in scanning tunneling microscopy have made this prospect a reality; single atoms can be placed at selected positions and structures can be built to a particular design atom-by-atom. Atoms and molecules may be manipulated in a variety of ways by using the interactions present in the tunnel junction of a scanning tunneling microscope. Some of these recent developments and some of the possible uses of atomic and molecular manipulation as a tool for science are discussed.

  19. 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.

  20. Optical dynamics of molecular aggregates

    NARCIS (Netherlands)

    de Boer, Steven

    2006-01-01

    The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si

  1. Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.

    Energy Technology Data Exchange (ETDEWEB)

    Ogata, S.

    1998-01-27

    Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.

  2. Homogenizing atomic dynamics by fractional differential equations

    Science.gov (United States)

    Tang, Shaoqiang; Ying, Yuping

    2017-10-01

    In this paper, we propose two ways to construct fractional differential equations (FDE) for approximating atomic chain dynamics. Taking harmonic chain as an example, we add a power function of fractional order to Taylor expansion of the dispersion relation, and determine the parameters by matching two selected wave numbers. This approximate function leads to an FDE after considering both directions for wave propagation. As an alternative, we consider the symbol of the force term, and approximate it by a similar function. It also induces an FDE. Both approaches produce excellent agreement with the harmonic chain dynamics. The accuracy may be improved by optimizing the selected wave numbers, or starting with higher order Taylor expansions. When resolved in the lattice constant, the resulting FDE's faithfully reproduce the lattice dynamics. When resolved in a coarse grid instead, they systematically generate homogenized algorithms. Numerical tests are performed to verify the proposed approaches. Moreover, FDE's are also constructed for diatomic chain and anharmonic lattice, to illustrate the generality of the proposed approaches.

  3. Dynamics and Thermodynamics of Many Particle Cold Atom Systems

    Science.gov (United States)

    2016-05-05

    AFRL-AFOSR-VA-TR-2016-0219 Dynamics and Thermodynamics of Many Particle Cold Atom Systems Anatoli Polkovnikov TRUSTEES OF BOSTON UNIVERSITY Final...TITLE AND SUBTITLE Dynamics and Thermodynamics of Many Particle Cold Atom Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-13-1-0039 5c. PROGRAM...FA9550-13-1-0039 “Dynamics and Thermodynamics of Many Particle Cold Atom Systems” by Anatoli Polkovnikov, Professor of Physics Department of Physics

  4. 1978 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  5. 1979 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  6. Quantum molecular dynamics simulations of dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  7. Bead-Fourier path integral molecular dynamics

    Science.gov (United States)

    Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto

    2003-06-01

    Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.

  8. Atomic Quadrupole Moment Measurement Using Dynamic Decoupling.

    Science.gov (United States)

    Shaniv, R; Akerman, N; Ozeri, R

    2016-04-01

    We present a method that uses dynamic decoupling of a multilevel quantum probe to distinguish small frequency shifts that depend on m_{j}^{2}, where m_{j}^{2} is the angular momentum of level |j⟩ along the quantization axis, from large noisy shifts that are linear in m_{j}, such as those due to magnetic field noise. Using this method we measured the electric-quadrupole moment of the 4D_{5/2} level in ^{88}Sr^{+} to be 2.973_{-0.033}^{+0.026}ea_{0}^{2}. Our measurement improves the uncertainty of this value by an order of magnitude and thus helps mitigate an important systematic uncertainty in ^{88}Sr^{+} based optical atomic clocks and verifies complicated many-body quantum calculations.

  9. Trapping of molecular Oxygen together with Lithium atoms

    CERN Document Server

    Akerman, Nitzan; Segev, Yair; Bibelnik, Natan; Narevicius, Julia; Narevicius, Edvardas

    2016-01-01

    We demonstrate simultaneous deceleration and trapping of a cold atomic and molecular mixture. This is the first step towards studies of cold atom-molecule collisions at low temperatures as well as application of sympathetic cooling. Both atoms and molecules are cooled in a supersonic expansion and are loaded into a moving magnetic trap which brings them to rest via the Zeeman interaction from an initial velocity of 375 m/s. We use a beam seeded with molecular Oxygen, and entrain it with Lithium atoms by laser ablation prior to deceleration. The deceleration ends with loading of the mixture into a static quadrupole trap, which is generated by two permanent magnets. We estimate $10^9$ trapped O$_2$ molecules and $10^5$ Li atoms with background pressure limited lifetime on the order of 1 second. With further improvements to Lithium entrainment we expect that sympathetic cooling of molecules is within reach.

  10. Trapping of Molecular Oxygen together with Lithium Atoms

    Science.gov (United States)

    Akerman, Nitzan; Karpov, Michael; Segev, Yair; Bibelnik, Natan; Narevicius, Julia; Narevicius, Edvardas

    2017-08-01

    We demonstrate simultaneous deceleration and trapping of a cold atomic and molecular mixture. This is the first step towards studies of cold atom-molecule collisions at low temperatures as well as application of sympathetic cooling. Both atoms and molecules are cooled in a supersonic expansion and are loaded into a moving magnetic trap that brings them to rest via the Zeeman interaction from an initial velocity of 375 m /s . We use a beam seeded with molecular oxygen, and entrain it with lithium atoms by laser ablation prior to deceleration. The deceleration ends with loading of the mixture into a static quadrupole trap, which is generated by two permanent magnets. We estimate 1 09 trapped O2 molecules and 1 05 Li atoms with background pressure limited lifetime on the order of 1 sec. With further improvements to lithium entrainment we expect that sympathetic cooling of molecules is within reach.

  11. New trends in atomic and molecular physics advanced technological applications

    CERN Document Server

    2013-01-01

    The field of Atomic and Molecular Physics (AMP) has reached significant advances in high–precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy , astrophysics , fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) To...

  12. Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

    Science.gov (United States)

    Continetti, R. E.; Balko, B. A.; Lee, Y. T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

  13. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  14. Atomic and Molecular Aspects of Astronomical Spectra

    CERN Document Server

    Sochi, Taha

    2012-01-01

    In the first section we present the atomic part where a C2+ atomic target was prepared and used to generate theoretical data to investigate recombination lines arising from electron-ion collisions in thin plasma. R-matrix method was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation. The data were used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, emissivities and dielectronic recombination coefficients. The data were cast in a line list containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature. The electron temperature investigation was also extended to include free electron energy analysis to investigate...

  15. 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.

  16. Molecular Dynamics study of Pb overlayer on Cu(100)

    Science.gov (United States)

    Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.

    1991-01-01

    Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.

  17. Molecular Dynamics study of Pb overlayer on Cu(100)

    Science.gov (United States)

    Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.

    1991-01-01

    Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.

  18. Historical Account And Branching To Rarefied Gas Dynamics Of Atomic and Molecular Beams : A Continuing And Fascinating Odyssey Commemorated By Nobel Prizes Awarded To 23 Laureates In Physics And Chemistry

    Science.gov (United States)

    Campargue, Roger

    2005-05-01

    This Historical Account derived in part from D. R. Herschbach was presented as an opening lecture of the Molecular Beam Session organized at the 24th International Symposium on Rarefied Gas Dynamics held in Bari, Italy, in July 2004. The emphasis is on the impressive results due to the molecular beam techniques in the last century. The first section summarizes the historical beam experiments performed by 14 Nobel Prize laureates having used the thermally effusive sources to establish the basic principles of Modern Physics. The second section is on the branching of Molecular Beams to Rarefied Gas Dynamics having permitted to investigate the physics of supersonic free jets and transform the molecular beam techniques. Finally, the last section relates the spectacular molecular beam experiments in helium free jet ultracooling, molecular spectroscopy, chemical reaction dynamics, clustering and modification of low density matter, and biomolecule mass spectrometry, rewarded by nine Nobel Prizes in Chemistry from 1986 to 2002.

  19. From Molecular Dynamics to Brownian Dynamics

    CERN Document Server

    Erban, Radek

    2014-01-01

    Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

  20. Atomic dynamics in the mode-mode competition system

    Institute of Scientific and Technical Information of China (English)

    Wu Qin; Fang Mao-Fa

    2004-01-01

    The atomic dynamical properties in the system with competing k-photon and l-photon transitions are studied fully by means of quantum theory. We discuss the influences of the mode-mode competition, the relative competing strengths of the atom and the two-mode field, and the initial state of the system on the atomic dynamics. We show that the presence of the mode-mode competition can result in quite a periodical collapses-revivals of the atomic inversion and the increase of the initial photons of the system can lead to the collapse-revival phenomenon and prolong the revival time of the atomic inversion.

  1. Dynamical Non-Equilibrium Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Giovanni Ciccotti

    2013-12-01

    Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.

  2. Dynamic splitting and merging of an atom cloud on an atom chip

    Institute of Scientific and Technical Information of China (English)

    Ke Min; Yan Bo; Cheng Feng; Wang Yu-Zhu

    2009-01-01

    Chip-based atom interferometers bring together the advantages of atom chips and Bose-Einstein condensates. Their central prerequisite is that a condensate can be coherently split into two halves with a determined relative phase. This paper demonstrates the dynamical splitting and merging of an atom cloud with two U-wires on an atom chip. Symmetrical and asymmetrical splittings are realized by applying a bias field with different directions and magnitudes. The trajectories of the splitting are consistent with theoretical calculations. The atom chip is a good candidate for constructing an atom interferometer.

  3. Fracture of Cu Nanowire upon Stretch by Atomic Scale Molecular Dynamic Simulation%铜纳米线拉伸断裂过程的原子尺度分子动力学模拟

    Institute of Scientific and Technical Information of China (English)

    陈念科; 李贤斌

    2014-01-01

    基于经典力学势函数的分子动力学模拟方法研究铜纳米线的拉伸断裂过程,并分析断裂前应力、应变和位错行为的关系及断裂后的形貌演化。结果表明:纳米线两端的锥形结构可阻塞位错运动,从而提高其断裂强度;断裂后断口处尖锐的尖端结构形貌会发生自发的回缩和钝化,该过程是尖端上储存的弹性能和的高能结构(如孤立原子、孪晶界和表面弯折等)的自我修复,最终在表面上形成许多能量较低的(111)小平面所致;其物理机理是在温度激活下的能量最小化过程。%To explore the fracture mechanism of metal nanowires,a fracture process of Cu nanowire upon stretch was theoretically studied by molecular dynamic (MD)simulations based on embedded-atom method (EAM)potential.The relationship between stress,strain and dislocation before fracture as well as the morphology evolution after fracture was analyzed.The results demonstrate that the tips on the two ends of the nanowire can stuck the dislocation motion.Then the stacking fault by the first partial dislocation could be annihilated by a full dislocation formed by another partial dislocation.This process can thus enhance the fracture strength.The sharp structure after fracture can retract and become obtuse spontaneously.The atomic scale analysis of the morphology change demonstrates that the fracture is a process of eliminating the high energy structures,such as isolated atoms,twin boundary and surface kink.The surface of the fracture finally emerge many (111)facets with lower energies. Therefore the physical mechanism is attributed to the rule of energy minimization.

  4. Molecular Dynamics Simulations of Helium Behaviour in Titanium Crystals

    Institute of Scientific and Technical Information of China (English)

    SUN Tie-Ying; LONG Xing-Gui; WANG Jun; HOU Qing; WU Zhong-Cheng; PENG Shu-Ming; LUO Shun-Zhong

    2008-01-01

    Molecular dynamics simulations are performed to investigate the behaviour of helium atoms in titanium at a temperature of 300 K.The nucleation and growth of helium bubble has been simulated up to 50 helium atoms.The approach to simulate the bubble growth is to add helium atoms one by one to the bubble and let the system evolve.The titanium cohesion is based on the tight binding scheme derived from the embedded atom method,and the helium-titanium interaction is characterized by fitted potential in the form of a Lennard-Jones function.The pressure in small helium bubbles is approximately calculated.The simulation results show that the pressure will decrease with the increasing bubble size,while increase with the increasing helium atoms.An analytic function about the quantitative relationship of the pressure with the bubble size and number of helium atoms is also fitted.

  5. The atomic structural dynamics of γ-Al2O3 supported Ir-Pt nanocluster catalysts prepared from a bimetallic molecular precursor: a study using aberration-corrected electron microscopy and X-ray absorption spectroscopy.

    Science.gov (United States)

    Small, Matthew W; Sanchez, Sergio I; Menard, Laurent D; Kang, Joo H; Frenkel, Anatoly I; Nuzzo, Ralph G

    2011-03-16

    This study describes a prototypical, bimetallic heterogeneous catalyst: compositionally well-defined Ir-Pt nanoclusters with sizes in the range of 1-2 nm supported on γ-Al(2)O(3). Deposition of the molecular bimetallic cluster [Ir(3)Pt(3)(μ-CO)(3)(CO)(3)(η-C(5)Me(5))(3)] on γ-Al(2)O(3), and its subsequent reduction with hydrogen, provides highly dispersed supported bimetallic Ir-Pt nanoparticles. Using spherical aberration-corrected scanning transmission electron microscopy (C(s)-STEM) and theoretical modeling of synchrotron-based X-ray absorption spectroscopy (XAS) measurements, our studies provide unambiguous structural assignments for this model catalytic system. The atomic resolution C(s)-STEM images reveal strong and specific lattice-directed strains in the clusters that follow local bonding configurations of the γ-Al(2)O(3) support. Combined nanobeam diffraction (NBD) and high-resolution transmission electron microscopy (HRTEM) data suggest the polycrystalline γ-Al(2)O(3) support material predominantly exposes (001) and (011) surface planes (ones commensurate with the zone axis orientations frequently exhibited by the bimetallic clusters). The data reveal that the supported bimetallic clusters exhibit complex patterns of structural dynamics, ones evidencing perturbations of an underlying oblate/hemispherical cuboctahedral cluster-core geometry with cores that are enriched in Ir (a result consistent with models based on surface energetics, which favor an ambient cluster termination by Pt) due to the dynamical responses of the M-M bonding to the specifics of the adsorbate and metal-support interactions. Taken together, the data demonstrate that strong temperature-dependent charge-transfer effects occur that are likely mediated variably by the cluster-support, cluster-adsorbate, and intermetallic bonding interactions.

  6. Fusing atomic W states via quantum Zeno dynamics.

    Science.gov (United States)

    Ji, Y Q; Shao, X Q; Yi, X X

    2017-05-03

    We propose a scheme for preparation of large-scale entangled W states based on the fusion mechanism via quantum Zeno dynamics. By sending two atoms belonging to an n-atom W state and an m-atom W state, respectively, into a vacuum cavity (or two separate cavities), we may obtain a (n + m - 2)-atom W state via detecting the two-atom state after interaction. The present scheme is robust against both spontaneous emission of atoms and decay of cavity, and the feasibility analysis indicates that it can also be realized in experiment.

  7. Molecular Dynamics for Dense Matter

    CERN Document Server

    Maruyama, Toshiki; Chiba, Satoshi

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...

  8. A Molecular Dynamics Approach to Grain Boundary Structure and Migration

    DEFF Research Database (Denmark)

    Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans

    1974-01-01

    It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...

  9. Atomic and molecular layer deposition for surface modification

    Science.gov (United States)

    Vähä-Nissi, Mika; Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija; Johansson, Leena-Sisko; Koskinen, Jorma T.; Harlin, Ali

    2014-06-01

    Atomic and molecular layer deposition (ALD and MLD, respectively) techniques are based on repeated cycles of gas-solid surface reactions. A partial monolayer of atoms or molecules is deposited to the surface during a single deposition cycle, enabling tailored film composition in principle down to molecular resolution on ideal surfaces. Typically ALD/MLD has been used for applications where uniform and pinhole free thin film is a necessity even on 3D surfaces. However, thin - even non-uniform - atomic and molecular deposited layers can also be used to tailor the surface characteristics of different non-ideal substrates. For example, print quality of inkjet printing on polymer films and penetration of water into porous nonwovens can be adjusted with low-temperature deposited metal oxide. In addition, adhesion of extrusion coated biopolymer to inorganic oxides can be improved with a hybrid layer based on lactic acid.

  10. The virtual atomic and molecular data centre (VAMDC) consortium

    Science.gov (United States)

    Dubernet, M. L.; Antony, B. K.; Ba, Y. A.; Babikov, Yu L.; Bartschat, K.; Boudon, V.; Braams, B. J.; Chung, H.-K.; Daniel, F.; Delahaye, F.; Del Zanna, G.; de Urquijo, J.; Dimitrijević, M. S.; Domaracka, A.; Doronin, M.; Drouin, B. J.; Endres, C. P.; Fazliev, A. Z.; Gagarin, S. V.; Gordon, I. E.; Gratier, P.; Heiter, U.; Hill, C.; Jevremović, D.; Joblin, C.; Kasprzak, A.; Krishnakumar, E.; Leto, G.; Loboda, P. A.; Louge, T.; Maclot, S.; Marinković, B. P.; Markwick, A.; Marquart, T.; Mason, H. E.; Mason, N. J.; Mendoza, C.; Mihajlov, A. A.; Millar, T. J.; Moreau, N.; Mulas, G.; Pakhomov, Yu; Palmeri, P.; Pancheshnyi, S.; Perevalov, V. I.; Piskunov, N.; Postler, J.; Quinet, P.; Quintas-Sánchez, E.; Ralchenko, Yu; Rhee, Y.-J.; Rixon, G.; Rothman, L. S.; Roueff, E.; Ryabchikova, T.; Sahal-Bréchot, S.; Scheier, P.; Schlemmer, S.; Schmitt, B.; Stempels, E.; Tashkun, S.; Tennyson, J.; Tyuterev, Vl G.; Vujčić, V.; Wakelam, V.; Walton, N. A.; Zatsarinny, O.; Zeippen, C. J.; Zwölf, C. M.

    2016-04-01

    The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases. .

  11. Dynamics of complex fluids in rotary atomization

    Science.gov (United States)

    Keshavarz, Bavand; McKinley, Gareth; MIT, Mechanical Engineering Department Team

    2016-11-01

    We study the dynamics of fragmentation for different Newtonian and viscoelastic liquids in rotary atomization. In this process, at the rim of a spinning cup, the centripetal acceleration destabilizes the formed liquid torus due to the Rayleigh-Taylor instability. The resulting ligaments leave the liquid torus with a remarkably repeatable spacing that scales linearly with the inverse of the rotation rate. Filaments then follow a well-defined geometrical path-line that is described by the involute of the circle. Knowing the geometry of this phenomenon we derive the detailed kinematics of this process and compare it with the experimental observations. We show that the ligaments elongate tangentially to the involute of the circle and thin radially as they separate from the cup. A theoretical form is derived for the spatial variation of the filament deformation rate. Once the ligaments are far from the cup they breakup into droplets since they are not stretched fast enough (compared to the critical rate of capillary thinning). We couple these derivations with the known properties of Newtonian and viscoelastic liquids to provide a physical analysis for this fragmentation process that is compared in detail with our experiments.

  12. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  13. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  14. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  15. Scalable molecular dynamics with NAMD.

    Science.gov (United States)

    Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus

    2005-12-01

    NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.

  16. Rheology via nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G.

    1982-10-01

    The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.

  17. Molecular dynamical modelling of endohedral fullerenes formation in plasma

    Science.gov (United States)

    Fedorov, A. S.; Kovaleva, E. A.; Lubkova, T. A.; Popov, Z. I.; Kuzubov, A. A.; Visotin, M. A.; Irle, S.

    2016-02-01

    The initial stages of fullerene and endohedral metallofullerene (EMF) synthesis in carbon-helium plasma at 1500 K and 2500 K have been simulated with quantum chemical molecular dynamics (MD) based on density-functional tight-binding (DFTB). The cases of formation of large (>100 atoms) sp2-carbon clusters with scandium atoms inside were observed. These clusters are considered as precursors of fullerenes or EMFs, and thus it is shown that formation of EMFs can be explained within the framework of "shrinking hot giant" mechanism. Also, the dependence of formation rates on plasma parameters, including temperature, buffer gas and metal atoms concentrations, has been studied.

  18. Atoms, molecules and photons An introduction to atomic-, molecular- and quantum-physics

    CERN Document Server

    Demtröder, Wolfgang

    2006-01-01

    This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed over the last two centuries both by many experimental discoveries and, from the theoretical side, by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of classical description. The interaction of electromagnetic radiation with atoms and molecules and its potential for spectroscopy is outlined in more detail and in particular lasers as modern spectroscopic tools are discussed more thoroughly. Many examples and problems with solutions are offered to encourage readers to actively engage in experimentation.

  19. Dynamical Properties of Scaled Atomic Wehrl Entropy of Multiphoton JCM in the Presence of Atomic Damping

    Directory of Open Access Journals (Sweden)

    S. Abdel-Khalek

    2013-01-01

    Full Text Available We study the dynamics of the atomic inversion, scaled atomic Wehrl entropy, and marginal atomic Q-function for a single two-level atom interacting with a one-mode cavity field taking in the presence of atomic damping. We obtain the exact solution of the master equation in the interaction picture using specific initial conditions. We examine the effects of atomic damping parameter and number of multiphoton transition on the scaled atomic Wehrl entropy, atomic Q-function, and their marginal distribution. We observe an interesting monotonic relation between the different physical quantities in the case of different values of the number of photon transition during the time evolution.

  20. Better, Cheaper, Faster Molecular Dynamics

    Science.gov (United States)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

  1. Molecular dynamical simulations of melting behaviors of metal clusters

    Directory of Open Access Journals (Sweden)

    Ilyar Hamid

    2015-04-01

    Full Text Available The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002] for the statically stable structures.

  2. 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.

  3. 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.

  4. 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.

  5. From the warm magnetized atomic medium to molecular clouds

    CERN Document Server

    Hennebelle, P; Vázquez-Semadeni, E; Klessen, R; Audit, E

    2008-01-01

    {It has recently been proposed that giant molecular complexes form at the sites where streams of diffuse warm atomic gas collide at transonic velocities.} {We study the global statistics of molecular clouds formed by large scale colliding flows of warm neutral atomic interstellar gas under ideal MHD conditions. The flows deliver material as well as kinetic energy and trigger thermal instability leading eventually to gravitational collapse.} {We perform adaptive mesh refinement MHD simulations which, for the first time in this context, treat self-consistently cooling and self-gravity.} {The clouds formed in the simulations develop a highly inhomogeneous density and temperature structure, with cold dense filaments and clumps condensing from converging flows of warm atomic gas. In the clouds, the column density probability density distribution (PDF) peaks at $\\sim 2 \\times 10^{21} \\psc$ and decays rapidly at higher values; the magnetic intensity correlates weakly with density from $n \\sim 0.1$ to $10^4 \\pcc$, an...

  6. Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former

    Science.gov (United States)

    Kim, Jeongmin; Sung, Bong June

    2015-06-01

    The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

  7. Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.

    Science.gov (United States)

    Kim, Jeongmin; Sung, Bong June

    2015-06-17

    The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

  8. Molecular dynamics of interface rupture

    Science.gov (United States)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  9. Molecular dynamics of interface rupture

    Science.gov (United States)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  10. Capillary dynamics driven by molecular self-layering.

    Science.gov (United States)

    Wu, Pingkeng; Nikolov, Alex; Wasan, Darsh

    2017-02-10

    Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction. Here, the capillary rise dynamics of simple molecular fluids in cylindrical capillary is explained by the molecular self-layering model. The proposed model considers the role of the molecular shape on self-layering and its effect on the molecularly thin film viscosity in regards to the advancing (dynamic) contact angle. The model was tested to explain the capillary rise dynamics of fluids of spherical, cylindrical, and disk shape molecules in borosilicate glass capillaries. The good agreement between the capillary rise data and SFA data from the literature for simple fluid self-layering shows the validity of the present model. The present model provides new insights into the design of many applications where dynamic wetting is important because it reveals the significant impact of molecular self-layering close to the wall on dynamic wetting.

  11. Quantum Dynamical Theory for Squeezed Atom Laser

    Institute of Scientific and Technical Information of China (English)

    JING Hui; HAN Yi-Ang; CHEN Jing-Ling; MIAO Yuan-Xiu

    2000-01-01

    A model for the squeezed output coupler of the trapped Bose-Einstein condensed atoms is established with a simple many-boson system of two states with linear coupling, by preparing an initially squeezed light field. In the Bogoliubov approximation, its solutions show that the quadrature squeezing effect mutually oscillates between the coupling light field and the output atomic field. This manifests that the initially squeezed light will transform into a coherent state after some period of coupling interaction while the output atomic field is in a squeezed state.

  12. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecul....... As a particularly intriguing example of this, the lateral pressure profiles of raft-like and non-raft systems indicate that the lipid composition of membrane domains may have a major impact on membrane protein activation.......We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...

  13. Observation of dynamic atom-atom correlation in liquid helium in real space.

    Science.gov (United States)

    Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

    2017-05-04

    Liquid (4)He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that (4)He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

  14. Cold atom dynamics in crossed laser beam waveguides

    CERN Document Server

    Torrontegui, E; Ruschhaupt, A; Guéry-Odelin, D; Muga, J G

    2010-01-01

    We study the dynamics of neutral cold atoms in an $L$-shaped crossed-beam optical waveguide formed by two perpendicular red-detuned lasers of different intensities and a blue-detuned laser at the corner. Complemented with a vibrational cooling process this setting works as a one-way device or "atom diode".

  15. Multi-wavelength Study of Diffuse Atomic and Molecular Gas

    Science.gov (United States)

    Federman, Steven Robert; Rice, Johnathan; Flagey, Nicolas; Ritchey, Adam M.; Welty, Daniel E.; Goldsmith, Paul; Langer, William; Pineda, Jorge L.; Lambert, David L.; Lemaire, Jean-Louis

    2017-06-01

    Diffuse atomic and molecular gas is revealed through a combination of absorption lines against background targets and emission. We describe a project that combines results on ultraviolet (UV) and visible absorption with those obtained from the Herschel key program GOTC+ (Galactic Observations of Terahertz C+) to develop a comprehensive picture of neutral diffuse gas in the Galaxy. [C II], H I, and CO emission acquired for the GOTC+ survey reveal the presence of warm neutral atomic gas, cold neutral atomic gas, CO-dark H2 gas (molecular gas not seen in CO emission), and denser molecular gas in different kinematic components. We derive the component structure (number of clouds and their column densities) seen in absorption at visible wavelengths from Ca II, Ca I, K I, CH, CH+, and CN and compare that to the emission from [C II], H I, and CO and its isotopologues. Absorption lines from additional atoms (including C I, O I, and Ni II) and molecules (CO) from UV spectra obtained with the Hubble Space Telescope are used to expand the kinematic correspondences. Preliminary results on physical conditions (gas temperature and density) inferred from analyses of CN chemistry and excitation of neutral and singly-ionized carbon, neutral oxygen, and CO are also presented.

  16. Decay dynamics in a strongly driven atom-molecule coupled system

    CERN Document Server

    Rakshit, Arpita; Deb, Bimalendu

    2013-01-01

    Within the framework of master equation, we study decay dynamics of an atom-molecule system strongly coupled by two photoassociation lasers. Summing over the infinite number of electromagnetic vacuum modes that are coupled to the laser-dressed atom-molecule system, we obtain an integro-differential master equation for the the system's reduced density matrix. The equation is numerically solved to describe system dynamics in the presence of decay. In particular, we discuss correlated spontaneous emission from a pair of electronically excited diatomic ro-vibrational states due to their laser induced coupling to the ground continuum of atomic scattering states. This allows us to calculate time-dependence of emitted radiation intensity. It exhibits quantum beats due to coherent dynamics. The phase difference between the two driving fields is found to significantly affect the decay dynamics and the beats. Our results demonstrate the possibility to control decay from the molecular excited states and the decoherence ...

  17. Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation.

    Science.gov (United States)

    Doi, Kentaro; Takeuchi, Hiroshi; Nii, Ryosuke; Akamatsu, Shingo; Kakizaki, Toshiya; Kawano, Satoyuki

    2013-08-28

    This study has investigated the formation patterns resulting from the self-assembly of deoxyribonucleic acid (DNA) on highly oriented pyrolytic graphite (HOPG), using both experimental and molecular dynamics approaches. Under optimized conditions based on pretreatment of HOPG surface and specific solution concentrations, DNA is found to self-assemble to form various patterned networks. The associated self-assembly mechanism is elucidated using coarse-grained molecular dynamics simulations and fractal dimension analysis. The results of this work demonstrate an effective technique allowing the formation of arrays of negatively charged biomacromolecules on negatively charged HOPG surfaces.

  18. Molecular Dynamics in the Vacuum Ultraviolet

    Science.gov (United States)

    1989-01-30

    CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of

  19. 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.

  20. Brownian motion from molecular dynamics

    CERN Document Server

    Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun

    2010-01-01

    Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.

  1. Atomic and molecular physics in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Toburen, L.H.

    1990-09-01

    The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

  2. Large scale molecular dynamics simulations of a liquid crystalline droplet with fast multipole implementations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Z.; Lupo, J.; Patnaik, S.S.; McKenney, A.; Pachter, R.

    1999-07-01

    The Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in the group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4{prime}-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.

  3. Atomic and molecular processes in JT-60U divertor plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Takenaga, H.; Shimizu, K.; Itami, K. [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment] [and others

    1997-01-01

    Atomic and molecular data are indispensable for the understanding of the divertor characteristics, because behavior of particles in the divertor plasma is closely related to the atomic and molecular processes. In the divertor configuration, heat and particles escaping from the main plasma flow onto the divertor plate along the magnetic field lines. In the divertor region, helium ash must be effectively exhausted, and radiation must be enhanced for the reduction of the heat load onto the divertor plate. In order to exhaust helium ash effectively, the difference between behavior of neutral hydrogen (including deuterium and tritium) and helium in the divertor plasma should be understood. Radiation from the divertor plasma generally caused by the impurities which produced by the erosion of the divertor plate and/or injected by gas-puffing. Therefore, it is important to understand impurity behavior in the divertor plasma. The ions hitting the divertor plate recycle through the processes of neutralization, reflection, absorption and desorption at the divertor plates and molecular dissociation, charge-exchange reaction and ionization in the divertor plasma. Behavior of hydrogen, helium and impurities in the divertor plasmas can not be understood without the atomic and molecular data. In this report, recent results of the divertor study related to the atomic and molecular processes in JT-60U were summarized. Behavior of neural deuterium and helium was discussed in section 2. In section 3, the comparisons between the modelling of the carbon impurity transport and the measurements of C II and C IV were discussed. In section 4, characteristics of the radiative divertor using Ne puffing were reported. The new diagnostic method for the electron density and temperature in the divertor plasmas using the intensity ratios of He I lines was described in section 5. (author)

  4. Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

    Science.gov (United States)

    Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

    2009-07-02

    Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or

  5. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  6. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    Energy Technology Data Exchange (ETDEWEB)

    Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  7. Molecular dynamics of membrane proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  8. Programming an Interpreter Using Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    C.A. Middelburg

    2007-01-01

    Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.

  9. Imaging and dynamics of light atoms and molecules on graphene.

    Science.gov (United States)

    Meyer, Jannik C; Girit, C O; Crommie, M F; Zettl, A

    2008-07-17

    Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunnelling microscope revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunnelling microscopy has limited applicability due to restrictions in, for example, sample conductivity, cleanliness, and data acquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM), has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high-atomic-number) atoms can now be detected by TEM even when embedded within a semiconductor material. But detecting an individual low-atomic-number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM owing to the very low contrast of light elements. Here we demonstrate a means to observe, by conventional TEM, even the smallest atoms and molecules: on a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic-scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.

  10. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Science.gov (United States)

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  11. The Atomic to Molecular Transition in the Interstellar Medium

    Science.gov (United States)

    Goldsmith, Paul F.

    2012-01-01

    Study of H2 in UV and IR continues to surprise us with complexity of excitation state, OPR, and role in astrochemistry. Atomic H in molecular clouds is a very powerful tool suggesting that they are not "young" but that it takes millions of years to convert primarily atomic hydrogen clouds to 99.9% molecular form. Laboratory data suggests that H2 formation is efficient over broader range of temperatures than thought to be the case a few years ago, but range is still limited. Issues of complex grain morphology and surface structure make this a very difficult field in which to obtain definitively meaningful results. Ongoing and future observations of CI and CII will improve our understanding of the structure of clouds, their total mass, and how they have evolved and will continue to do so.

  12. Dynamical and non-additive atomic van der Waals phases

    CERN Document Server

    Impens, François; Neto, Paulo A Maia

    2013-01-01

    We investigate dynamical corrections to the van der Waals phase induced by the non-unitary evolution of atomic waves propagating near a perfectly conducting surface. These corrections reflect the interplay between field retardation effects and the dynamics of the external atomic degrees of freedom. The dynamical atom-surface interaction phase shift contains both local and non-local contributions. We derive the local contributions and show that they are equivalent to coarse-graining the instantaneous van der Waals potential over the time scale corresponding to the round-trip travel time of light between atom and surface. We show that the non-local phase contributions are non-additive, and propose to use this property in a multiple-path van der Waals interferometer in order to isolate them from the standard (and much larger) quasi-static van der Waals phase.

  13. Dynamic of cold-atom tips in anharmonic potentials

    Directory of Open Access Journals (Sweden)

    Tobias Menold

    2016-10-01

    Full Text Available Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion.Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics.Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control.

  14. Super-atom molecular orbital excited states of fullerenes.

    Science.gov (United States)

    Johansson, J Olof; Bohl, Elvira; Campbell, Eleanor E B

    2016-09-13

    Super-atom molecular orbitals are orbitals that form diffuse hydrogenic excited electronic states of fullerenes with their electron density centred at the centre of the hollow carbon cage and a significant electron density inside the cage. This is a consequence of the high symmetry and hollow structure of the molecules and distinguishes them from typical low-lying molecular Rydberg states. This review summarizes the current experimental and theoretical studies related to these exotic excited electronic states with emphasis on femtosecond photoelectron spectroscopy experiments on gas-phase fullerenes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'.

  15. Rapid formation of molecular clouds from turbulent atomic gas

    Science.gov (United States)

    Glover, S. C. O.; Mac Low, M.-M.

    The characteristic lifetimes of molecular clouds remain uncertain and a topic of frequent debate, with arguments having recently been advanced both in support of short-lived clouds, with lifetimes of a few Myr or less (see e.g. Elmegreen 2000; Hartmann et al. 2001) and in support of much longer-lived clouds, with lifetimes of the order of 10 Myr or more (see e.g. Tassis & Mouschovias, 2004; Goldsmith & Li, 2005). An argument that has previously been advanced in favour of longer lived clouds is the apparent difficulty involved in converting sufficient atomic hydrogen to molecular hydrogen within the short timescale required by the rapid cloud formation scenario. However, previous estimates of the time required for this conversion to occur have not taken into account the effects of the supersonic turbulence which is inferred to be present in the atomic gas. In this contribution, we present results from a set of high resolution three-dimensional simulations of turbulence in gravitationally unstable atomic gas. These simulations were performed using a modified version of the ZEUS-MP hydrodynamical code (Norman 2000), and include a detailed treatment of the thermal balance of the gas and of the formation of molecular hydrogen. The effects of photodissociation of H2 by the Galactic UV field are also included, with a simple local approximation used to compute the effects of H2 self-shielding. The results of our simulations demonstrate that H2 formation occurs rapidly in turbulent atomic gas. Starting from purely atomic gas, large quantities of molecular gas can be produced on timescales of less than a Myr, given turbulent velocity dispersions and magnetic field strengths consistent with observations. Moreover, as our simulations underestimate the effectiveness of H2 self-shielding and dust absorption, we can be confident that the molecular fractions which we compute are strong lower limits on the true values. The formation of large quantities of molecular gas on the

  16. Dual-Beam Atom Laser Driven by Spinor Dynamics

    Science.gov (United States)

    Thompson, Robert; Lundblad, Nathan; Maleki, Lute; Aveline, David

    2007-01-01

    An atom laser now undergoing development simultaneously generates two pulsed beams of correlated Rb-87 atoms. (An atom laser is a source of atoms in beams characterized by coherent matter waves, analogous to a conventional laser, which is a source of coherent light waves.) The pumping mechanism of this atom laser is based on spinor dynamics in a Bose-Einstein condensate. By virtue of the angular-momentum conserving collisions that generate the two beams, the number of atoms in one beam is correlated with the number of atoms in the other beam. Such correlations are intimately linked to entanglement and squeezing in atomic ensembles, and atom lasers like this one could be used in exploring related aspects of Bose-Einstein condensates, and as components of future sensors relying on atom interferometry. In this atom-laser apparatus, a Bose-Einstein condensate of about 2 x 10(exp 6) Rb-87 atoms at a temperature of about 120 micro-K is first formed through all-optical means in a relatively weak singlebeam running-wave dipole trap that has been formed by focusing of a CO2-laser beam. By a technique that is established in the art, the trap is loaded from an ultrahigh-vacuum magnetooptical trap that is, itself, loaded via a cold atomic beam from an upstream two-dimensional magneto-optical trap that resides in a rubidium-vapor cell that is differentially pumped from an adjoining vacuum chamber, wherein are performed scientific observations of the beams ultimately generated by the atom laser.

  17. Simulation of Helium Behaviour in Titanium Crystals Using Molecular Dynamics

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; HOU Qing; SUN Tie-Ying; WU Zhong-Cheng; LONG Xing-Gui; WU Xing-Chun; LUO Shun-Zhong

    2006-01-01

    @@ The behaviour of helium in Ti crystals at 300 K has been investigated by means of the molecular dynamics. The study is focused on the influences of He-Ti interaction on the aggregation of helium atoms in the substrate. When a Born-Mayer potential is used to describe the He-Ti interaction, the He atoms are unable to cluster with each other due to the weak bridge barrier that cannot trap the helium atoms, Whereas using a He-Ti potential that is constructed by fitting the ab initio pairwise He-Ti potential, the clustering of He atoms can be observed. The results indicate that suitable He-Ti potential plays an important role in the formation of He clusters in metals.Moreover, it is noted that the shape of the formed He cluster is irregular, and the produced defect prefers to congregating on one side of the He cluster rather than spreading symmetrically around it.

  18. Molecular dynamics simulation of thermal stability of nanocrystalline vanadium

    Institute of Scientific and Technical Information of China (English)

    WEI; Mingzhi; XIAO; Shifang; YUAN; Xiaojian; HU; Wangyu

    2006-01-01

    The microstructure and thermal stability of nanocrystalline vanadium with an average grain size ranging from 2.86 to 7.50 nm are calculated by means of the analytic embedded-atom method and molecular dynamics. The grain boundary and nanocrystalline grain atoms are differentiated by the common neighbor analysis method. The results indicate that the fraction of grain boundary increases with the grain size decreasing, and the mean energy of atoms is higher than that of coarse crystals. The thermal-stable temperatures of nanocrystalline vanadium are determined from the evolution of atomic energy, fraction of grain boundary and radial distribution function. It is shown that the stable temperature decreases obviously with the grain size decreasing. In addition the reasons which cause the grain growth of nanocrystalline vanadium are discussed.

  19. Molecular dynamics simulations of nanoscale metal tips under electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Parviainen, S., E-mail: stefan.parviainen@helsinki.fi [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FIN-00014 Helsinki (Finland); Djurabekova, F.; Pohjonen, A.; Nordlund, K. [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FIN-00014 Helsinki (Finland)

    2011-07-15

    Vacuum arcing is a plasma discharge over a metal surface under high electric fields. Plasma formation requires the supply of neutral atoms, which under high vacuum condition can only come from the surface itself. Nevertheless, the mechanisms by which the atoms are supplied are not known. In the present work, we propose a model for the onset of surface roughness and field-enhanced atom evaporation. Specifically, we describe a dislocation mechanism of tip growth from near-surface voids. We also simulate surface charging and resistive heating using a hybrid electrodynamics and molecular dynamics (ED and MD) code for dynamic simulations of electronic effects. We study the morphological evolution of the nanoscale protrusion under the electronic effects, such as the stretching of the tip by the stress induced by the electric field.

  20. Atoms, Molecules and Photons An Introduction to Atomic-, Molecular- and Quantum Physics

    CERN Document Server

    Demtröder, Wolfgang

    2010-01-01

    This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed over the last two centuries both by many experimental discoveries and, from the theoretical side, by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of classical description. The interaction of electromagnetic radiation with atoms and molecules and its potential for spectroscopy is outlined in more detail and in particular lasers as modern spectroscopic tools are discussed more thoroughly. Many examples and problems with solutions are offered to encourage readers to actively engage in applying and adapting the fundamental physics presented in this textbook to specific situations. Completely revised new edition with new sections covering all actual developments, like x-ray optics, ion-cyclotron-resonance spectrometer, attosecond lasers, ultraprecission frequency measurement ...

  1. 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.

  2. Testing chiral dynamics in pionic atoms

    Science.gov (United States)

    Friedman, E.; Gal, A.

    2004-01-01

    The energy dependence of chirally expanded πN isoscalar and isovector amplitudes b0(E) and b1(E), respectively, for zero-momentum off-shell pions near threshold, is used to impose the minimal substitution requirement E→E-VC on the properly constructed pion optical potential within a large-scale fit to 100 pionic-atom data across the periodic table which also include the recently established 'deeply bound' pionic atoms of Pb and Sn. This fit cannot be reconciled with the well-known free-space values of the πN threshold amplitudes. In contrast, introducing the empirically known energy dependence for on-shell pions leads to a better fit and to satisfactory values for the πN threshold amplitudes. The difference between these two approaches is briefly discussed.

  3. Molecular dynamics simulation of Ni3Al melting

    Institute of Scientific and Technical Information of China (English)

    Rongshan Wang; Huaiyu Hou; Xiaodong Ni; Guoliang Chen

    2008-01-01

    With the Voter-Chert version of embedded-atom model (EAM) potential and molecular dynamics, the melting of Ni3A1 alloy was simulated by one-phase (conventional) and two-phase approaches. It is shown that the simulated melting point is dependent on the potential and the simulation method. The structures of the melts obtained by different simulation methods were analyzed by the pair correlation function, the coordination number, and the distribution of atom pair type (indexed by the Honeycutt-Andersen pair analysis technique). The results show that the structures are very similar.

  4. Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

    Institute of Scientific and Technical Information of China (English)

    WEN Yu-Hua; ZHOU Fu-Xin; LIU Yue-Wu

    2001-01-01

    The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied.The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference,but the grain interior becomes more disordered, and their structural difference diminishes gradually; however,the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

  5. Reactions of carbon atoms in pulsed molecular beams

    Energy Technology Data Exchange (ETDEWEB)

    Reisler, H. [Univ. of Southern California, Los Angeles (United States)

    1993-12-01

    This research program consists of a broad scope of experiments designed to unravel the chemistry of atomic carbon in its two spin states, P and D, by using well-controlled initial conditions and state-resolved detection of products. Prerequisite to the proposed studies (and the reason why so little is known about carbon atom reactions), is the development of clean sources of carbon atoms. Therefore, in parallel with the studies of its chemistry and reaction dynamics, the authors continuously explore new, state-specific and efficient ways of producing atomic carbon. In the current program, C({sup 3}P) is produced via laser ablation of graphite, and three areas of study are being pursued: (i) exothermic reactions with small inorganic molecules (e.g., O{sub 2}, N{sub 2}O, NO{sub 2}) that can proceed via multiple pathways; (ii) the influence of vibrational and translational energy on endothermic reactions involving H-containing reactants that yield CH products (e.g., H{sub 2}O H{sub 2}CO); (iii) reactions of C({sup 3}P) with free radicals (e.g., HCO, CH{sub 3}O). In addition, the authors plan to develop a source of C({sup 1}D) atoms by exploiting the pyrolysis of diazotetrazole and its salts in the ablation source. Another important goal involves collaboration with theoreticians in order to obtain relevant potential energy surfaces, rationalize the experimental results and predict the roles of translational and vibrational energies.

  6. Molecular dynamics investigation of radiation damage in semiconductors

    Science.gov (United States)

    Good, Brian S.

    1991-01-01

    Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.

  7. Caloric Effects in Methylammonium Lead Iodide from Molecular Dynamics Simulations

    OpenAIRE

    Liu, Shi; Cohen, Ronald E.

    2016-01-01

    Organic-inorganic hybrid perovskite architecture could serve as a robust platform for materials design to realize functionalities beyond photovoltaic applications. We explore caloric effects in organometal halide perovskites, taking methylammonium lead iodide (MAPbI$_3$) as an example, using all-atom molecular dynamics simulations with a first-principles based interatomic potential. The adiabatic thermal change is estimated directly by introducing different driving fields in the simulations. ...

  8. Molecular dynamics investigation of radiation damage in semiconductors

    Science.gov (United States)

    Good, Brian S.

    1991-01-01

    Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.

  9. Atomic and molecular layer deposition for surface modification

    Energy Technology Data Exchange (ETDEWEB)

    Vähä-Nissi, Mika, E-mail: mika.vaha-nissi@vtt.fi [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Johansson, Leena-Sisko, E-mail: leena-sisko.johansson@aalto.fi [Aalto University, School of Chemical Technology, Department of Forest Products Technology, PO Box 16100, FI‐00076 AALTO (Finland); Koskinen, Jorma T.; Harlin, Ali [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland)

    2014-06-01

    Atomic and molecular layer deposition (ALD and MLD, respectively) techniques are based on repeated cycles of gas–solid surface reactions. A partial monolayer of atoms or molecules is deposited to the surface during a single deposition cycle, enabling tailored film composition in principle down to molecular resolution on ideal surfaces. Typically ALD/MLD has been used for applications where uniform and pinhole free thin film is a necessity even on 3D surfaces. However, thin – even non-uniform – atomic and molecular deposited layers can also be used to tailor the surface characteristics of different non-ideal substrates. For example, print quality of inkjet printing on polymer films and penetration of water into porous nonwovens can be adjusted with low-temperature deposited metal oxide. In addition, adhesion of extrusion coated biopolymer to inorganic oxides can be improved with a hybrid layer based on lactic acid. - Graphical abstract: Print quality of a polylactide film surface modified with atomic layer deposition prior to inkjet printing (360 dpi) with an aqueous ink. Number of printed dots illustrated as a function of 0, 5, 15 and 25 deposition cycles of trimethylaluminum and water. - Highlights: • ALD/MLD can be used to adjust surface characteristics of films and fiber materials. • Hydrophobicity after few deposition cycles of Al{sub 2}O{sub 3} due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO{sub 2}. • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt.

  10. 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

  11. SPILADY: A parallel CPU and GPU code for spin-lattice magnetic molecular dynamics simulations

    Science.gov (United States)

    Ma, Pui-Wai; Dudarev, S. L.; Woo, C. H.

    2016-10-01

    Spin-lattice dynamics generalizes molecular dynamics to magnetic materials, where dynamic variables describing an evolving atomic system include not only coordinates and velocities of atoms but also directions and magnitudes of atomic magnetic moments (spins). Spin-lattice dynamics simulates the collective time evolution of spins and atoms, taking into account the effect of non-collinear magnetism on interatomic forces. Applications of the method include atomistic models for defects, dislocations and surfaces in magnetic materials, thermally activated diffusion of defects, magnetic phase transitions, and various magnetic and lattice relaxation phenomena. Spin-lattice dynamics retains all the capabilities of molecular dynamics, adding to them the treatment of non-collinear magnetic degrees of freedom. The spin-lattice dynamics time integration algorithm uses symplectic Suzuki-Trotter decomposition of atomic coordinate, velocity and spin evolution operators, and delivers highly accurate numerical solutions of dynamic evolution equations over extended intervals of time. The code is parallelized in coordinate and spin spaces, and is written in OpenMP C/C++ for CPU and in CUDA C/C++ for Nvidia GPU implementations. Temperatures of atoms and spins are controlled by Langevin thermostats. Conduction electrons are treated by coupling the discrete spin-lattice dynamics equations for atoms and spins to the heat transfer equation for the electrons. Worked examples include simulations of thermalization of ferromagnetic bcc iron, the dynamics of laser pulse demagnetization, and collision cascades.

  12. Programming an interpreter using molecular dynamics

    OpenAIRE

    2008-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...

  13. Programming an Interpreter Using Molecular Dynamics

    OpenAIRE

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...

  14. Dynamics of atom trapping in an rf-dressed potential

    CERN Document Server

    Chakraborty, A; Ram, S P; Tiwari, S K; Rawat, H S

    2016-01-01

    The dynamics of atom trapping in a radio-frequency-dressed-state potential formed by static and radio frequency (rf) fields has been studied using the Direct Simulation Monte Carlo (DSMC) technique. Using the simulations, a case of formation of a toroidal trap for cold $^{87}Rb$ atoms is investigated for atoms trapped in a static quadrupole magnetic trap and exposed to an rf-field with temporally increasing amplitude and decreasing frequency. We first calculate the adiabatic rf-dressed potential for an atom interacting with these fields and then apply DSMC algorithm to simulate the motion of the atom in this time dependent adiabatic potential. In the simulations the Landau-Zener (LZ) transition probability is calculated to know if the atom is in the trappable or untrappable dressed state. The results show that, initially at lower rf-field strength, the rf-field ejects atoms from the trap and leads to evaporative cooling of the atom cloud. However at higher rf-field strength, the atoms make LZ transition to th...

  15. A dynamical atomic simulation for the Ni-Al Wulff nanoparticle

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jianfeng [Department of Applied Physics, Hunan Agricultural University, Changsha 410128 (China); Yang, Jianyu, E-mail: wuliyangjianyu@yahoo.com.cn [Hunan Institute of Engineering, Xiangtan 411104 (China)

    2013-06-01

    Ni-Al bimetallic nanoparticle structures are studied from a kinetic point of view. The diffusion and growth of Ni (or Al) atoms on Al (or Ni) cores with the Wulff structure are simulated by molecular dynamics and nudged elastic band methods. An analytic embedded atom model is applied to the two metals. The energy barriers of several typical diffusion processes of the adatoms on the nanoparticle surface are calculated. Results show that the incorporation of the Ni atoms into the Al core easily occurs, and the reverse process does not readily proceed. The growth simulations reveal that a better core-shell nanoparticle is obtained when the Al atoms are deposited on the Ni core at lower temperatures, and the deposition of the Ni atoms on the Al core leads to an amorphous surface. - Highlights: • The diffusion barrier of Ni (or Al) on Al (or Ni) Wulff nanoparticle is studied. • Ni atom can diffuse easily into Al core, and Al atom generally segregate on surface. • A core-shell nanoparticle is obtained for the deposition of Al atoms on Ni core. • Amorphous nanoparticle surface is obtained by depositing Ni atoms on Al core.

  16. Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

    Directory of Open Access Journals (Sweden)

    Fernan Saiz

    2016-06-01

    Full Text Available The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.

  17. Visualizing global properties of a molecular dynamics trajectory.

    Science.gov (United States)

    Zhou, Hao; Li, Shangyang; Makowski, Lee

    2016-01-01

    Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule.

  18. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

    Science.gov (United States)

    Soteras, Ignacio; Curutchet, Carles; Bidon-Chanal, Axel; Dehez, François; Ángyán, János G; Orozco, Modesto; Chipot, Christophe; Luque, F Javier

    2007-11-01

    The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.

  19. Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies

    Science.gov (United States)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

    Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.

  20. Molecular dynamics using quasielastic neutron scattering

    CERN Document Server

    Mitra, S

    2003-01-01

    Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)

  1. Dynamics of atom-field entanglement in a bimodal cavity

    CERN Document Server

    Deçordi, G L

    2015-01-01

    We investigate some aspects of the dynamics and entanglement of bipartite quantum system (atom-quantized field), coupled to a third ``external" subsystem (quantized field). We make use of the Raman coupled model; a three-level atom in a lambda configuration interacting with two modes of the quantized cavity field. We consider the far off resonance limit, which allows the derivation of an effective Hamiltonian of a two-level atom coupled to the fields. We also make a comparison with the situation in which one of the modes is treated classically rather than prepared in a quantum field (coherent state).

  2. Entanglement dynamics of a strongly driven trapped atom

    CERN Document Server

    Roghani, Maryam; Breuer, Heinz-Peter

    2011-01-01

    We study the entanglement between the internal electronic and the external vibrational degrees of freedom of a trapped atom which is driven by two lasers into electromagnetically-induced transparency. It is shown that basic features of the intricate entanglement dynamics can be traced to Landau-Zener splittings (avoided crossings) in the spectrum of the atom-laser field Hamiltonian. We further construct an effective Hamiltonian that describes the behavior of entanglement under dissipation induced by spontaneous emission processes. The proposed approach is applicable to a broad range of scenarios for the control of entanglement between electronic and translational degrees of freedom of trapped atoms through suitable laser fields.

  3. Nonlinear coherent dynamics of an atom in an optical lattice

    CERN Document Server

    Argonov, V Y

    2006-01-01

    We consider a simple model of lossless interaction between a two-level single atom and a standing-wave single-mode laser field which creates a one-dimensional optical lattice. Internal dynamics of the atom is governed by the laser field which is treated to be classical with a large number of photons. Center-of-mass classical atomic motion is governed by the optical potential and the internal atomic degree of freedom. The resulting Hamilton-Schr\\"odinger equations of motion are a five-dimensional nonlinear dynamical system with two integrals of motion. The main focus of the paper is chaotic atomic motion that may be quantified strictly by positive values of the maximal Lyapunov exponent. It is shown that atom, depending on the value of its total energy, can either oscillate chaotically in a well of the optical potential or fly ballistically with weak chaotic oscillations of its momentum or wander in the optical lattice changing the direction of motion in a chaotic way. In the regime of chaotic wandering atomic...

  4. Femtosecond electron diffraction: heralding the era of atomically resolved dynamics

    Science.gov (United States)

    Sciaini, Germán; Miller, R. J. Dwayne

    2011-09-01

    One of the great dream experiments in Science is to directly observe atomic motions as they occur. Femtosecond electron diffraction provided the first 'light' of sufficient intensity to achieve this goal by attaining atomic resolution to structural changes on the relevant timescales. This review covers the technical progress that made this new level of acuity possible and gives a survey of the new insights gained from an atomic level perspective of structural dynamics. Atomic level views of the simplest possible structural transition, melting, are discussed for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated with the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron-lattice systems are also discussed in which optically induced changes in the potential energy landscape lead to ballistic structural changes. Concepts such as the structural order parameters are now directly observable at the atomic level of inspection to give a remarkable view of the extraordinary degree of cooperativity involved in strongly correlated electron-lattice systems. These recent examples, in combination with time-resolved real space imaging now possible with electron probes, are truly defining an emerging field that holds great promise to make a significant impact in how we understand structural dynamics. This article is dedicated to the memory of Professor David John Hugh Cockayne, a world leader in electron microscopy, who sadly passed away in December.

  5. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Zwier, Timothy

    2012-07-20

    At the 2012 Atomic and Molecular Interactions Gordon Conference, there will be talks in several broadly defined and partially overlapping areas:  Intramolecular and single-collision reaction dynamics;  Photophysics and photochemistry of excited states;  Clusters, aerosols and solvation;  Interactions at interfaces;  Conformations and folding of large molecules;  Interactions under extreme conditions of temperature and pressure. The theme of the Gordon Research Seminar on Atomic & Molecular Interactions, in keeping with the tradition of the Atomic and Molecular Interactions Gordon Research Conference, is far-reaching and involves fundamental research in the gas and condensed phases along with application of these ideas to practical chemical fields. The oral presentations, which will contain a combination of both experiment and theory, will focus on four broad categories:  Ultrafast Phenomena;  Excited States, Photoelectrons, and Photoions;  Chemical Reaction Dynamics;  Biomolecules and Clusters.

  6. Molecular dynamics study of nanojoining between axially positioned Ag nanowires

    Science.gov (United States)

    Cui, Jianlei; Theogene, Barayavuga; Wang, Xuewen; Mei, Xuesong; Wang, Wenjun; Wang, Kedian

    2016-08-01

    The miniaturization of electronics devices into nanometer scale is indispensable for next-generation semiconductor technology. Ag nanowires (Ag NWs) are considered to be the promising candidates for future electronic circuit owing to the excellent electrical and thermal properties. The nanojoining of axially positioned Ag NWs was performed by molecular dynamics simulation. Through the detailed atomic evolution during the nanojoining, the results indicate that the temperature and the distance between Ag NWs in axial direction have a great impact on nanojoining effect. When the nanojoining temperature is relatively high, the atoms are disordered and the atomic queues become to distort with strong thermodynamic properties and weak effect of metal bonds. At the relatively low temperature, the Ag NWs can be well connected with good junction quality and their own morphology, which is similar to the cold welding without fusion, while the distance between Ag NWs should be controlled for interaction and diffusion of interfacial atoms at nanowires head. When the Ag NWs are placed on Si and SiO2 substrate, because the atomic species and lattice structure of substrate material can differently affect the motions of Ag atoms through the interactive force between the atoms, the nanojoining quality of Ag NWs on Si substrate is better than that on the SiO2 substrate. So, for getting effective and reliable nanojoining without nanosolders and other materials, the temperature, distance and substrate surface should be reasonably controlled and selected, providing helpful theoretical guidance for experiment and application of nanojoining.

  7. Atomic and Molecular Data: Division B / Commission 14

    CERN Document Server

    Mashonkina, Lyudmila; Wahlgren, Glenn M; Allard, France; Barklem, Paul; Beiersdorfer, Peter; Fraser, Helen; Nave, Gillian; Nilsson, Hampus

    2015-01-01

    Commission 14 has been operating for almost a century. It was one of the 32 Standing IAU Commissions and established in 1919. The main purpose of Commission 14 is to foster interactions between the astronomical community and those conducting research on atoms, molecules, and solid state particles to provide data vital to reducing and analysing astronomical observations and performing theoretical investigations. Although Commission 14 terminated at the Honolulu General Assembly, the field Atomic and Molecular Data remains with the IAU. By call of the IAU, the Commission 14 OC initiated a proposal for a new Commission on Laboratory Astrophysics that was approved. Commission on Laboratory Astrophysics will be a natural evolution of Commission 14.

  8. Atomic and Molecular Data for Optical Stellar Spectroscopy

    CERN Document Server

    Heiter, U; Asplund, M; Barklem, P S; Bergemann, M; Magrini, L; Masseron, T; Mikolaitis, Š; Pickering, J C; Ruffoni, M P

    2015-01-01

    High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2- to 10-m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available ...

  9. Tunneling Dynamics Between Atomic Bright Solitons

    CERN Document Server

    Zhao, Li-Chen; Yang, Zhan-Ying; Yang, Wen-Li

    2016-01-01

    We investigate tunneling behavior between two bright solitons in a Bose-Einstein condensate with attractive contact interactions between atoms. The explicit tunneling properties including tunneling particles and oscillation period are described analytically, which indicates that the periodic tunneling form is a nonlinear Josephson type oscillation. The results suggest that the breathing behavior of solitons comes from the tunneling mechanism in an effective double-well potential, which is quite different from the modulational instability mechanism for Akhmediev breather and K-M breather. Furthermore, we obtain a phase diagram for two soliton interaction which admits tunneling property, particle-like property, interference property, and a resonant interaction case. The explicit conditions for them are clarified based on the defined critical distance $d_c$ and spatial interference period $D$.

  10. The Molecular Dynamics Simulations of Atomic Radius Difference for Liquid Cu%原子半径差对液态金属Cu的分子动力学模拟

    Institute of Scientific and Technical Information of China (English)

    张妍

    2011-01-01

    Two metal systems of pure Cu and CuCu'( Cu'represents atoms which radius is 10% larger than normal size Cu, the number ratio of Cu:Cu' = 3:1 ) have been studied by moleclar dynamics simulations. It is found that the glass transition temperature of CuCu'is larger than Cu from the radial distribution function. In addition, the number of Cu'atoms around the Cu is more than Cu in the system of CuCu', the degree of atomic ordering of the CuCu'system is better than that of Cu. The results show that larger of atomic radius difference make for the better glass forming ability.%运用分子动力学模拟方法,对Cu和CuCu'(Cu'的原子半径比Cu的大10%,两者的原子数比例为3∶1)两种金属体系进行了模拟研究.通过对径向分布函数的分析,发现CuCu'的玻璃转变温度比Cu高;另外,在CuCu'体系中铜原子周围的Cu'原子数目的分布多于铜原子,CuCu'体系的有序度高于Cu体系,说明合金中原子半径差的增大有利于非晶的形成.

  11. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled...

  12. Molecular dynamics simulations of diffusion mechanisms in NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Soule De Bas, B.; Farkas, D

    2003-03-14

    Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.

  13. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    Directory of Open Access Journals (Sweden)

    Yajiang Hao

    2015-07-01

    Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  14. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    CERN Document Server

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  15. Dynamics of single Fe atoms in graphene vacancies.

    Science.gov (United States)

    Robertson, Alex W; Montanari, Barbara; He, Kuang; Kim, Judy; Allen, Christopher S; Wu, Yimin A; Olivier, Jaco; Neethling, Jan; Harrison, Nicholas; Kirkland, Angus I; Warner, Jamie H

    2013-04-10

    Focused electron beam irradiation has been used to create mono and divacancies in graphene within a defined area, which then act as trap sites for mobile Fe atoms initially resident on the graphene surface. Aberration-corrected transmission electron microscopy at 80 kV has been used to study the real time dynamics of Fe atoms filling the vacancy sites in graphene with atomic resolution. We find that the incorporation of a dopant atom results in pronounced displacements of the surrounding carbon atoms of up to 0.5 Å, which is in good agreement with density functional theory calculations. Once incorporated into the graphene lattice, Fe atoms can transition to adjacent lattice positions and reversibly switch their bonding between four and three nearest neighbors. The C atoms adjacent to the Fe atoms are found to be more susceptible to Stone-Wales type bond rotations with these bond rotations associated with changes in the dopant bonding configuration. These results demonstrate the use of controlled electron beam irradiation to incorporate dopants into the graphene lattice with nanoscale spatial control.

  16. The 2011 Dynamics of Molecular Collisions Conference

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [JILA, NIST

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  17. European Virtual Atomic And Molecular Data Center - VAMDC

    Science.gov (United States)

    Dimitrijevic, M. S.; Sahal-Brechot, S.; Kovacevic, A.; Jevremovic, D.; Popovic, L. C.

    2010-07-01

    Reliable atomic and molecular data are of great importance for different applications in astrophysics, atmospheric physics, fusion, environmental sciences, combustion chemistry, and in industrial applications from plasmas and lasers to lighting. Currently, very important resources of such data are highly fragmented, presented in different, nonstandardized ways, available through a variety of highly specialized and often poorly documented interfaces, so that the full exploitation of all their scientific worth is limited, hindering research in many topics like e.g. the characterization of extrasolar planets, understanding the chemistry of our local solar system and of the wider universe, the study of the terrestrial atmosphere and quantification of climate change; the development of the fusion rersearch, etc. The Virtual Atomic and Molecular Data Centre (http://www.vamdc.eu, VAMDC) is an European Union funded FP7 project aiming to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. It will also provide a forum for training potential users and dissemination of expertise worldwide. Partners in the Consortium of the Project are: 1) Centre National de Recherche Scientifique - CNRS (Paris, Reims, Grenoble, Bordeaux, Dijon, Toulouse); 2) The Chancellor, Masters and Scholars of the University of Cambridge - CMSUC; 3) University College London - UCL; 4) Open University - OU; (Milton Keynes, England); 5) Universitaet Wien - UNIVIE; 6) Uppsala Universitet - UU; 7) Universitaet zu Koeln - KOLN; 8) Istituto Nazionale di Astrofisica - INAF (Catania, Cagliari); 9) Queen's University Belfast - QUB; 10) Astronomska Opservatorija - AOB (Belgrade, Serbia); 11) Institute of Spectroscopy RAS - ISRAN (Troitsk, Russia); 12) Russian Federal Nuclear Center - All-Russian Institute of Technical Physics - RFNC-VNIITF (Snezhinsk, Chelyabinsk Region, Russia; 13) Institute of Atmospheric Optics - IAO (Tomsk, Russia

  18. 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.

  19. MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES

    Directory of Open Access Journals (Sweden)

    I. M. Neelov

    2014-07-01

    Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.

  20. Molecular dynamics simulation of flow in pores

    Science.gov (United States)

    Blömer, Jan

    2001-08-01

    The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.

  1. Efficient compression of molecular dynamics trajectory files.

    Science.gov (United States)

    Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James

    2012-10-15

    We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.

  2. Molecular transport through capillaries made with atomic-scale precision

    Science.gov (United States)

    Radha, B.; Esfandiar, A.; Wang, F. C.; Rooney, A. P.; Gopinadhan, K.; Keerthi, A.; Mishchenko, A.; Janardanan, A.; Blake, P.; Fumagalli, L.; Lozada-Hidalgo, M.; Garaj, S.; Haigh, S. J.; Grigorieva, I. V.; Wu, H. A.; Geim, A. K.

    2016-10-01

    Nanometre-scale pores and capillaries have long been studied because of their importance in many natural phenomena and their use in numerous applications. A more recent development is the ability to fabricate artificial capillaries with nanometre dimensions, which has enabled new research on molecular transport and led to the emergence of nanofluidics. But surface roughness in particular makes it challenging to produce capillaries with precisely controlled dimensions at this spatial scale. Here we report the fabrication of narrow and smooth capillaries through van der Waals assembly, with atomically flat sheets at the top and bottom separated by spacers made of two-dimensional crystals with a precisely controlled number of layers. We use graphene and its multilayers as archetypal two-dimensional materials to demonstrate this technology, which produces structures that can be viewed as if individual atomic planes had been removed from a bulk crystal to leave behind flat voids of a height chosen with atomic-scale precision. Water transport through the channels, ranging in height from one to several dozen atomic planes, is characterized by unexpectedly fast flow (up to 1 metre per second) that we attribute to high capillary pressures (about 1,000 bar) and large slip lengths. For channels that accommodate only a few layers of water, the flow exhibits a marked enhancement that we associate with an increased structural order in nanoconfined water. Our work opens up an avenue to making capillaries and cavities with sizes tunable to ångström precision, and with permeation properties further controlled through a wide choice of atomically flat materials available for channel walls.

  3. Petascale computations for Large-scale Atomic and Molecular collisions

    CERN Document Server

    McLaughlin, Brendan M

    2014-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Synchrotron Radiation facilities and from Satellite observations. We also indicate future directions and implementation of the R-matrix codes on emerging GPU architectures.

  4. PAMOP: Petascale Atomic, Molecular and Optical Collision Calculations

    CERN Document Server

    McLaughlin, Brendan M; Pindzola, Michael S; Müller, Alfred

    2015-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.

  5. Experimental Techniques for Studies in Atomic & Molecular Physics

    OpenAIRE

    Heijkenskjöld, Filip

    2008-01-01

    This thesis is based on a selection of six different experimental techniques used for studies in atomic and molecular physics. The techniques analysed in the thesis are compared to find similarities in strategies and ways to avoid sources of error. Paper 1 deals with collision based spectroscopy with 60 keV Xe6+ ions on sodium and argon gas targets. Information on energy of Rydberg states in Xe5+ is unveiled by optical spectroscopy in the wavelength range from vacuum ultraviolet (VUV) to visi...

  6. Atomic Force Microscopy of dynamic protein DNA interactions

    NARCIS (Netherlands)

    Noort, van Simon Johannes Theodorus

    1999-01-01

    In this thesis a dedicated Atomic Force Microscopy (AFM) setup is used for imaging biochemical reactions with molecular resolution. The basis for the high resolution of AFM is the combination of a small probe, close proximity to the sample and a short-range interaction between the probe and the samp

  7. Coarse-grained molecular dynamics simulations of biomolecules

    Directory of Open Access Journals (Sweden)

    Ken Takahashi

    2014-03-01

    Full Text Available Coarse-grained molecular dynamics (CGMD simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.

  8. Carbon nanotubes as nanodelivery systems an insight through molecular dynamics simulations

    CERN Document Server

    Lim, Melvin Choon Giap

    2013-01-01

    This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.

  9. A large scale molecular dynamics calculation of a lipid bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)

    1998-03-01

    Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)

  10. Combined molecular dynamics-spin dynamics simulations of bcc iron

    Energy Technology Data Exchange (ETDEWEB)

    Perera, Meewanage Dilina N [ORNL; Yin, Junqi [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Brown, Greg [ORNL

    2014-01-01

    Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.

  11. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    Science.gov (United States)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

  12. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    Science.gov (United States)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

  13. Model based control of dynamic atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chibum [Department of Mechanical System Design Engineering, Seoul National University of Science and Technology, Seoul 139-743 (Korea, Republic of); Salapaka, Srinivasa M., E-mail: salapaka@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-04-15

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H{sub ∞} control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  14. Model based control of dynamic atomic force microscope.

    Science.gov (United States)

    Lee, Chibum; Salapaka, Srinivasa M

    2015-04-01

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  15. Crystal structural and diffusion property in titanium carbides: A molecular dynamics study

    Science.gov (United States)

    Lv, Yanan; Gao, Weimin

    2016-09-01

    Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.

  16. Self-consistent generalized Langevin equation theory of the dynamics of multicomponent atomic liquids

    Science.gov (United States)

    Lázaro-Lázaro, Edilio; Mendoza-Méndez, Patricia; Elizondo-Aguilera, Luis Fernando; Perera-Burgos, Jorge Adrián; Ramírez-González, Pedro Ezequiel; Pérez-Ángel, Gabriel; Castañeda-Priego, Ramón; Medina-Noyola, Magdaleno

    2017-05-01

    A fundamental challenge of the theory of liquids is to understand the similarities and differences in the macroscopic dynamics of both colloidal and atomic liquids, which originate in the (Newtonian or Brownian) nature of the microscopic motion of their constituents. Starting from the recently discovered long-time dynamic equivalence between a colloidal and an atomic liquid that share the same interparticle pair potential, in this work we develop a self-consistent generalized Langevin equation theory for the dynamics of equilibrium multicomponent atomic liquids, applicable as an approximate but quantitative theory describing the long-time diffusive dynamical properties of simple equilibrium atomic liquids. When complemented with a Gaussian-like approximation, this theory is also able to provide a reasonable representation of the passage from a ballistic to diffusive behavior. We illustrate the applicability of the resulting theory with three particular examples, namely, a monodisperse and a polydisperse monocomponent hard-sphere liquid and a highly size-asymmetric binary hard-sphere mixture. To assess the quantitative accuracy of our results, we perform event-driven molecular dynamics simulations, which corroborate the general features of the theoretical predictions.

  17. The Effect of Cholesterol on Short- and Long-Chain Monounsaturated Lipid Bilayers as Determined by Molecular Dynamics Simulations and X-Ray Scattering

    National Research Council Canada - National Science Library

    Kučerka, Norbert; Perlmutter, Jason D; Pan, Jianjun; Tristram-Nagle, Stephanie; Katsaras, John; Sachs, Jonathan N

    2008-01-01

    ...) monounsaturated phospholipids. Bilayer structural information is derived from all-atom molecular dynamics simulations, which are validated via direct comparison to x-ray scattering experiments...

  18. Deterministic Entanglement via Molecular Dissociation in Integrated Atom Optics

    OpenAIRE

    Zhao, Bo; Chen, Zeng-Bing; Pan, Jian-Wei; Schmiedmayer, J.; Recati, Alessio; Astrakharchik, Grigory E.; Calarco, Tommaso

    2005-01-01

    Deterministic entanglement of neutral cold atoms can be achieved by combining several already available techniques like the creation/dissociation of neutral diatomic molecules, manipulating atoms with micro fabricated structures (atom chips) and detecting single atoms with almost 100% efficiency. Manipulating this entanglement with integrated/linear atom optics will open a new perspective for quantum information processing with neutral atoms.

  19. A Robust Ramsey Interferometer for Atomic Timekeeping in Dynamic Environments

    Science.gov (United States)

    Kotru, Krish; Brown, Justin; Butts, David; Choy, Jennifer; Galfond, Marissa; Johnson, David M.; Kinast, Joseph; Timmons, Brian; Stoner, Richard

    2014-05-01

    We present a laser-based approach to atomic timekeeping, in which atomic phase information is extracted using modified Raman pulses in a Ramsey sequence. We overcome systematic effects associated with differential AC Stark shifts by employing atom optics derived from Raman adiabatic rapid passage (ARP). ARP drives coherent transfer between two hyperfine ground states by sweeping the frequency difference of two optical fields and maintaining a large single-photon detuning. Compared to resonant, pulsed Raman transitions, ARP atom optics afford a >150x reduction in sensitivity to differential AC Stark shifts in a Ramsey interferometer. We also demonstrate that ARP preserves fringe contrast in Ramsey interferometers for cloud displacements reaching the 1/e2 intensity radius of the laser beam. ARP can thus be expected to improve the robustness of clock interferometers operating in dynamic environments. Copyright ©2014 by The Charles Stark Draper Laboratory, Inc. All rights reserved.

  20. Photochemistry of molecular and atomic oxygen in the terrestrial nightglow

    Science.gov (United States)

    Lednyts'kyy, Olexandr; Von Savigny, Christian; Sinnhuber, Miriam

    2016-07-01

    The electronic states of molecular oxygen ({O}_2) are in constant communication through collisions in high vibrational levels of {O}_2 in the MLT (Mesosphere/Lower Thermosphere) region. We assume that the Herzberg {O}_2 electronic states transfer energy to O-atoms to generate the green line. Our Multiple Nightglow Chemistry model is based on more than 80 (odd oxygen and odd hydrogen) aeronomical reactions to implement this concept. We retrieved atomic oxygen concentration ([O]) profiles in the MLT region with help of SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) and SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) infrared radiometer observations of the nightglow. Particularly, we obtained volume emission rate (VER) profiles (due to the infrared atmospheric {O}_2(a^1Δ_g) nightglow at 1.27 μm) from SABER to retrieve [O] profiles. We discussed quenching profiles that correspond to retrieved [O] profiles to reflect complex molecularity of infrared atmospheric and green line nightglow emissions.

  1. An extension of dynamic droplet deformation models to secondary atomization

    NARCIS (Netherlands)

    Bartz, F.O.; Schmehl, R.; Koch, R.; Bauer, H.J.

    2010-01-01

    A detailed model for secondary atomization of liquid droplets by aerodynamic forces is presented. As an empirical extension of dynamic droplet deformation models, it accounts for temporal variations of the relative velocity between droplet and gas phase during the deformation and breakup process and

  2. Combining optimal control theory and molecular dynamics for protein folding.

    Science.gov (United States)

    Arkun, Yaman; Gur, Mert

    2012-01-01

    A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  3. Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

    Energy Technology Data Exchange (ETDEWEB)

    Li, M.; Wang, C. Z.; Mandelev, M.; Ho, K. M.

    2008-05-13

    Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of {beta} relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of {beta} relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long

  4. The Cologne Database for Molecular Spectroscopy, CDMS, in the Virtual Atomic and Molecular Data Centre, VAMDC

    CERN Document Server

    Endres, Christian P; Schilke, Peter; Stutzki, Jürgen; Müller, Holger S P

    2016-01-01

    The CDMS was founded 1998 to provide in its catalog section line lists of molecular species which may be observed in various astronomical sources using radio astronomy. The line lists contain transition frequencies with qualified accuracies, intensities, quantum numbers, as well as further auxilary information. They have been generated from critically evaluated experimental line lists, mostly from laboratory experiments, employing established Hamiltonian models. Seperate entries exist for different isotopic species and usually also for different vibrational states. As of December 2015, the number of entries is 792. They are available online as ascii tables with additional files documenting information on the entries. The Virtual Atomic and Molecular Data Centre was founded more than 5 years ago as a common platform for atomic and molecular data. This platform facilitates exchange not only between spectroscopic databases related to astrophysics or astrochemistry, but also with collisional and kinetic databases...

  5. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  6. Molecular dynamics simulation of radiation damage cascades in diamond

    Energy Technology Data Exchange (ETDEWEB)

    Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  7. Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent.

    Science.gov (United States)

    Sader, Safaa; Wu, Chun

    2017-03-01

    Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide. This wild type complex was used to build the ternary complex with R487K and E571K mutants. Three 500ns molecular dynamics simulations were performed on complex systems of wild type and two mutants. The detailed energetic, structural and dynamic analysis were performed on the simulation data. Our binding data indicated a significant impairment of Amsacrine binding energy in the two mutants compared with the wild type. The order of weakening (R487K>E571K) was in agreement with the order of experimental drug resistance fold (R489K>E571K). Our binding energy decomposition further indicated that weakening of the ligand-protein interaction rather than the ligand-DNA interaction was the major contributor of the binding energy difference between R487K and E571K. In addition, key residues contributing to the binding energy (ΔG) or the decrease of the binding energy (ΔΔG) were identified through the energy decomposition analysis. The change in ligand binding pose, dynamics of protein, DNA and ligand upon the mutations were thoroughly analyzed and discussed. Deciphering the molecular basis of drug resistance is crucial to overcome drug resistance using rational drug design. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Molecular dynamics studies of entangled polymer chains

    NARCIS (Netherlands)

    Bulacu, Monica Iulia

    2008-01-01

    The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a

  9. A thread calculus with molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2010-01-01

    We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o

  10. Programming an interpreter using molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi

  11. Programming an interpreter using molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the

  12. Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials

    CERN Document Server

    Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard

    2009-01-01

    We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...

  13. Modeling hybrid perovskites by molecular dynamics.

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  14. Modeling hybrid perovskites by molecular dynamics

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  15. Molecular Dynamics Studies of Matrix Metalloproteases.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas

    2017-01-01

    Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.

  16. Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

    Science.gov (United States)

    Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

    2007-01-01

    The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

  17. Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

    Energy Technology Data Exchange (ETDEWEB)

    Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)

    2015-09-28

    An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

  18. Molecular ions in ultracold atomic gases: computed electronic interactions for \\MgHion with Rb

    CERN Document Server

    Tacconi, Mario

    2007-01-01

    The electronic structures of the manifold of potential energy surfaces generated in the lower energy range by the interaction of the MgH$^+$(X$^1\\Sigma^+$) cationic molecule with Rb($^2$S), neutral atom are obtained over a broad range of Jacobi coordinates from strongly correlated \\emph{ab initio} calculations which use a Multireference (MR) wavefunction within a Complete Active Space (CAS) approach. The relative features of the lowest five surfaces are analyzed in terms of possible collisional outcomes when employed to model the ultracold dynamics of ionic molecular partners.

  19. Molecular dynamics simulations on PGLa using NMR orientational constraints.

    Science.gov (United States)

    Sternberg, Ulrich; Witter, Raiker

    2015-11-01

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  20. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  1. Dynamic molecular crystals with switchable physical properties.

    Science.gov (United States)

    Sato, Osamu

    2016-06-21

    The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials.

  2. Dynamics of entanglement between two atomic samples with spontaneous scattering

    CERN Document Server

    Lisi, A D; Illuminati, F; Lisi, Antonio Di; Siena, Silvio De; Illuminati, Fabrizio

    2003-01-01

    We investigate the effects of spontaneous scattering on the evolution of entanglement of two atomic samples, probed by phase shift measurements on optical beams interacting with both samples. We develop a formalism of conditional quantum evolutions and present a wave function analysis implemented in numerical simulations of the state vector dynamics. This method allows to track the evolution of entanglement and to compare it with the predictions obtained when spontaneous scattering is neglected. We provide numerical evidence that the interferometric scheme to entangle atomic samples is only marginally affected by the presence of spontaneous scattering, and should thus be robust even in more realistic situations.

  3. Atomic Tunnelling Dynamics of Two Squeezed Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    LI Jin-Hui; KUANG Le-Man

    2003-01-01

    In this paper, tunnelling dynamics of squeezed Bose-Einstein condensates (BEC's) in the presence of the nonlinear self-interaction of each species, the interspecies nonlinear interaction, and the Josephson-like tunnelling interaction is investigated by using the second quantization approach. The influence of BEC squeezing on macroscopic quantum self-trapping (MQST) and quantum coherent atomic tunnelling is analyzed in detail. It is shown that the MQST and coherent atomic tunnelling between two squeezed BEC's can be manipulated through changing squeezing amplitude and squeezing phase of BEC squeezed states.

  4. Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

    Directory of Open Access Journals (Sweden)

    Eric Paquet

    2015-01-01

    Full Text Available Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.

  5. 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...

  6. VALD - an atomic and molecular database for astrophysics

    Energy Technology Data Exchange (ETDEWEB)

    Heiter, U; Barklem, P; Kochukhov, O; Piskunov, N [Department of Astronomy and Space Physics, Uppsala University (Sweden); Fossati, L; Obbrugger, M; Stuetz, Ch; Weiss, W W [Institute of Astronomy, University of Vienna (Austria); Kildiyarova, R [Institute of Spectroscopy, Russian Academy of Sciences, Moscow region, Troitsk (Russian Federation); Kupka, F [Max-Planck-Institute for Astrophysics, Garching (Germany); Plez, B [Universite Montpellier II, GRAAL, CNRS - UMR 5024 (France); Ryabchikova, T [Institute of Astronomy, Russian Academy of Sciences, Moscow (Russian Federation); Stempels, H C [School of Physics and Astronomy, University of St Andrews, Scotland (United Kingdom)], E-mail: ulrike@astro.uu.se

    2008-10-15

    The VALD database of atomic and molecular data aims to ensure a robust and consistent analysis of astrophysical spectra. We offer a convenient e-mail and web-based user interface to a vast collection of spectral line parameters for all chemical elements and in the future also for molecules. An international team is working on the following tasks: collecting line parameters from relevant theoretical and experimental publications, computing line parameters, evaluating the data quality by comparison of similar data from different sources and by comparison with astrophysical observations, and incorporating the data into VALD. A unique feature of VALD is its capability to provide the most comprehensive spectral line lists for specific astrophysical plasma conditions defined by the user.

  7. Electronically coarse-grained molecular dynamics using quantum Drude oscillators

    Science.gov (United States)

    Jones, A. P.; Crain, J.; Cipcigan, F. S.; Sokhan, V. P.; Modani, M.; Martyna, G. J.

    2013-12-01

    Standard molecular dynamics (MD) simulations generally make use of a basic description of intermolecular forces which consists of fixed, pairwise, atom-centred Coulomb, van der Waals and short-range repulsive terms. Important interactions such as many-body polarisation and many-body dispersion which are sensitive to changes in the environment are usually neglected, and their effects treated effectively within mean-field approximations to reproduce a single thermodynamic state point or physical environment. This leads to difficulties in modelling the complex interfaces of interest today where the behaviour may be quite different from the regime of parameterisation. Here, we describe the construction and properties of a Gaussian coarse-grained electronic structure, which naturally generates many-body polarisation and dispersion interactions. The electronic structure arises from a fully quantum mechanical treatment of a set of distributed quantum Drude oscillators (QDOs), harmonic atoms which interact with each other and other moieties via electrostatic (Coulomb) interactions; this coarse-grained approach is capable of describing many-body polarisation and dispersion but not short-range interactions which must be parametrised. We describe how on-the-fly forces due to this exchange-free Gaussian model may be generated with linear scale in the number of atoms in the system using an adiabatic path integral molecular dynamics for quantum Drude oscillators technique (APIMD-QDO). We demonstrate the applicability of the QDO approach to realistic systems via a study of the liquid-vapour interface of water.

  8. Molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine

    NARCIS (Netherlands)

    Cascales, J.J.L.; Berendsen, H.J.C.; delaTorre, J.G.

    1996-01-01

    A molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine in its liquid-crystalline state with atomic detail was carried out. From an analysis of a trajectory of 184 ps of length, we obtained information about the dynamics and structure of water between suc

  9. The Atom in a Molecule: Implications for Molecular Structure and Properties

    Science.gov (United States)

    2016-05-23

    Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  10. Bifurcation, chaos, and scan instability in dynamic atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cantrell, John H., E-mail: john.h.cantrell@nasa.gov [Research Directorate, NASA Langley Research Center, Hampton, Virginia 23681 (United States); Cantrell, Sean A., E-mail: scantrell@nlsanalytics.com [NLS Analytics, LLC, 375 Dundee Road, Glencoe, Illinois 60022 (United States)

    2016-03-28

    The dynamical motion at any point on the cantilever of an atomic force microscope can be expressed quite generally as a superposition of simple harmonic oscillators corresponding to the vibrational modes allowed by the cantilever shape. Central to the dynamical equations is the representation of the cantilever-sample interaction force as a polynomial expansion with coefficients that account for the interaction force “stiffness,” the cantilever-to-sample energy transfer, and the displacement amplitude of cantilever oscillation. Renormalization of the cantilever beam model shows that for a given cantilever drive frequency cantilever dynamics can be accurately represented by a single nonlinear mass-spring model with frequency-dependent stiffness and damping coefficients [S. A. Cantrell and J. H. Cantrell, J. Appl. Phys. 110, 094314 (2011)]. Application of the Melnikov method to the renormalized dynamical equation is shown to predict a cascade of period doubling bifurcations with increasing cantilever drive force that terminates in chaos. The threshold value of the drive force necessary to initiate bifurcation is shown to depend strongly on the cantilever setpoint and drive frequency, effective damping coefficient, nonlinearity of the cantilever-sample interaction force, and the displacement amplitude of cantilever oscillation. The model predicts the experimentally observed interruptions of the bifurcation cascade for cantilevers of sufficiently large stiffness. Operational factors leading to the loss of image quality in dynamic atomic force microscopy are addressed, and guidelines for optimizing scan stability are proposed using a quantitative analysis based on system dynamical parameters and choice of feedback loop parameter.

  11. Random Matrix Theory in molecular dynamics analysis.

    Science.gov (United States)

    Palese, Luigi Leonardo

    2015-01-01

    It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.

  12. PREFACE: 7th Asian International Seminar on Atomic and Molecular Physics

    Science.gov (United States)

    Deshmukh, Pranawa C.; Chakraborty, Purushottam; Williams, Jim F.

    2007-09-01

    These proceedings arose from the 7th Asian International Seminar on Atomic and Molecular Physics (AISAMP) which was held at the Indian Institute of Technology, Madras from 4-7 December 2006. The history of the AISAMP has been reviewed by Takayanagi http://www.physics.iitm.ac.in/~aisamp7/history.html. This international seminar/conference series grew out of the Japan-China meetings which were launched in 1985, the fourth of which was held in 1992 and carried a second title: The First Asian International Seminar on Atomic and Molecular Physics (AISAMP), thus providing a formal medium for scientists in this part of the world to report periodically and exchange their scientific thoughts. The founding nations of Japan and China were joined subsequently by Korea, Taiwan, India and Australia. The aims of the symposia included bringing together leading experts and students of atomic and molecular physics, the discussion of important problems, learning and sharing modern techniques and expanding the horizons of modern atomic and molecular physics. The fields of interest ranged from atomic and molecular structure and dynamics to photon, electron and positron scattering, to quantum information processing, the effects of symmetry and many body interactions, laser cooling, cold traps, electric and magnetic fields and to atomic and molecular physics with synchrotron radiation. Particular interest was evident in new techniques and the changes of the physical properties from atomic to condensed matter. Details of the 7th AISAMP, including the topics for the special sessions and the full programme, are available online at the conference website http://www.physics.iitm.ac.in/~aisamp7/. In total, 95 presentations were made at the 7th AISAMP, these included the Invited Talks and Contributed Poster Presentations, of which 52 appear in the present Proceedings after review by expert referees, refereed to the usual standard of the Institute of Physics journal: Journal of Physics B: Atomic

  13. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A

    2006-01-01

    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the characteri

  14. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A

    2006-01-01

    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the

  15. Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

    Directory of Open Access Journals (Sweden)

    Rajab Al-Sayegh

    2015-01-01

    Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

  16. Controlling the dynamics of a single atom in lateral atom manipulation.

    Science.gov (United States)

    Stroscio, Joseph A; Celotta, Robert J

    2004-10-01

    We studied the dynamics of a single cobalt (Co) atom during lateral manipulation on a copper (111) surface in a low-temperature scanning tunneling microscope. The Co binding site locations were revealed in a detailed image that resulted from lateral Co atom motion within the trapping potential of the scanning tip. Random telegraph noise, corresponding to the Co atom switching between hexagonal close-packed (hcp) and face-centered cubic (fcc) sites, was seen when the tip was used to try to position the Co atom over the higher energy hcp site. Varying the probe tip height modified the normal copper (111) potential landscape and allowed the residence time of the Co atom in these sites to be varied. At low tunneling voltages (less than approximately 5 millielectron volts), the transfer rate between sites was independent of tunneling voltage, current, and temperature. At higher voltages, the transfer rate exhibited a strong dependence on tunneling voltage, indicative of vibrational heating by inelastic electron scattering.

  17. Dynamical localization: Hydrogen atoms in magnetic and microwave fields

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuto, F.; Casati, G. [Dipartimento di Fisica dellUniversita, Via Castelnuovo 7, 22100 Como (Italy); Shepelyansky, D.L. [Laboratoire de Physique Quantique, UMR C5626 du CNRS, Universite Paul Sabatier, 31062, Toulouse (France)

    1997-03-01

    We show that dynamical localization for excited hydrogen atoms in magnetic and microwave fields takes place at quite low microwave frequency ({omega}n{sup 3}{lt}1). Estimates of the localization length are given for different parameter regimes, showing that the quantum delocalization border drops significantly as compared to the case of zero magnetic field. This opens up broad possibilities for laboratory investigations. {copyright} {ital 1997} {ital The American Physical Society}

  18. Liouville-von Neumann molecular dynamics

    Science.gov (United States)

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-01

    We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.

  19. The Cologne Database for Molecular Spectroscopy, CDMS, in the Virtual Atomic and Molecular Data Centre, VAMDC

    Science.gov (United States)

    Endres, Christian P.; Schlemmer, Stephan; Schilke, Peter; Stutzki, Jürgen; Müller, Holger S. P.

    2016-09-01

    The Cologne Database for Molecular Spectroscopy, CDMS, was founded 1998 to provide in its catalog section line lists of mostly molecular species which are or may be observed in various astronomical sources (usually) by radio astronomical means. The line lists contain transition frequencies with qualified accuracies, intensities, quantum numbers, as well as further auxiliary information. They have been generated from critically evaluated experimental line lists, mostly from laboratory experiments, employing established Hamiltonian models. Separate entries exist for different isotopic species and usually also for different vibrational states. As of December 2015, the number of entries is 792. They are available online as ascii tables with additional files documenting information on the entries. The Virtual Atomic and Molecular Data Centre, VAMDC, was founded more than 5 years ago as a common platform for atomic and molecular data. This platform facilitates exchange not only between spectroscopic databases related to astrophysics or astrochemistry, but also with collisional and kinetic databases. A dedicated infrastructure was developed to provide a common data format in the various databases enabling queries to a large variety of databases on atomic and molecular data at once. For CDMS, the incorporation in VAMDC was combined with several modifications on the generation of CDMS catalog entries. Here we introduce related changes to the data structure and the data content in the CDMS. The new data scheme allows us to incorporate all previous data entries but in addition allows us also to include entries based on new theoretical descriptions. Moreover, the CDMS entries have been transferred into a mySQL database format. These developments within the VAMDC framework have in part been driven by the needs of the astronomical community to be able to deal efficiently with large data sets obtained with the Herschel Space Telescope or, more recently, with the Atacama Large

  20. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

  1. Molecular dynamics simulation of thermodynamical properties of copper clusters

    Institute of Scientific and Technical Information of China (English)

    Wu Zhi-Min; Wang Xin-Qiang; Yang Yuan-Yuan

    2007-01-01

    The melting and freezing processes of CuN (N = 180, 256, 360, 408, 500, 628 and 736) nanoclusters are simulated by using micro-canonical molecular dynamics simulation technique. The potential energies and the heat capacities as a function of temperature are obtained. The results reveal that the melting and freezing points increase almost linearly with the atom number in the cluster increasing. All copper nanoclusters have negative heat capacity around the melting and freezing points, and hysteresis effect in the melting/freezing transition is derived in CuN nanoclusters for the first time.

  2. Isomorphic phase transformation in shocked Cerium using molecular dynamics

    OpenAIRE

    Germann T.C.; Chen S.-P.; Dupont V.

    2011-01-01

    Cerium (Ce) undergoes a significant (∼16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plas...

  3. 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.

  4. Self-assembling, reactivity and molecular dynamics of fullerenol nanoparticles.

    Science.gov (United States)

    Vraneš, Milan; Borišev, Ivana; Tot, Aleksandar; Armaković, Stevan; Armaković, Sanja; Jović, Danica; Gadžurić, Slobodan; Djordjevic, Aleksandar

    2016-12-21

    In this work structuring of water and insight into intermolecular interactions between water and fullerenol are studied throughout the process of forming nanoagglomerates at different temperatures applying both experimental and computational approaches. The obtained fullerenol nanoparticles (FNPs) are firstly characterized using dynamic light scattering, atomic force microscopy and transmission electron microscopy. The density, electrical conductivity and dynamic viscosity of aqueous fullerenol solutions are measured in the temperature range of 293.15 to 315.15 K. From the experimental density results other important thermodynamic values, such as apparent molar volumes and the partial molar volumes of water and fullerenol, are also calculated. To support the conclusion derived from the experimental density and calculated volumetric parameters, and to better understand the nature of the interactions with water, molecular dynamics simulations and radial distribution functions are also employed.

  5. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    Science.gov (United States)

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  6. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  7. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

    This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

  8. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

    Science.gov (United States)

    2017-01-01

    Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition

  9. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    Science.gov (United States)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-02-21

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular

  10. Weak links between fast mobility and local structure in molecular and atomic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  11. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  12. Molecular Scale Dynamics of Large Ring Polymers

    Science.gov (United States)

    Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.

    2014-10-01

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.

  13. 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.

  14. Neutron Star Crust and Molecular Dynamics Simulation

    CERN Document Server

    Horowitz, C J; Schneider, A; Berry, D K

    2011-01-01

    In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.

  15. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  16. Molecular dynamics simulations of thermal effects in nanometric cutting process

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Understanding the basic action of how material removing in nanoscale is a critical issue of producing well-formed components.In order to clarify thermal effects on material removal at atomic level,molecular dynamics(MD)simulations of nanometric cutting of mono-crystalline copper are performed with Morse,EAM and Tersoff potential.The effects of cutting speed on temperature distribution are investigated.The simulation results demonstrate that the temperature distribution shows a roughly concentric shape around shear zone and a steep temperature gradient lies in diamond tool,a relative high temperature is located in shear zone and machined surface,but the highest temperature is found in chip.At a high cutting speed mode,the atoms in shear zone with high temperature implies a large stress is built up in a local region.

  17. A hybrid algorithm for parallel molecular dynamics simulations

    CERN Document Server

    Mangiardi, Chris M

    2016-01-01

    This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with AVX and AVX-2 processors as well as Xeon-Phi co-processors.

  18. Lightweight computational steering of very large scale molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States)

    1996-09-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.

  19. A hybrid algorithm for parallel molecular dynamics simulations

    Science.gov (United States)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  20. Molecular dynamics simulation of annealed ZnO surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  1. Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

    Directory of Open Access Journals (Sweden)

    Casuyac Miqueas

    2016-01-01

    Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

  2. Current-induced atomic dynamics, instabilities, and Raman signals

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Brandbyge, Mads; Hedegard, Per

    2012-01-01

    We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Jou...... of these in the Raman signals....

  3. Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena.

    Science.gov (United States)

    Prasad, Manish; Sinno, Talid

    2004-11-01

    An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.

  4. The evolution of the atomic and molecular interstellar medium in star-forming galaxies

    NARCIS (Netherlands)

    Popping, Gergö

    2014-01-01

    In this thesis I developed models to make predictions for the atomic and molecular gas content of galaxies. Main results of my thesis include that the atomic hydrogen content of galaxies remained relatively constant with over the last 10 Billion years, whereas the molecular hydrogen content decrease

  5. 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.)

  6. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  7. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo

  8. Catalysis and communication in dynamic molecular networks

    NARCIS (Netherlands)

    Fanlo Virgos, Hugo

    2015-01-01

    The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

  9. Critical Dynamics in Quenched 2D Atomic Gases

    Science.gov (United States)

    Larcher, F.; Dalfovo, F.; Proukakis, N. P.

    2016-05-01

    Non-equilibrium dynamics across phase transitions is a subject of intense investigations in diverse physical systems. One of the key issues concerns the validity of the Kibble-Zurek (KZ) scaling law for spontaneous defect creation. The KZ mechanism has been recently studied in cold atoms experiments. Interesting open questions arise in the case of 2D systems, due to the distinct nature of the Berezinskii-Kosterlitz-Thouless (BKT) transition. Our studies rely on the stochastic Gross-Pitaevskii equation. We perform systematic numerical simulations of the spontaneous emergence and subsequent dynamics of vortices in a uniform 2D Bose gas, which is quenched across the BKT phase transition in a controlled manner, focusing on dynamical scaling and KZ-type effects. By varying the transverse confinement, we also look at the extent to which such features can be seen in current experiments. Financial support from EPSRC and Provincia Autonoma di Trento.

  10. Molecular Exchange Dynamics in Block Copolymer Micelles

    Science.gov (United States)

    Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy

    2012-02-01

    Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.

  11. Virtual-Wall Model for Molecular Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Lijuan Qian

    2016-12-01

    Full Text Available A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.

  12. Enhanced molecular dynamics for simulating porous interphase layers in batteries.

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)

    2009-10-01

    Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

  13. Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation.

    Science.gov (United States)

    Hong, Seung Do; Ha, Man Yeong; Balachandar, S

    2009-11-01

    The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. With increasing characteristic energy, the static contact angle in equilibrium with a solid surface in the absence of a body force decreases because the hydrophobic surface changes its characteristics to the hydrophilic surface. In order to consider the effect of moving water droplet on the dynamic contact angles, we apply the constant acceleration to an individual oxygen and hydrogen atom. In the presence of a body force, the water droplet changes its shape with larger advancing contact angle than the receding angle. The dynamic contact angles are compared with the static contact angle in order to see the effect of the presence of a body force.

  14. MDMovie: a molecular dynamics viewing tool.

    Science.gov (United States)

    Greenberg, J P

    1996-10-01

    The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.

  15. Thermal relaxation of molecular oxygen in collisions with nitrogen atoms

    Science.gov (United States)

    Andrienko, Daniil A.; Boyd, Iain D.

    2016-07-01

    Investigation of O2-N collisions is performed by means of the quasi-classical trajectory method on the two lowest ab initio potential energy surfaces at temperatures relevant to hypersonic flows. A complete set of bound-bound and bound-free transition rates is obtained for each precollisional rovibrational state. Special attention is paid to the vibrational and rotational relaxations of oxygen as a result of chemically non-reactive interaction with nitrogen atoms. The vibrational relaxation of oxygen partially occurs via the formation of an intermediate NO2 complex. The efficient energy randomization results in rapid vibrational relaxation at low temperatures, compared to other molecular systems with a purely repulsive potential. The vibrational relaxation time, computed by means of master equation studies, is nearly an order of magnitude lower than the relaxation time in N2-O collisions. The rotational nonequilibrium starts to play a significant effect at translational temperatures above 8000 K. The present work provides convenient relations for the vibrational and rotational relaxation times as well as for the quasi-steady dissociation rate coefficient and thus fills a gap in data due to a lack of experimental measurements for this system.

  16. A dynamic magneto-optical trap for atom chips

    CERN Document Server

    Rushton, Jo; Bateman, James; Himsworth, Matt

    2016-01-01

    We describe a dynamic magneto-optical trap (MOT) suitable for the use with vacuum systems in which optical access is limited to a single window. This technique facilitates the long-standing desire of producing integrated atom chips, many of which are likely to have severely restricted optical access compared with conventional vacuum chambers. This "switching-MOT" relies on the synchronized pulsing of optical and magnetic fields at audio frequencies. The trap's beam geometry is obtained using a planar mirror surface, and does not require a patterned substrate or bulky optics inside the vacuum chamber. Central to the design is a novel magnetic field geometry that requires no external quadrupole or bias coils which leads toward a very compact system. We have implemented the trap for $^{85}$Rb and shown that it is capable of capturing 2 million atoms and directly cooling below the Doppler temperature.

  17. A dynamic magneto-optical trap for atom chips

    Science.gov (United States)

    Rushton, Jo; Roy, Ritayan; Bateman, James; Himsworth, Matt

    2016-11-01

    We describe a dynamic magneto-optical trap (MOT) suitable for the use with vacuum systems in which optical access is limited to a single window. This technique facilitates the long-standing desire of producing integrated atom chips, many of which are likely to have severely restricted optical access compared with conventional vacuum chambers. This ‘switching-MOT’ relies on the synchronized pulsing of optical and magnetic fields at audio frequencies. The trap’s beam geometry is obtained using a planar mirror surface, and does not require a patterned substrate or bulky optics inside the vacuum chamber. Central to the design is a novel magnetic field geometry that requires no external quadrupole or bias coils which leads toward a very compact system. We have implemented the trap for 85Rb and shown that it is capable of capturing 2 million atoms and directly cooling below the Doppler temperature.

  18. Crossed-molecular-beams reactive scattering of oxygen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Baseman, R.J.

    1982-11-01

    The reactions of O(/sup 3/P) with six prototypical unsaturated hydrocarbons, and the reaction of O(/sup 1/D) with HD, have been studied in high-resolution crossed-molecular-beams scattering experiments with mass-spectrometric detection. The observed laboratory-product angular and velocity distributions unambiguously identify parent-daughter ion pairs, distinguish different neutral sources of the same ion, and have been used to identify the primary products of the reactions. The derived center-of-mass product angular and translational energy distributions have been used to elucidate the detailed reaction dynamics. These results demonstrate that O(/sup 3/P)-unsaturated hydrocarbon chemistry is dominated by single bond cleavages, leading to radical products exclusively.

  19. Molecular dynamics simulations of D2O ice photodesorption

    CERN Document Server

    Arasa, C; Cuppen, H M; van Dishoeck, E F; Kroes, G J; 10.1063/1.3582910

    2011-01-01

    Molecular dynamics calculations have been performed to study the ultraviolet photodissociation of D2O in an amorphous D2O ice surface at 10-90 K, in order to investigate the influence of isotope effects on the photodesorption processes. As for H2O, the main processes after UV photodissociation are trapping and desorption. There are three desorption processes: D atom, OD radical, and D2O molecule photodesorption. D2O desorption takes places either by direct desorption of a recombined D2O molecule, or when an energetic D atom produced by photodissociation kicks a surrounding D2O molecule out of the surface by transferring part of its momentum. Desorption probabilities are compared quantitatively with those for H2O obtained from previous MD simulations of UV photodissociation of amorphous water ice. The main conclusions are the same, but the average D atom photodesorption probability is smaller than that of the H atom (by about a factor of 0.9) because D has lower kinetic energy than H, whereas the average OD ra...

  20. Molecular dynamics analysis on buckling of defective carbon nanotubes.

    Science.gov (United States)

    Kulathunga, D D T K; Ang, K K; Reddy, J N

    2010-09-01

    Owing to their remarkable mechanical properties, carbon nanotubes have been employed in many diverse areas of applications. However, similar to any of the many man-made materials used today, carbon nanotubes (CNTs) are also susceptible to various kinds of defects. Understanding the effect of defects on the mechanical properties and behavior of CNTs is essential in the design of nanotube-based devices and composites. It has been found in various past studies that these defects can considerably affect the tensile strength and fracture of CNTs. Comprehensive studies on the effect of defects on the buckling and vibration of nanotubes is however lacking in the literature. In this paper, the effects of various configurations of atomic vacancy defects, on axial buckling of single-walled carbon nanotubes (SWCNTs), in different thermal environments, is investigated using molecular dynamics simulations (MDS), based on a COMPASS force field. Our findings revealed that even a single missing atom can cause a significant reduction in the critical buckling strain and load of SWCNTs. In general, increasing the number of missing atoms, asymmetry of vacancy configurations and asymmetric distribution of vacancy clusters seemed to lead to higher deterioration in buckling properties. Further, SWCNTs with a single vacancy cluster, compared to SWCNTs with two or more vacancy clusters having the same number of missing atoms, appeared to cause higher deterioration of buckling properties. However, exceptions from the above mentioned trends could be expected due to chemical instabilities of defects. Temperature appeared to have less effect on defective CNTs compared to pristine CNTs.

  1. Molecular dynamics simulation of graphene bombardment with Si ion

    Science.gov (United States)

    Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

    2014-03-01

    Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

  2. Molecular dynamics analysis on buckling of defective carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Kulathunga, D D T K; Ang, K K [Department of Civil Engineering, National University of Singapore (Singapore); Reddy, J N, E-mail: cveangkk@nus.edu.s [Department of Mechanical Engineering, Texas A and M University, College Station, TX 77843-3123 (United States)

    2010-09-01

    Owing to their remarkable mechanical properties, carbon nanotubes have been employed in many diverse areas of applications. However, similar to any of the many man-made materials used today, carbon nanotubes (CNTs) are also susceptible to various kinds of defects. Understanding the effect of defects on the mechanical properties and behavior of CNTs is essential in the design of nanotube-based devices and composites. It has been found in various past studies that these defects can considerably affect the tensile strength and fracture of CNTs. Comprehensive studies on the effect of defects on the buckling and vibration of nanotubes is however lacking in the literature. In this paper, the effects of various configurations of atomic vacancy defects, on axial buckling of single-walled carbon nanotubes (SWCNTs), in different thermal environments, is investigated using molecular dynamics simulations (MDS), based on a COMPASS force field. Our findings revealed that even a single missing atom can cause a significant reduction in the critical buckling strain and load of SWCNTs. In general, increasing the number of missing atoms, asymmetry of vacancy configurations and asymmetric distribution of vacancy clusters seemed to lead to higher deterioration in buckling properties. Further, SWCNTs with a single vacancy cluster, compared to SWCNTs with two or more vacancy clusters having the same number of missing atoms, appeared to cause higher deterioration of buckling properties. However, exceptions from the above mentioned trends could be expected due to chemical instabilities of defects. Temperature appeared to have less effect on defective CNTs compared to pristine CNTs.

  3. Quantum State Control of Trapped Atomic and Molecular Ions

    Science.gov (United States)

    Seck, Christopher M.

    Full quantum control of a molecule would have a significant impact in molecular coherent control (alignment and orientation) and ultracold and quantum chemistry, quantum computing and simulation as well as hybrid quantum devices, and precision spectroscopy of importance to fundamental physics research. Precision spectroscopy of even simple diatomic molecules offers the possibility of uncovering physics beyond the standard model, specifically time variation of the proton-to-electron mass ratio, which is currently constrained by astronomical molecular observations at the 10-16 1/yr level and laboratory atomic measurements at the 10-17 1/yr level. To achieve this level of measurement and to avoid the complications of diatomic structure on traditional spectroscopy methods, molecular quantum logic spectroscopy (mQLS) will be the spectroscopy technique of choice. We discuss development of in-house external-cavity diode laser (ECDL) systems and improvements to the Libbrecht-Hall circuit, which is a well-known, low-noise current driver for narrow-linewidth diode lasers. However, as the current approaches the maximum set limit, the noise in the laser current increases dramatically. This behavior is documented and simple circuit modifications to alleviate this issue are explored. We cool trapped AlH+ molecules to their ground rotational-vibrational quantum state using an electronically-exciting broadband laser to simultaneously drive cooling resonances from many different rotational levels. We demonstrate rotational cooling on the 140(20) ms timescale from room temperature to 3.8 K, with the ground state population increasing from 3% to 95.4%. Since QLS does not require the high gate fidelities usually associated with quantum computation and quantum simulation, it is possible to make simplifying choices in ion species and quantum protocols at the expense of some fidelity. We demonstrate sideband cooling and motional state detection protocols for 138Ba+ of sufficient fidelity

  4. Self-diffusion dynamic behavior of atomic clusters on Re(0 0 0 1) surface

    Energy Technology Data Exchange (ETDEWEB)

    Liu Fusheng [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu Wangyu, E-mail: wangyuhu2001cn@yahoo.com.cn [Department of Applied Physics, Hunan University, Changsha 410082 (China); Deng Huiqiu; Luo Wenhua; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)

    2009-08-15

    Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of rhenium atomic clusters up to seven atoms on Re(0 0 0 1) surface have been studied in the temperature ranges from 600 K to 1900 K. The simulation time varies from 20 ns to 200 ns according to the cluster sizes and the temperature. The heptamer and trimer are more stable comparing to other neighboring non-compact clusters. The diffusion coefficients of clusters are derived from the mean square displacement of cluster's mass-center, and diffusion prefactors D{sub 0} and activation energies E{sub a} are derived from the Arrhenius relation. It is found that the Arrhenius relation of the adatom can be divided into two parts at different temperature range. The activation energy of clusters increases with the increasing of the atom number in clusters. The prefactor of the heptamer is 2-3 orders of magnitude higher than a usual prefactor because of a large number of nonequivalent diffusion processes. The trimer and heptamer are the nuclei at different temperature range according to the nucleation theory.

  5. Dynamics of hydrogen-like atom bounded by maximal acceleration

    CERN Document Server

    Friedman, Yaakov

    2012-01-01

    The existence of a maximal acceleration for massive objects was conjectured by Caianiello 30 years ago based on the Heisenberg uncertainty relations. Many consequences of this hypothesis have been studied, but until now, there has been no evidence that boundedness of the acceleration may lead to quantum behavior. In previous research, we predicted the existence of a universal maximal acceleration and developed a new dynamics for which all admissible solutions have an acceleration bounded by the maximal one. Based on W. K\\"{u}ndig's experiment, as reanalyzed by Kholmetskii et al, we estimated its value to be of the order $10^{19}m/s^2$. We present here a solution of our dynamical equation for a classical hydrogen-like atom and show that this dynamics leads to some aspects of quantum behavior. We show that the position of an electron in a hydrogen-like atom can be described only probabilistically. We also show that in this model, the notion of "center of mass" must be modified. This modification supports the no...

  6. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    Energy Technology Data Exchange (ETDEWEB)

    Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)

    2015-09-28

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  7. Large Scale Molecular Dynamics Simulations of Homogeneous Nucleation

    CERN Document Server

    Tanaka, Kyoko K

    2013-01-01

    We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 {\\mu}s (56 million time-steps). They cover a wide range of supersaturation ratios, S=1.55 to 10^4, and temperatures from kT = 0.3 to 1.0 {\\epsilon} (where {\\epsilon} is the depth of the LJ potential, and k the Boltzmann constant). We have resolved nucleation rates as low as 10^{17} cm^{-3} s^{-1} (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem....

  8. Molecular dynamics simulations through GPU video games technologies

    Science.gov (United States)

    Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

    2016-01-01

    Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

  9. 2008 Atomic and Molecular Interactions GRC-July 6-11, 2008

    Energy Technology Data Exchange (ETDEWEB)

    Arthur Suits

    2009-06-03

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2008 conference continues these traditions. At the 2008 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Spectroscopy; (2) Molecules in Strong Fields; (3) Photodissociation Dynamics; (4) Astrochemistry; and (5) Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed. Limited funds are available to support attendance for students and post-docs. Advisors should email the conference chair requesting such support, and the students should apply online as usual.

  10. Molecular Dynamic Simulation for HMX/NTO Supramolecular Explosive

    Institute of Scientific and Technical Information of China (English)

    林鹤; 朱顺官; 张琳; 彭新华; 李洪珍; 陈阳

    2012-01-01

    Based on the crystal engineering, six models of octahydro-1,3 ,5 ,7-tetranitro-1,3 ,5 ,7-tetrazocine ( HMX )/3-nitro-1,2,4-triazol-5-one(NTO) supramolecular explosive were designed. The probable formation of HMX/NTO supramolecular explosive was investigated by the molecular dynamic (MD) method. Interaction between oxygen atoms in HMX and hydrogen atoms in NTO or between hydrogen atoms in HMX and oxygen atoms in NTO were studied by the radial distribution function (RDF). It shows that there are strong hydrogen bonds and Van Der Waals forces between HMX and NTO, in which the hydrogen bonds between oxygen atoms in the NTO and hydrogen atoms in HMX are the main host-guest interactions. The distributions of bond length, bond angle and dihedral angle were simulated by MD. It shows that the structure of HMX is seriously distorted. The binding energies and X-ray powder diffraction (XRD) patterns were calculated on the basis of the final HMX/NTO supramolecular structures. The results show that the binding energies of six supramolecular models are Ebinding (1 1 1) 〉E binding (1 0 0) 〉E binding (0 2 0) 〉E binding (random) 〉Ebinding (1 0 2) 〉 Ebinding(0 1 1), and the XRD patterns of six supramolecular models are quite different from pure HMX or NTO. Based on the investigation for growth morphology, binding energies and RDF, the model of HMX supercell substituted by NTO along the ( 1 1 1 ) surface of HMX is easier to form.

  11. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...

  12. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

    2015-12-15

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

  13. Conduction of molecular electronic devices: Qualitative insights through atom-atom polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Stuyver, T.; Fias, S., E-mail: sfias@vub.ac.be; De Proft, F.; Geerlings, P. [ALGC, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel (Belgium); Fowler, P. W. [Department of Chemistry, University of Sheffield, Sheffield S3 7HF (United Kingdom)

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  14. Conduction of molecular electronic devices: qualitative insights through atom-atom polarizabilities.

    Science.gov (United States)

    Stuyver, T; Fias, S; De Proft, F; Fowler, P W; Geerlings, P

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  15. Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions

    Energy Technology Data Exchange (ETDEWEB)

    Amaran, Saieswari; Kosloff, Ronnie [Fritz Haber Research Centre and The Department of Physical Chemistry, Hebrew University, Jerusalem 91904 (Israel); Tomza, Michał; Skomorowski, Wojciech; Pawłowski, Filip; Moszynski, Robert [Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw (Poland); Rybak, Leonid; Levin, Liat; Amitay, Zohar [The Shirlee Jacobs Femtosecond Laser Research Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Berglund, J. Martin; Reich, Daniel M.; Koch, Christiane P. [Theoretische Physik, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel (Germany)

    2013-10-28

    Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.

  16. 2nd International Symposium "Atomic Cluster Collisions : Structure and Dynamics from the Nuclear to the Biological Scale"

    CERN Document Server

    Solov'yov, Andrey; ISACC 2007; Latest advances in atomic cluster collisions

    2008-01-01

    This book presents a 'snapshot' of the most recent and significant advances in the field of cluster physics. It is a comprehensive review based on contributions by the participants of the 2nd International Symposium on Atomic Cluster Collisions (ISACC 2007) held in July 19-23, 2007 at GSI, Darmstadt, Germany. The purpose of the Symposium is to promote the growth and exchange of scientific information on the structure and properties of nuclear, atomic, molecular, biological and complex cluster systems studied by means of photonic, electronic, heavy particle and atomic collisions. Particular attention is devoted to dynamic phenomena, many-body effects taking place in cluster systems of a different nature - these include problems of fusion and fission, fragmentation, collective electron excitations, phase transitions, etc.Both the experimental and theoretical aspects of cluster physics, uniquely placed between nuclear physics on the one hand and atomic, molecular and solid state physics on the other, are discuss...

  17. Thermal Transport in Carbon Nanotubes using Molecular Dynamics

    Science.gov (United States)

    Moore, Andrew; Khatun, Mahfuza

    2011-10-01

    We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.

  18. Molecular dynamics simulations of amyloid fibrils: an in silico approach

    Institute of Scientific and Technical Information of China (English)

    Wei Ye; Wei Wang; Cheng Jiang; Qingfen Yu; Haifeng Chen

    2013-01-01

    Amyloid fibrils play causal roles in the pathogenesis of amyloid-related degenerative diseases such as Alzheimer's disease,type Ⅱ diabetes mellitus,and the prion-related transmissible spongiform encephalopathies.The mechanism of fibril formation and protein aggregation is still hotly debated and remains an important open question in order to develop therapeutic method of these diseases.However,traditional molecular biological and crystallographic experiments could hardly observe atomic details and aggregation process.Molecular dynamics (MD) simulations could provide explanations for experimental results and detailed pathway of protein aggregation.In this review,we focus on the applications of MD simulations on several amyloidogenic protein systems.Furthermore,MD simulations could help us to understand the mechanism of amyloid aggregation and how to design the inhibitors.

  19. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

    Science.gov (United States)

    Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A

    2012-12-11

    It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.

  20. Molecular dynamics simulations of carbon nanotube-based gears

    Science.gov (United States)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn

    1997-09-01

    We use a molecular dynamics simulation to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with 0957-4484/8/3/001/img1. Brenner's reactive hydrocarbon potential is used to model interatomic forces within each molecular gear. A Lennard - Jones 6 - 12 potential or the Buckingham 0957-4484/8/3/001/img2 potential plus electrostatic interaction terms are used for intermolecular interactions between gears. A number of gear and gear/shaft configurations are simulated on parallel computers. One gear is powered by forcing the atoms near the end of the nanotube to rotate, and a second gear is allowed to rotate by keeping the atoms near the end of its nanotube constrained to a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. Results suggest that these gears can operate at up to 50 - 100 GHz in a vacuum at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering the temperature and/or rotation rate.

  1. Chaotic dynamics and fractal structures in experiments with cold atoms

    Science.gov (United States)

    Daza, Alvar; Georgeot, Bertrand; Guéry-Odelin, David; Wagemakers, Alexandre; Sanjuán, Miguel A. F.

    2017-01-01

    We use tools from nonlinear dynamics for the detailed analysis of cold-atom experiments. A powerful example is provided by the recent concept of basin entropy, which allows us to quantify the final-state unpredictability that results from the complexity of the phase-space geometry. We show here that this enables one to reliably infer the presence of fractal structures in phase space from direct measurements. We illustrate the method with numerical simulations in an experimental configuration made of two crossing laser guides that can be used as a matter-wave splitter.

  2. Atomic dynamics of tin nanoparticles embedded into porous glass

    Energy Technology Data Exchange (ETDEWEB)

    Parshin, P. P.; Zemlyanov, M. G., E-mail: zeml@isssph.kiae.ru; Panova, G. Kh.; Shikov, A. A. [Russian Research Centre Kurchatov Institute (Russian Federation); Kumzerov, Yu. A.; Naberezhnov, A. A. [Russian Academy of Sciences, Ioffe Physicotechnical Institute (Russian Federation); Sergueev, I.; Crichton, W. [European Synchrotron Radiation Facility (France); Chumakov, A. I. [Russian Research Centre Kurchatov Institute (Russian Federation); Rueffer, R. [European Synchrotron Radiation Facility (France)

    2012-03-15

    The method of resonant nuclear inelastic absorption of synchrotron radiation has been used to study the phonon spectrum for tin nanoparticles (with a natural isotope mixture) embedded into a porous glassy (silica) matrix with an average pore diameter of 7 nm in comparison to the analogous spectrum of bulk tin enriched with {sup 119}Sn isotope. Differences between the spectra have been observed, which are related to both the dimensional effects and specific structural features of the porous glass-tin nanocomposite. Peculiarities in the dynamics of tin atoms embedded into nanopores of glass are interpreted in terms of a qualitative model of the nanocomposite structure.

  3. Molecular Dynamics Study of a Dual-Cation Ionomer Electrolyte.

    Science.gov (United States)

    Chen, Xingyu; Chen, Fangfang; Jónsson, Erlendur; Forsyth, Maria

    2017-01-18

    The poly(N1222 )x Li1-x [AMPS] ionomer system (AMPS=2-acrylamido-2-methylpropane sulfonic acid) with dual cations has previously shown decoupled Li ion dynamics from polymer segmental motions, characterized by the glass-transition temperature, which can result in a conductive electrolyte material whilst retaining an appropriate modulus (i.e. stiffness) so that it can suppress dendrite formation, thereby improving safety when used in lithium-metal batteries. To understand this ion dynamics behavior, molecular dynamics techniques have been used in this work to simulate structure and dynamics in these materials. These simulations confirm that the Li ion transport is decoupled from the polymer particularly at intermediate N1222(+) concentrations. At 50 mol % N1222(+) concentration, the polymer backbone is more rigid than for higher N1222(+) concentrations, but with increasing temperature Li ion dynamics are more significant than polymer or quaternary ammonium cation motions. Herein we suggest an ion-hopping mechanism for Li(+) , arising from structural rearrangement of ionic clusters that could explain its decoupled behavior. Higher temperatures favor an aggregated ionic structure as well as enhancing these hopping motions. The simulations discussed here provide an atomic-level understanding of ion dynamics that could contribute to designing an improved ionomer with fast ion transport and mechanical robustness.

  4. Quantum Trajectory Approach to Molecular Dynamics Simulation with Surface Hopping

    CERN Document Server

    Feng, Wei; Li, Xin-Qi; Fang, Weihai

    2012-01-01

    The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic state. In this work we propose a quantum trajectory approach to the MD simulation with surface hopping, from an insight that an effective "observation" is actually implied in theMDsimulation through tracking the forces experienced, just like checking the meter's result in the quantum measurement process. This treatment can build the nonadiabatic surface hopping on a dynamical foundation, instead of the usual artificial and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.

  5. Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts

    Directory of Open Access Journals (Sweden)

    Kazuaki Z. Takahashi

    2017-01-01

    Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.

  6. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  7. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...

  8. Molecular dynamics simulations of glycerol glass-forming liquid

    Energy Technology Data Exchange (ETDEWEB)

    Blieck, J. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Lerbret, A. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2005-10-31

    Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q {approx} 0.6 A{sup -1} are observed. Our results are also found compatible with predictions of the Mode Coupling Theory.

  9. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    Science.gov (United States)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  10. High temperature phonon dispersion in graphene using classical molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K. [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam-603102 (India); Valsakumar, M. C., E-mail: anees@igcar.gov.in [School of Engineering Sciences and Technology, University of Hyderabad, Hyderabad-500046 (India)

    2014-04-24

    Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.

  11. Dynamic assembly of molecularly imprinted polymer nanoparticles.

    Science.gov (United States)

    Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei

    2017-09-11

    Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. The dynamic properties of the two-level entangled atom in an optical field

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The interaction of an optical field and one of the entangled atoms is analyzed in detail in this paper. Furthermore, the dynamic properties of the two-level entangled atom are manifested. The properties of the action are dependent on the initial state of the atom. After detecting the atom out of the field, we can obtain the state of the other atom moving in the field. It is shown that the state of the atom out of the field influences the dynamic properties of the atom in the field.

  13. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    Science.gov (United States)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  14. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    Science.gov (United States)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  15. Molecular Dynamics Simulations of Surface Processes: Oxygen Recombination on Silica Surfaces at High Temperature

    Science.gov (United States)

    2007-07-01

    size-scalable cluster approach with SixOy clusters of increasing size cleaved from the β- cristobalite unit cell. In this study the hybrid Hartree...values of the β- cristobalite cell and extending the Molecular Dynamics Simulations of Surface Processes: Oxygen Recombination on Silica Surfaces at... cristobalite surface is reported as a function of the distance of the N atom from the Si active atom. The dashed line shows the interaction

  16. Simulation of Structure and Energies of NinAlm Nanoclusters (n + m = 13) by Molecular Dynamics

    OpenAIRE

    Rojas T., Justo; Departamento de Física, Instituto Peruano de Energía Nuclear. Lima, Perú Facultad de Ciencias Físicas, Universidad Nacional Mayor de San Marcos. Lima, Perú; Rojas A., Chachi; Facultad de Ciencias Físicas, Universidad Nacional Mayor de San Marcos. Lima, Perú; Arroyo C., Juan; Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos. Lima, Perú

    2014-01-01

    By simulation with the Molecular Dynamics method and the thermal temper technique, the more stablegeometric structures and their respective energy were determined in the Nin Alm (n + m = 13)nanoclusters. The atomic interaction in the cluster was modelized with the Embeded Atom Method (EAM)(the Voter & Chen version). The most stable geometric structures of the cluster and their minimal energywere obtained from 200 generating spatial coordinates along the high energy path. The initial inter...

  17. Insights from molecular dynamics simulations for computational protein design.

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-02-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

  18. Efimov Superchemistry:Quantum Dynamical Theory for Coherent Atom-Trimer Conversion in a Repulsive Atomic Bose-Einstein Condensate

    Institute of Scientific and Technical Information of China (English)

    JING Hui; GENG Zhen-Duo

    2008-01-01

    @@ We show that by making a generalized atom-molecule dark state,coherent creation of triatomic molecules can be enhanced in a repulsive atomic Bose-Einstein condensate.The dynamics of heteronuclear trimer creation is significantJy different from the homonuclear case and further enhancement can be realized by controlling its chemical reaction channels,The possibility of manipulating atom-trimer conversion provides an appealing research area for current coherent matter-wave optics.

  19. Quantum Dynamics of Cooled Atoms in the Presence of Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    YI Xue-Xi; SU Jun-Chen

    2001-01-01

    Under the Markov approximation, the quantum dynamics of cooled atoms in the presence of Bose-Einstein condensates is studied. A master equation governing the evolution of such a system is derived. Using this master equation, the distribution of the atoms in the excited states at finite temperature and the dynamics of the excited atom at zero temperature are given and discussed.

  20. Open quantum system parameters from molecular dynamics

    CERN Document Server

    Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander

    2015-01-01

    We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...

  1. 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.

  2. Characterization of Rare Events in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carsten Hartmann

    2013-12-01

    Full Text Available A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.

  3. Unraveling the molecular effects of mutation L270P on Wiskkot-Aldrich syndrome protein: insights from molecular dynamics approach.

    Science.gov (United States)

    Palaniappan, Chandrasekaran; Rao, Sethumadhavan; Ramalingam, Rajasekaran

    2016-09-01

    Missense mutation L270P disrupts the auto-inhibited state of "Wiskkot-Aldrich syndrome protein" (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42.

  4. Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

    CERN Document Server

    Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2011-01-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

  5. The MOLDY short-range molecular dynamics package

    Science.gov (United States)

    Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

    2011-12-01

    We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as

  6. 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...

  7. Molecular dynamics modelling of solidification in metals

    Energy Technology Data Exchange (ETDEWEB)

    Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  8. Molecular crowding and protein enzymatic dynamics.

    Science.gov (United States)

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

    The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding.

  9. 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.

  10. 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

  11. Control-volume representation of molecular dynamics.

    Science.gov (United States)

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2012-05-01

    A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.

  12. Learning generative models of molecular dynamics.

    Science.gov (United States)

    Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J

    2012-01-01

    We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.

  13. Dynamic Maintenance and Visualization of Molecular Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

    2004-12-16

    Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

  14. Adsorbed water on iron surface by molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, F.W.; Campos, T.M.B.; Cividanes, L.S., E-mail: flaviano@ita.br; Simonetti, E.A.N.; Thim, G.P.

    2016-01-30

    Graphical abstract: - Highlights: • We developed a new force field to describe the Fe–H{sub 2}O interaction. • We developed a new force field to describe the flexible water model at low temperature. • We analyze the orientation of water along the iron surface. • We calculate the vibrational spectra of water near the iron surface. • We found a complex relationship between water orientation and the atomic vibrational spectra at different sites of adsorption along the iron surface. - Abstract: The adsorption of H{sub 2}O molecules on metal surfaces is important to understand the early process of water corrosion. This process can be described by computational simulation using molecular dynamics and Monte Carlo. However, this simulation demands an efficient description of the surface interactions between the water molecule and the metallic surface. In this study, an effective force field to describe the iron-water surface interactions was developed and it was used in a molecular dynamics simulation. The results showed a very good agreement between the simulated vibrational-DOS spectrum and the experimental vibrational spectrum of the iron–water interface. The water density profile revealed the presence of a water double layer in the metal interface. Furthermore, the horizontal mapping combined with the angular distribution of the molecular plane allowed the analysis of the water structure above the surface, which in turn agrees with the model of the double layer on metal surfaces.

  15. A new formalism for molecular dynamics in internal coordinates

    Science.gov (United States)

    Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel

    2001-03-01

    Internal coordinate molecular dynamics (ICMD) has been used in the past in simulations for large molecules as an alternative way of increasing step size with a reduced operational dimension that is not achievable by MD in Cartesian coordinates. A new ICMD formalism for flexible molecular systems is presented, which is based on the spectroscopic B-matrix rather than the A-matrix of previous methods. The proposed formalism does not require an inversion of a large matrix as in the recursive formulations based on robot dynamics, and takes advantage of the sparsity of the B-matrix, ensuring computational efficiency for flexible molecules. Each molecule's external rotations about an arbitrary atom center, which may differ from its center of mass, are parameterized by the SU(2) Euler representation, giving singularity free parameterization. Although the formalism is based on the use of nonredundant generalized (internal and external) coordinates, an MD simulation in linearly dependent coordinates can be done by finding a transformation to a new set of independent coordinates. Based on the clear separability in the generalized coordinates between fast varying degrees of freedom and slowly varying ones, a multiple time step algorithm is introduced that avoids the previous nontrivial interaction distance classification. Also presented is a recursive method for computing nonzero A-matrix elements that is much easier to apply to a general molecular structure than the previous method.

  16. Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

    Science.gov (United States)

    Yong, Chin W

    2016-08-22

    DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

  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. 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)

  19. Acoustic properties in glycerol glass-former: Molecular dynamics simulation

    Science.gov (United States)

    Busselez, Remi; Pezeril, Thomas; Institut des Materiaux et Molecules du Mans Team

    2013-03-01

    Study of high-frequency collective dynamics around TeraHertz region in glass former has been a subject of intense investigations and debates over the past decade. In particular, the presence of the Boson peak characteristic of glassy material and its relation to other glass anomalies. Recently, experiments and simulations have underlined possible relation between Boson peak and transverse acoustic modes in glassy materials. In particular, simulations of simple Lennard Jones glass former have shown a relation between Ioffe-Regel criterion in transverse modes and Boson peak. We present here molecular dynamics simulation on high frequency dynamics of glycerol. In order to study mesoscopic order (0.5-5nm-1), we made use of large simulation box containing 80000 atoms. Analysis of collective longitudinal and transverse acoustic modes shows striking similarities in comparison with simulation of Lennard-Jones particles. In particular, it seems that a connection may exist between Ioffe-Regel criterion for transverse modes and Bose Peak frequency. However,in our case we show that this connection may be related with structural correlation arising from molecular clusters.

  20. Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

    Science.gov (United States)

    2015-08-01

    Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software by N Scott Weingarten and James P Larentzos Approved for...0687 ● AUG 2015 US Army Research Laboratory Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular...Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software 5a. CONTRACT NUMBER 5b