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Sample records for short-range molecular dynamics

  1. Kernel optimization for short-range molecular dynamics

    Science.gov (United States)

    Hu, Changjun; Wang, Xianmeng; Li, Jianjiang; He, Xinfu; Li, Shigang; Feng, Yangde; Yang, Shaofeng; Bai, He

    2017-02-01

    To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the "if-clause" of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version.

  2. 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

  3. Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

    International Nuclear Information System (INIS)

    Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

    2011-01-01

    The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.

  4. Molecular dynamics simulations of short-range force systems on 1024-node hypercubes

    International Nuclear Information System (INIS)

    Plimpton, S.J.

    1990-01-01

    In this paper, two parallel algorithms for classical molecular dynamics are presented. The first assigns each processor to a subset of particles; the second assigns each to a fixed region of 3d space. The algorithms are implemented on 1024-node hypercubes for problems characterized by short-range forces, diffusion (so that each particle's neighbors change in time), and problem size ranging from 250 to 10000 particles. Timings for the algorithms on the 1024-node NCUBE/ten and the newer NCUBE 2 hypercubes are given. The latter is found to be competitive with a CRAY-XMP, running an optimized serial algorithm. For smaller problems the NCUBE 2 and CRAY-XMP are roughly the same; for larger ones the NCUBE 2 is up to twice as fast. Parallel efficiencies of the algorithms and communication parameters for the two hypercubes are also examined

  5. Ab initio molecular dynamics model for density, elastic properties and short range order of Co-Fe-Ta-B metallic glass thin films

    International Nuclear Information System (INIS)

    Hostert, C; Music, D; Schneider, J M; Bednarcik, J; Keckes, J; Kapaklis, V; Hjörvarsson, B

    2011-01-01

    Density, elastic modulus and the pair distribution function of Co-Fe-Ta-B metallic glasses were obtained by ab initio molecular dynamics simulations and measured for sputtered thin films using x-ray reflectivity, nanoindentation and x-ray diffraction using high energy photons. The computationally obtained density of 8.19 g cm -3 for Co 43 Fe 20 Ta 5.5 B 31.5 and 8.42 g cm -3 for Co 45.5 Fe 24 Ta 6 B 24.5 , as well as the Young’s moduli of 273 and 251 GPa, respectively, are consistent with our experiments and literature data. These data, together with the good agreement between the theoretical and the experimental pair distribution functions, indicate that the model established here is useful to describe the density, elasticity and short range order of Co-Fe-Ta-B metallic glass thin films. Irrespective of the investigated variation in chemical composition, (Co, Fe)-B cluster formation and Co-Fe interactions are identified by density-of-states analysis. Strong bonds within the structural units and between the metallic species may give rise to the comparatively large stiffness. (paper)

  6. Dynamical arrest in dense short-ranged attractive colloids

    International Nuclear Information System (INIS)

    Foffi, G; Sciortino, F; Zaccarelli, E; Tartaglia, P

    2004-01-01

    We study thermodynamic and dynamic properties of model colloidal systems interacting with a hard core repulsion and a short-range attraction, and provide an overall picture of their phase diagrams which shows a very rich phenomenology. We focus on the slow dynamic properties of this model, investigating in detail the glass transition lines (both repulsive and attractive), the glass-glass transitions and the location of the higher order singularities. We discuss the relative location of the glass lines and of the metastable liquid-gas binodal, an issue relevant for the understanding of low density arrested states of matter

  7. In-medium short-range dynamics of nucleons: Recent theoretical and experimental advances

    Energy Technology Data Exchange (ETDEWEB)

    Atti, Claudio Ciofi degli, E-mail: ciofi@pg.infn.it

    2015-08-14

    The investigation of in-medium short-range dynamics of nucleons, usually referred to as the study of short-range correlations (SRCs), is a key issue in nuclear and hadronic physics. As a matter of fact, even in the simplified assumption that the nucleus could be described as a system of protons and neutrons interacting via effective nucleon–nucleon (NN) interactions, several non trivial problems arise concerning the description of in-medium (NN short-range dynamics, namely: (i) the behavior of the NN interaction at short inter-nucleon distances in medium cannot be uniquely constrained by the experimental NN scattering phase shifts due to off-shell effects; (ii) by rigorous renormalization group (RG) techniques entire families of phase equivalent interactions differing in the short-range part can be derived; (iii) the in-medium NN interaction may be, in principle, different from the free one; (iv) when the short inter-nucleon separation is of the order of the nucleon size, the question arises of possible effects from quark and gluon degrees of freedom. For more than fifty years, experimental evidence of SRCs has been searched by means of various kinds of nuclear reactions, without however convincing results, mainly because the effects of SRCs arise from non observable quantities, like, e.g., the momentum distributions, and have been extracted from observable cross sections where short- and long-range effects, effects from nucleonic and non nucleonic degrees of freedom, and effects from final state interaction, could not be unambiguously separated out. Recent years, however, were witness of new progress in the field: from one side, theoretical and computational progress has allowed one to solve ab initio the many-nucleon non relativistic Schrödinger equation in terms of realistic NN interactions, obtaining realistic microscopic wave functions, unless the case of parametrized wave functions used frequently in the past, moreover the development of advanced

  8. Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations.

    Science.gov (United States)

    Kundu, Mainak; He, Ting-Fang; Lu, Yangyi; Wang, Lijuan; Zhong, Dongping

    2018-05-03

    Short-range electron transfer (ET) in proteins is an ultrafast process on the similar timescales as local protein-solvent fluctuations thus the two dynamics are coupled. Here, we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with eleven mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical timescales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.

  9. OTDM Networking for Short Range High-Capacity Highly Dynamic Networks

    DEFF Research Database (Denmark)

    Medhin, Ashenafi Kiros

    This PhD thesis aims at investigating the possibility of designing energy-efficient high-capacity (up to Tbit/s) optical network scenarios, leveraging on the effect of collective switching of many bits simultaneously, as is inherent in high bit rate serial optical data signals. The focus...... is on short range highly dynamic networks, catering to data center needs. The investigation concerns optical network scenarios, and experimental implementations of high bit rate serial data packet generation and reception, scalable optical packet labeling, simple optical label extraction and stable ultra...

  10. Attractive short-range interatomic potential in the lattice dynamics of niobium and tantalum

    International Nuclear Information System (INIS)

    Onwuagba, B.N.; Pal, S.

    1987-01-01

    It is shown in the framework of the pseudopotential approach that there is a sizable attractive short-range component of the interatomic potential due to the s-d interaction which has the same functional form in real space as the Born-Mayer repulsion due to the overlap of core electron wave functions centred on neighbouring ions. The magnitude of this attractive component is such as to completely cancel the conventional Born-Mayer repulsion, making the resultant short-range interatomic potential attractive rather than repulsive. Numerical calculations show that the attractive interatomics potential, which represents the local-field correction, leads to a better understanding of the occurrence of the soft modes in the phonon dispersion curves of niobium and tantalum

  11. Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

    Science.gov (United States)

    Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

    2015-01-01

    The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.

  12. Short-range dynamics and prediction of mesoscale flow patterns in the MISTRAL field experiment

    Energy Technology Data Exchange (ETDEWEB)

    Weber, R.O.; Kaufmann, P.; Talkner, P. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    In a limited area of about 50 km by 50 km with complex topography, wind measurements on a dense network were performed during the MISTRAL field experiment in 1991-1992. From these data the characteristic wind fields were identified by an automated classification method. The dynamics of the resulting twelve typical regional flow patterns is studied. It is discussed how transitions between the flow patterns take place and how well the transition probabilities can be described in the framework of a Markov model. Guided by this discussion, a variety of prediction models were tested which allow a short-term forecast of the flow pattern type. It is found that a prediction model which uses forecast information from the synoptic scale has the best forecast skill. (author) 2 figs., 7 refs.

  13. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

    Science.gov (United States)

    Narth, Christophe; Lagardère, Louis; Polack, Étienne; Gresh, Nohad; Wang, Qiantao; Bell, David R; Rackers, Joshua A; Ponder, Jay W; Ren, Pengyu Y; Piquemal, Jean-Philip

    2016-02-15

    We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. Copyright © 2016 Wiley Periodicals, Inc.

  14. Static and Dynamic Accuracy of an Innovative Miniaturized Wearable Platform for Short Range Distance Measurements for Human Movement Applications

    Directory of Open Access Journals (Sweden)

    Stefano Bertuletti

    2017-06-01

    Full Text Available Magneto-inertial measurement units (MIMU are a suitable solution to assess human motor performance both indoors and outdoors. However, relevant quantities such as step width and base of support, which play an important role in gait stability, cannot be directly measured using MIMU alone. To overcome this limitation, we developed a wearable platform specifically designed for human movement analysis applications, which integrates a MIMU and an Infrared Time-of-Flight proximity sensor (IR-ToF, allowing for the estimate of inter-object distance. We proposed a thorough testing protocol for evaluating the IR-ToF sensor performances under experimental conditions resembling those encountered during gait. In particular, we tested the sensor performance for different (i target colors; (ii sensor-target distances (up to 200 mm and (iii sensor-target angles of incidence (AoI (up to 60 ∘ . Both static and dynamic conditions were analyzed. A pendulum, simulating the oscillation of a human leg, was used to generate highly repeatable oscillations with a maximum angular velocity of 6 rad/s. Results showed that the IR-ToF proximity sensor was not sensitive to variations of both distance and target color (except for black. Conversely, a relationship between error magnitude and AoI values was found. For AoI equal to 0 ∘ , the IR-ToF sensor performed equally well both in static and dynamic acquisitions with a distance mean absolute error <1.5 mm. Errors increased up to 3.6 mm (static and 11.9 mm (dynamic for AoI equal to ± 30 ∘ , and up to 7.8 mm (static and 25.6 mm (dynamic for AoI equal to ± 60 ∘ . In addition, the wearable platform was used during a preliminary experiment for the estimation of the inter-foot distance on a single healthy subject while walking. In conclusion, the combination of magneto-inertial unit and IR-ToF technology represents a valuable alternative solution in terms of accuracy, sampling frequency, dimension and power consumption

  15. Short-time dynamics of lysozyme solutions with competing short-range attraction and long-range repulsion: Experiment and theory

    Science.gov (United States)

    Riest, Jonas; Nägele, Gerhard; Liu, Yun; Wagner, Norman J.; Godfrin, P. Douglas

    2018-02-01

    Recently, atypical static features of microstructural ordering in low-salinity lysozyme protein solutions have been extensively explored experimentally and explained theoretically based on a short-range attractive plus long-range repulsive (SALR) interaction potential. However, the protein dynamics and the relationship to the atypical SALR structure remain to be demonstrated. Here, the applicability of semi-analytic theoretical methods predicting diffusion properties and viscosity in isotropic particle suspensions to low-salinity lysozyme protein solutions is tested. Using the interaction potential parameters previously obtained from static structure factor measurements, our results of Monte Carlo simulations representing seven experimental lysoyzme samples indicate that they exist either in dispersed fluid or random percolated states. The self-consistent Zerah-Hansen scheme is used to describe the static structure factor, S(q), which is the input to our calculation schemes for the short-time hydrodynamic function, H(q), and the zero-frequency viscosity η. The schemes account for hydrodynamic interactions included on an approximate level. Theoretical predictions for H(q) as a function of the wavenumber q quantitatively agree with experimental results at small protein concentrations obtained using neutron spin echo measurements. At higher concentrations, qualitative agreement is preserved although the calculated hydrodynamic functions are overestimated. We attribute the differences for higher concentrations and lower temperatures to translational-rotational diffusion coupling induced by the shape and interaction anisotropy of particles and clusters, patchiness of the lysozyme particle surfaces, and the intra-cluster dynamics, features not included in our simple globular particle model. The theoretical results for the solution viscosity, η, are in qualitative agreement with our experimental data even at higher concentrations. We demonstrate that semi

  16. Brownian motion in short range random potentials

    International Nuclear Information System (INIS)

    Romero, A.H.; Romero, A.H.; Sancho, J.M.

    1998-01-01

    A numerical study of Brownian motion of noninteracting particles in random potentials is presented. The dynamics are modeled by Langevin equations in the high friction limit. The random potentials are Gaussian distributed and short ranged. The simulations are performed in one and two dimensions. Different dynamical regimes are found and explained. Effective subdiffusive exponents are obtained and commented on. copyright 1998 The American Physical Society

  17. Short-range communication system

    Science.gov (United States)

    Alhorn, Dean C. (Inventor); Howard, David E. (Inventor); Smith, Dennis A. (Inventor)

    2012-01-01

    A short-range communication system includes an antenna, a transmitter, and a receiver. The antenna is an electrical conductor formed as a planar coil with rings thereof being uniformly spaced. The transmitter is spaced apart from the plane of the coil by a gap. An amplitude-modulated and asynchronous signal indicative of a data stream of known peak amplitude is transmitted into the gap. The receiver detects the coil's resonance and decodes same to recover the data stream.

  18. Short-range fundamental forces

    International Nuclear Information System (INIS)

    Antoniadis, I.; Baessler, S.; Buchner, M.; Fedorov, V.V.; Hoedl, S.; Nesvizhevsky, V.V.; Pignol, G.; Protasov, K.V.; Lambrecht, A.; Reynaud, S.; Sobolev, Y.

    2010-01-01

    We consider theoretical motivations to search for extra short-range fundamental forces as well as experiments constraining their parameters. The forces could be of two types: 1) spin-independent forces; 2) spin-dependent axion-like forces. Different experimental techniques are sensitive in respective ranges of characteristic distances. The techniques include measurements of gravity at short distances, searches for extra interactions on top of the Casimir force, precision atomic and neutron experiments. We focus on neutron constraints, thus the range of characteristic distances considered here corresponds to the range accessible for neutron experiments

  19. Short-range interactions between surfactants, silica species and EDTA⁴- salt during self-assembly of siliceous mesoporous molecular sieve: a UV Raman study.

    Science.gov (United States)

    Song, Jiayin; Liu, Liping; Li, Peng; Xiong, Guang

    2012-11-01

    The effects of surfactants, counterions and additive salts on the formation of siliceous mesoporous molecular sieves during self-assembly process were investigated by UV Raman spectroscopy, X-ray diffraction (XRD) and transmission electron microscopy (TEM) techniques. The surfactant molecules experience the rearrangement after adding the silica species and adjusting the pH value. The obvious change of the Raman bands related to the surfactants supports a cooperative interaction between surfactant and inorganic species during self-assembly process. The addition of EDTANa(4) to the system induces the interaction between the COO(-) groups of EDTA(4-) and silanol groups of silica and a strong interaction between the EDTA(4-) and the N(+)(CH(3))(3) groups of the surfactant. The above interactions may be the main reason for the salt effect. The new information from the change of the chemical bonds allows for a further analysis to the interactions of different salts between surfactants and silica species at molecular level. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Intentionally Short Range Communications (ISRC)

    Science.gov (United States)

    1993-05-01

    molecular oxygen in the atmosphere at 60 GHz (figure 9 LIppolito, 1981]). The MMW range is similar to that of the UV links. 3.3.1 Variable Range Similar to...option also requires that the signal be strong enough to overcome the noise from the solar and background sources, although the molecular oxygen and... emisions . Lasing will occur only within the cavity when the alignment is correct and not lasing othem ise. Such a cavity is dcteclable only when an observer

  1. Magnetic short range order in Gd

    International Nuclear Information System (INIS)

    Child, H.R.

    1976-01-01

    Quasielastic neutron scattering has been used to investigate magnetic short range order in Gd for 80 0 K 0 K. Short range order exists throughout this range from well below T/sub C/ = 291 0 K to well above it and can be reasonably well described by an anisotropic Orstein-Zernike form for chi

  2. Narrow resonances and short-range interactions

    International Nuclear Information System (INIS)

    Gelman, Boris A.

    2009-01-01

    Narrow resonances in systems with short-range interactions are discussed in an effective field theory (EFT) framework. An effective Lagrangian is formulated in the form of a combined expansion in powers of a momentum Q 0 | 0 --a resonance peak energy. At leading order in the combined expansion, a two-body scattering amplitude is the sum of a smooth background term of order Q 0 and a Breit-Wigner term of order Q 2 (δε) -1 which becomes dominant for δε 3 . Such an EFT is applicable to systems in which short-distance dynamics generates a low-lying quasistationary state. The EFT is generalized to describe a narrow low-lying resonance in a system of charged particles. It is shown that in the case of Coulomb repulsion, a two-body scattering amplitude at leading order in a combined expansion is the sum of a Coulomb-modified background term and a Breit-Wigner amplitude with parameters renormalized by Coulomb interactions.

  3. Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system

    KAUST Repository

    Allsopp, Nicholas; Ruocco, Giancarlo; Fratalocchi, Andrea

    2012-01-01

    We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the short-range atomic dynamics

  4. Molecular dynamics and Monte Carlo calculations in statistical mechanics

    International Nuclear Information System (INIS)

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

    1976-01-01

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

  5. Short-range correlations with pseudopotentials

    International Nuclear Information System (INIS)

    Osman, A.

    1976-01-01

    Short-range correlations in nuclei are considered on an unitary-model operator approach. Short-range pseudopotentials have been added to achieve healing in the correlated wave functions. With the introduction of the pseudopotentials, correlated basis wave functions are constructed. The matrix element for effective interaction in nuclei is developed. The required pseudopotentials have been calculated for the Hamda-Johnston, Yale and Reid potentials and for the nuclear nucleon-nucleon potential A calculated by us according to meson exchange between nucleons. (Osman, A.)

  6. Short range order of selenite glasses

    Czech Academy of Sciences Publication Activity Database

    Neov, S.; Gerasimova, I.; Yordanov, S.; Lakov, L.; Mikula, Pavol; Lukáš, Petr

    1999-01-01

    Roč. 40, č. 2 (1999), s. 111-112 ISSN 0031-9090 R&D Projects: GA AV ČR KSK1010104 Keywords : short range * selenite glasses Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.822, year: 1999

  7. Magnetic short-range order in Gd

    International Nuclear Information System (INIS)

    Child, H.R.

    1978-01-01

    The magnetic short-range order in a ferromagnetic, isotopically enriched 160 Gd metal single crystal has been investigated by quasielastic scattering of 81-meV neutrons. Since Gd behaves as an S-state ion in the metal, little anisotropy is expected in its magnetic behavior. However, the data show that there is anisotropic short-range order present over a large temperature interval both above and below T/sub C/. The data have been analyzed in terms of an Ornstein-Zernike Lorentzian form with anisotropic correlation ranges. These correlation ranges as deduced from the observed data behave normally above T/sub C/ but seem to remain constant over a fairly large interval below T/sub C/ before becoming unobservable at lower temperatures. These observations suggest that the magnetic ordering in Gd may be a more complicated phenomenon than first believed

  8. 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....

  9. Nonlocality and short-range wetting phenomena.

    Science.gov (United States)

    Parry, A O; Romero-Enrique, J M; Lazarides, A

    2004-08-20

    We propose a nonlocal interfacial model for 3D short-range wetting at planar and nonplanar walls. The model is characterized by a binding-potential functional depending only on the bulk Ornstein-Zernike correlation function, which arises from different classes of tubelike fluctuations that connect the interface and the substrate. The theory provides a physical explanation for the origin of the effective position-dependent stiffness and binding potential in approximate local theories and also obeys the necessary classical wedge covariance relationship between wetting and wedge filling. Renormalization group and computer simulation studies reveal the strong nonperturbative influence of nonlocality at critical wetting, throwing light on long-standing theoretical problems regarding the order of the phase transition.

  10. Nonlocality and Short-Range Wetting Phenomena

    Science.gov (United States)

    Parry, A. O.; Romero-Enrique, J. M.; Lazarides, A.

    2004-08-01

    We propose a nonlocal interfacial model for 3D short-range wetting at planar and nonplanar walls. The model is characterized by a binding-potential functional depending only on the bulk Ornstein-Zernike correlation function, which arises from different classes of tubelike fluctuations that connect the interface and the substrate. The theory provides a physical explanation for the origin of the effective position-dependent stiffness and binding potential in approximate local theories and also obeys the necessary classical wedge covariance relationship between wetting and wedge filling. Renormalization group and computer simulation studies reveal the strong nonperturbative influence of nonlocality at critical wetting, throwing light on long-standing theoretical problems regarding the order of the phase transition.

  11. Short range order in liquid pnictides

    International Nuclear Information System (INIS)

    Mayo, M; Makov, G; Yahel, E; Greenberg, Y

    2013-01-01

    Liquid pnictides have anomalous physical properties and complex radial distribution functions. The quasi-crystalline model of liquid structure is applied to interpret the three-dimensional structure of liquid pnictides. It is shown that all the column V elements can be characterized by a short range order lattice symmetry similar to that of the underlying solid, the A7 structure, which originates from a Peierls distorted simple cubic lattice. The evolution of the liquid structure down the column as well as its temperature and pressure dependence is interpreted by means of the effect of thermodynamic parameters on the Peierls distortion. Surprisingly, it is found that the Peierls effect increases with temperature and the nearest neighbour distances exhibit negative thermal expansion. (paper)

  12. 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.

  13. Molecular dynamics for fermions

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    2000-02-01

    The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

  14. Short range order of selenite glasses

    Czech Academy of Sciences Publication Activity Database

    Neov, Dimitar; Gerasimova, I.; Yordanov, S.; Lakov, L.; Mikula, Pavol; Lukáš, Petr; Dimitriev, Y.

    1999-01-01

    Roč. 40, č. 2 (1999), s. 111-112 ISSN 0031-9090 R&D Projects: GA ČR GV202/97/K038; GA AV ČR KSK1048601 Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 0.822, year: 1999

  15. The nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-03-01

    MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

  16. Freely cooling granular gases with short-ranged attractive potentials

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Eric; Subramaniam, Shankar, E-mail: shankar@iastate.edu [Department of Mechanical Engineering, Center for Multiphase Flow Research, Iowa State University, Ames, Iowa 50011 (United States)

    2015-04-15

    We treat the case of an undriven gas of inelastic hard-spheres with short-ranged attractive potentials via an extension of the pseudo-Liouville operator formalism. New evolution equations for the granular temperature and coordination number are obtained. The granular temperature exhibits deviation from both Haff’s law and the case of long-ranged potentials. We verify this departure using soft-sphere discrete element method simulations. Excellent agreement is found for the duration of the simulation even beyond where exclusively binary collisions are expected. Simulations show the emergence of strong spatial-velocity correlations on the length scale of the last peak in the pair-correlation function but do not show strong correlations beyond this length scale. We argue that molecular chaos may remain an adequate approximation if the system is modelled as a Smoluchowski type equation with aggregation and break-up processes.

  17. Combining 2-m temperature nowcasting and short range ensemble forecasting

    Directory of Open Access Journals (Sweden)

    A. Kann

    2011-12-01

    Full Text Available During recent years, numerical ensemble prediction systems have become an important tool for estimating the uncertainties of dynamical and physical processes as represented in numerical weather models. The latest generation of limited area ensemble prediction systems (LAM-EPSs allows for probabilistic forecasts at high resolution in both space and time. However, these systems still suffer from systematic deficiencies. Especially for nowcasting (0–6 h applications the ensemble spread is smaller than the actual forecast error. This paper tries to generate probabilistic short range 2-m temperature forecasts by combining a state-of-the-art nowcasting method and a limited area ensemble system, and compares the results with statistical methods. The Integrated Nowcasting Through Comprehensive Analysis (INCA system, which has been in operation at the Central Institute for Meteorology and Geodynamics (ZAMG since 2006 (Haiden et al., 2011, provides short range deterministic forecasts at high temporal (15 min–60 min and spatial (1 km resolution. An INCA Ensemble (INCA-EPS of 2-m temperature forecasts is constructed by applying a dynamical approach, a statistical approach, and a combined dynamic-statistical method. The dynamical method takes uncertainty information (i.e. ensemble variance from the operational limited area ensemble system ALADIN-LAEF (Aire Limitée Adaptation Dynamique Développement InterNational Limited Area Ensemble Forecasting which is running operationally at ZAMG (Wang et al., 2011. The purely statistical method assumes a well-calibrated spread-skill relation and applies ensemble spread according to the skill of the INCA forecast of the most recent past. The combined dynamic-statistical approach adapts the ensemble variance gained from ALADIN-LAEF with non-homogeneous Gaussian regression (NGR which yields a statistical mbox{correction} of the first and second moment (mean bias and dispersion for Gaussian distributed continuous

  18. The role of short-range Cys171-Cys178 disulfide bond in maintaining cutinase active site integrity: A molecular dynamics simulation

    International Nuclear Information System (INIS)

    Matak, Mehdi Youssefi; Moghaddam, Majid Erfani

    2009-01-01

    Understanding structural determinants in enzyme active site integrity can provide a good knowledge to design efficient novel catalytic machineries. Fusarium solani pisi cutinase with classic triad Ser-His-Asp is a promising enzyme to scrutinize these structural determinants. We performed two MD simulations: one, with the native structure, and the other with the broken Cys171-Cys178 disulfide bond. This disulfide bond stabilizes a turn in active site on which catalytic Asp175 is located. Functionally important H-bonds and atomic fluctuations in catalytic pocket have been changed. We proposed that this disulfide bond within active site can be considered as an important determinant of cutinase active site structural integrity.

  19. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  20. Magnetic short range order and the exchange coupling in magnets

    International Nuclear Information System (INIS)

    Antropov, V.P.

    2006-01-01

    We discuss our recent results of time-dependent density functional simulations of magnetic properties of Fe and Ni at finite temperatures. These results indicated that a strong magnetic short range order is responsible for the magnetic properties of elementary Ni and any itinerant magnet in general. We demonstrated that one can use the value of the magnetic short range order parameter to produce new quantitative classification of magnets. We also discuss the nature of the exchange coupling and its connection with the short range order. The spin-wave like propagating and diffusive excitations in paramagnetic localized systems with small short range order have been predicted while in the itinerant systems the short range order is more complicated. The possible smallness of the quantum factor in the itinerant magnets with short range order is discussed

  1. Numerical challenges of short range wake field calculations

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Thomas; Gjonaj, Erion; Weiland, Thomas [Technische Universitaet Darmstadt (Germany). Institut fuer Theorie Elektromagnetischer Felder (TEMF)

    2011-07-01

    For present and future accelerator projects with ultra short bunches the accurate and reliable calculation of short range wake fields is an important issue. However, the numerical calculation of short range wake fields is a numerical challenging task. The presentation gives an overview over the numerical challenges and techniques for short range wake field calculations. Finally, some simulation results obtained by the program PBCI developed at the TU Darmstadt are presented.

  2. Isobar configurations in nuclei and short range correlations

    CERN Document Server

    Weber, H J

    1979-01-01

    Recent results on short range correlations and isobar configurations are reviewed, and in particular a unitary version of the isobar model, coupling constants and rho -meson transition potentials, a comparison with experiments, the CERN N*-knockout from /sup 4/He, QCD and the NN interaction of short range. (42 refs).

  3. Molecular dynamics of bacteriorhodopsin.

    Science.gov (United States)

    Lupo, J A; Pachter, R

    1997-02-01

    A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

  4. Molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Dehmer, J.L.

    1982-01-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed

  5. Short-range quantitative precipitation forecasting using Deep Learning approaches

    Science.gov (United States)

    Akbari Asanjan, A.; Yang, T.; Gao, X.; Hsu, K. L.; Sorooshian, S.

    2017-12-01

    Predicting short-range quantitative precipitation is very important for flood forecasting, early flood warning and other hydrometeorological purposes. This study aims to improve the precipitation forecasting skills using a recently developed and advanced machine learning technique named Long Short-Term Memory (LSTM). The proposed LSTM learns the changing patterns of clouds from Cloud-Top Brightness Temperature (CTBT) images, retrieved from the infrared channel of Geostationary Operational Environmental Satellite (GOES), using a sophisticated and effective learning method. After learning the dynamics of clouds, the LSTM model predicts the upcoming rainy CTBT events. The proposed model is then merged with a precipitation estimation algorithm termed Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN) to provide precipitation forecasts. The results of merged LSTM with PERSIANN are compared to the results of an Elman-type Recurrent Neural Network (RNN) merged with PERSIANN and Final Analysis of Global Forecast System model over the states of Oklahoma, Florida and Oregon. The performance of each model is investigated during 3 storm events each located over one of the study regions. The results indicate the outperformance of merged LSTM forecasts comparing to the numerical and statistical baselines in terms of Probability of Detection (POD), False Alarm Ratio (FAR), Critical Success Index (CSI), RMSE and correlation coefficient especially in convective systems. The proposed method shows superior capabilities in short-term forecasting over compared methods.

  6. Impact of additional surface observation network on short range ...

    Indian Academy of Sciences (India)

    Stations (AWS) surface observations (temperature and moisture) on the short range forecast over the Indian ... models, which are able to resolve mesoscale fea- ... J. Earth Syst. Sci. ..... terization of the snow field in a cloud model; J. Climate.

  7. Measurements of short-range ordering in Ni3Al

    International Nuclear Information System (INIS)

    Okamoto, J.K.; Ahn, C.C.

    1992-01-01

    This paper reports on extended electron energy-loss fine structure (EXELFS) that has been used to measure short-range ordering in Ni 3 Al. Films of fcc Ni 3 Al with suppressed short-range order synthesized by vacuum evaporation of Ni 3 Al onto room temperature substrates. EXELFS data were taken from both Al K and Ni L 23 edges. The development of short-range order was observed after the samples were annealed for various times at temperatures below 350 degrees C. Upon comparison with ab initio planewave EXELFS calculations, it was found that the Warren-Cowley short-range order parameter a(1nn) changed by about -0.1 after 210 minutes of annealing at 150 degrees C

  8. Physical adsorption and molecular dynamics

    International Nuclear Information System (INIS)

    Cohan, N.V.

    1981-01-01

    Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

  9. Hard probes of short-range nucleon-nucleon correlations

    Energy Technology Data Exchange (ETDEWEB)

    J. Arrington, D. W. Higinbotham, G. Rosner, M. Sargsian

    2012-10-01

    The strong interaction of nucleons at short distances leads to a high-momentum component to the nuclear wave function, associated with short-range correlations between nucleons. These short-range, high-momentum structures in nuclei are one of the least well understood aspects of nuclear matter, relating to strength outside of the typical mean-field approaches to calculating the structure of nuclei. While it is difficult to study these short-range components, significant progress has been made over the last decade in determining how to cleanly isolate short-range correlations in nuclei. We have moved from asking if such structures exist, to mapping out their strength in nuclei and studying their microscopic structure. A combination of several different measurements, made possible by high-luminosity and high-energy accelerators, coupled with an improved understanding of the reaction mechanism issues involved in studying these structures, has led to significant progress, and provided significant new information on the nature of these small, highly-excited structures in nuclei. We review the general issues related to short-range correlations, survey recent experiments aimed at probing these short-range structures, and lay out future possibilities to further these studies.

  10. A method of short range system analysis for nuclear utilities

    International Nuclear Information System (INIS)

    Eng, R.; Mason, E.A.; Benedict, M.

    1976-01-01

    An optimization procedure has been formulated and tested that is capable of solving for the optimal generation schedule of several nuclear power reactors in an electric power utility system, under short-range, resource-limited, conditions. The optimization procedure utilizes a new concept called the Opportunity Cost of Nuclear Power (OCNP) to optimally assign the resource-limited nuclear energy to the different weeks and hours in the short-range planning horizon. OCNP is defined as the cost of displaced energy when optimally distributed nuclear energy is marginally increased. Under resource-limited conditions, the short-range 'value' of nuclear power to a utility system is not its actual generation cost, but the cost of the next best alternative supply of energy, the OCNP. OCNP is a function of a week's system reserve capacity, the system's economic loading order, the customer demand function, and the nature of the available utility system generating units. The optimized OCNP value of the short-range planning period represents the utility's short-range energy replacement cost incurred when selling nuclear energy to a neighbouring utility. (author)

  11. Short-range components of nuclear forces: Experiment versus mythology

    International Nuclear Information System (INIS)

    Kukulin, V. I.; Platonova, M. N.

    2013-01-01

    The present-day situation around the description of various (central, spin-orbit, and tensor) components of short-range nuclear forces is discussed. A traditional picture of these interactions based on the idea of one-meson exchange is contrasted against numerous results of recent experiments. As is shown in the present study, these results often deviate strongly from the predictions of traditional models. One can therefore state that such models are inapplicable to describing short-range nuclear forces and that it is necessary to go over from a traditional description to some alternative QCD-based (or QCD-motivated) picture. This means that, despite the widespread popularity of traditional concepts of short-range nuclear forces and their applicability in many particular cases, these concepts are not more than scientific myths that show their inconsistency when analyzed from the viewpoint of the modern experiment

  12. Electronically driven short-range lattice instability: Possible role in superconductive pairing

    International Nuclear Information System (INIS)

    Szasz, A.

    1991-01-01

    A superconducting pairing mechanism is suggested, mediating by collective and coherent cluster fluctuations in the materials. The model, based on a geometrical frustration, proposes a dynamic effect driven by a special short-range electronic instability. Experimental support for this model is discussed

  13. A short-range ensemble prediction system for southern Africa

    CSIR Research Space (South Africa)

    Park, R

    2012-10-01

    Full Text Available system for southern Africa R PARK, WA LANDMAN AND F ENGELBRECHT CSIR, PO Box 395, Pretoria, South Africa, 0001 Email: xxxxxxxxxxxxxx@csir.co.za ? www.csir.co.za INTRODUCTION This research has been conducted in order to develop a short-range ensemble... stream_source_info Park_2012.pdf.txt stream_content_type text/plain stream_size 7211 Content-Encoding ISO-8859-1 stream_name Park_2012.pdf.txt Content-Type text/plain; charset=ISO-8859-1 A short-range ensemble prediction...

  14. Gas Phase Molecular Dynamics

    International Nuclear Information System (INIS)

    Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

    1999-01-01

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule

  15. Small Device For Short-Range Antenna Measurements Using Optics

    DEFF Research Database (Denmark)

    Yanakiev, Boyan Radkov; Nielsen, Jesper Ødum; Christensen, Morten

    2011-01-01

    This paper gives a practical solution for implementing an antenna radiation pattern measurement device using optical fibers. It is suitable for anechoic chambers as well as short range channel sounding. The device is optimized for small size and provides a cheap and easy way to make optical antenna...

  16. High-Capacity Short-Range Optical Communication Links

    DEFF Research Database (Denmark)

    Tatarczak, Anna

    Over the last decade, we have observed a tremendous spread of end-user mobile devices. The user base of a mobile application can grow or shrink by millions per day. This situation creates a pressing need for highly scalable server infrastructure; a need nowadays satisfied through cloud computing...... offered by data centers. As the popularity of cloud computing soars, the demand for high-speed, short-range data center links grows. Vertical cavity surface emitting lasers (VCSEL) and multimode fibers (MMF) prove especially well-suited for such scenarios. VCSELs have high modulation bandwidths......, we achieve 10 Gbps over 400 m and then conrm the approach in an optimized system at 25 Gbps over 300 m. The techniques described in this thesis leverage additional degrees of freedom to better utilize the available resources of short-range links. The proposed schemes enable higher speeds and longer...

  17. Schroedinger operators with point interactions and short range expansions

    International Nuclear Information System (INIS)

    Albeverio, S.; Hoeegh-Krohn, R.; Oslo Univ.

    1984-01-01

    We give a survey of recent results concerning Schroedinger operators with point interactions in R 3 . In the case where the point interactions are located at a discrete set of points we discuss results about the resolvent, the spectrum, the resonances and the scattering quantities. We also discuss the approximation of point interactions by short range local potentials (short range or low energy expansions) and the one electron model of a 3-dimensional crystal. Moreover we discuss Schroedinger operators with Coulomb plus point interactions, with applications to the determination of scattering lengths and of level shifts in mesic atoms. Further applications to the multiple well problem, to multiparticle systems, to crystals with random impurities, to polymers and quantum fields are also briefly discussed. (orig.)

  18. Thermodynamic properties of short-range square well fluid

    Science.gov (United States)

    López-Rendón, R.; Reyes, Y.; Orea, P.

    2006-08-01

    The interfacial properties of short-range square well fluid with λ =1.15, 1.25, and 1.375 were determined by using single canonical Monte Carlo simulations. Simulations were carried out in the vapor-liquid region. The coexistence curves of these models were calculated and compared to those previously reported in the literature and good agreement was found among them. We found that the surface tension curves for any potential model of short range form a single master curve when we plot γ* vs T /Tc. It is demonstrated that the critical reduced second virial coefficient B2* as a function of interaction range or Tc* is not constant.

  19. Recent results on short-range gravity experiment

    International Nuclear Information System (INIS)

    Hata, Maki; Akiyama, Takashi; Ikeda, Yuki; Kawamura, Hirokazu; Narita, Keigo; Ninomiya, Kazufumi; Ogawa, Naruya; Sato, Toshiaki; Seitaibashi, Etsuko; Sekiguchi, Yuta; Tsutsui, Ryosuke; Yazawa, Kazumasa; Murata, Jiro

    2009-01-01

    According to the ADD model, deviation from Newton's inverse square law is expected at below sub-millimeter scale. Present study is an experimental investigation of the Newton's gravitational law at a short range scale. We have developed an experimental setup using torsion balance bar, and succeeded to confirm the inverse square law at a centimeter scale. In addition, composition dependence of gravitational constant G is also tested at the centimeter scale, motivated to test the weak equivalence principle.

  20. Chemical and topological short-range order in metallic glasses

    International Nuclear Information System (INIS)

    Vincze, I.; Schaafsma, A.S.; Van der Woude, F.; Kemeny, T.; Lovas, A.

    1980-10-01

    Moessbauer spectroscopy is applied to the study of chemical short-range order in (Fe,Ni)B metallic glasses. It is found that the atomic arrangement in melt-quenched glasses closely resembles that of the crystalline counterparts (Fe 3 B is tetragonal, Ni 3 B is orthorombic). The distribution of transition metal atoms is not random at high Ni concentrations: Ni atoms prefer a neighbourhood with a higher boron coordination. (P.L.)

  1. Short-range correlations in quark and nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Froemel, Frank

    2007-06-15

    In the first part of this thesis, the role of short-range correlations in quark matter is explored within the framework of the Nambu-Jona-Lasinio model. Starting from a next-to-leading order expansion in the inverse number of the quark colors, a fully self-consistent model constructed that employs the close relations between spectral functions and self-energies. In contrast to the usual quasiparticle approximations, this approach allows the investigation of the collisional broadening of the quark spectral function. Numerical calculations at various chemical potentials and zero temperature show that the short-range correlations do not only induce a finite width of the spectral function but also have some influence on the structure of the chiral phase transition. In the second part of this thesis, the temperature and density dependence of the nucleon spectral function in symmetric nuclear matter is investigated. The short-range correlations can be well described by a simple, self-consistent model on the one-particle-two-hole and two-particle-one-hole level (1p2h, 2p1h). The thermodynamically consistent description of the mean-field properties of the nucleons is ensured by incorporating a Skyrme-type potential. Calculations at temperatures and densities that can also be found in heavy-ion collisions or supernova explosions and the formation of neutron stars show that the correlations saturate at high temperatures and densities. (orig.)

  2. Thomas-Fermi molecular dynamics

    International Nuclear Information System (INIS)

    Clerouin, J.; Pollock, E.L.; Zerah, G.

    1992-01-01

    A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

  3. Symmetry of quantum molecular dynamics

    International Nuclear Information System (INIS)

    Burenin, A.V.

    2002-01-01

    The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

  4. Short-range clustering and decomposition in copper-nickel and copper-nickel-iron alloys

    International Nuclear Information System (INIS)

    Aalders, T.J.A.

    1982-07-01

    The thermodynamic equilibrium state of short-range clustering and the kinetics of short-range clustering and decomposition has been studied for a number of CuNi(Fe)-alloys by means of neutron scattering. The validity of the theories, which are usually applied to describe spinodal decomposition, nucleation and growth, coarsening etc., was investigated. It was shown that for the investigated substances the conventional theory of spinodal decomposition is valid for the relaxation of short-range clustering only for the case that the initial and final states do not differ too much. The dynamical scaling procedure described by Lebowitz et al. did not lead to a time-independent scaled function F(x) for the relaxation of short-range clustering, for the early stages of decomposition and for the case that an alloy, which was already decomposed at the quench temperature T 1 , was annealed at a temperature T 2 (T 1 ). For the later stages of decomposition, however, the scaling procedure was indeed successful. The coarsening of the alloys could, except for the later stages, be described by the Lifshitz-Slyozov theory. (Auth.)

  5. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  6. Evolution of short range order in Ar: Liquid to glass and solid transitions-A computational study

    Science.gov (United States)

    Shor, Stanislav; Yahel, Eyal; Makov, Guy

    2018-04-01

    The evolution of the short range order (SRO) as a function of temperature in a Lennard-Jones model liquid with Ar parameters was determined and juxtaposed with thermodynamic and kinetic properties obtained as the liquid was cooled (heated) and transformed between crystalline solid or glassy states and an undercooled liquid. The Lennard-Jones system was studied by non-equilibrium molecular dynamics simulations of large supercells (approximately 20000 atoms) rapidly cooled or heated at selected quenching rates and at constant pressure. The liquid to solid transition was identified by discontinuities in the atomic volume and molar enthalpy; the glass transition temperature range was identified from the temperature dependence of the self-diffusion. The SRO was studied within the quasi-crystalline model (QCM) framework and compared with the Steinhardt bond order parameters. Within the QCM it was found that the SRO evolves from a bcc-like order in the liquid through a bct-like short range order (c/a=1.2) in the supercooled liquid which persists into the glass and finally to a fcc-like ordering in the crystalline solid. The variation of the SRO that results from the QCM compares well with that obtained with Steinhardt's bond order parameters. The hypothesis of icosahedral order in liquids and glasses is not supported by our results.

  7. Molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to 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 about 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 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 the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

  8. Molecular dynamics for dense matter

    Science.gov (United States)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to 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 about 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 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 the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  9. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

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

  10. Analyses of kinetic glass transition in short-range attractive colloids based on time-convolutionless mode-coupling theory.

    Science.gov (United States)

    Narumi, Takayuki; Tokuyama, Michio

    2017-03-01

    For short-range attractive colloids, the phase diagram of the kinetic glass transition is studied by time-convolutionless mode-coupling theory (TMCT). Using numerical calculations, TMCT is shown to recover all the remarkable features predicted by the mode-coupling theory for attractive colloids: the glass-liquid-glass reentrant, the glass-glass transition, and the higher-order singularities. It is also demonstrated through the comparisons with the results of molecular dynamics for the binary attractive colloids that TMCT improves the critical values of the volume fraction. In addition, a schematic model of three control parameters is investigated analytically. It is thus confirmed that TMCT can describe the glass-glass transition and higher-order singularities even in such a schematic model.

  11. Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach

    International Nuclear Information System (INIS)

    Galván-Colín, Jonathan; Valladares, Ariel A.; Valladares, Renela M.; Valladares, Alexander

    2015-01-01

    Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu x Zr 100−x (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature

  12. Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach

    Energy Technology Data Exchange (ETDEWEB)

    Galván-Colín, Jonathan, E-mail: jgcolin@ciencias.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Ariel A., E-mail: valladar@unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Renela M.; Valladares, Alexander [Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-542, México, D.F. 04510, México (Mexico)

    2015-10-15

    Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu{sub x}Zr{sub 100−x} (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature.

  13. Level shifts induced by a short-range potential

    International Nuclear Information System (INIS)

    Karnakov, B.M.; Mur, V.D.

    1984-01-01

    Formulas are derived which express the shifts of levels with energies Esub(n)sup((0)) << rsub(c)sup(-2) in a field Vsub(f)(r) induced by a short-range potential U(r) of radius rsub(c) in terms of the low energy scattering parameters (scattering length and effective radius) with a moment l in the potential. If the interaction between the particle and center is nonresonant, the method developed is identical to perturbation theory on the scattering length. The theory is extended to systems with random degeneracy (Vsub(f) is the Coulomb potential). Formulas describing quasi-intersection of terms are obtained for the case of resonance interaction with the center in a partial wave with l not equal to 0 when energetically close levels are present in both U and Vsub(f). Some features of the level shift are mentioned for the case when the level possesses an anomalously small coupling energy and its coresponding wave function becomes delocalized with decrease of the coupling energy to zero. The problem is discussed of the level shift when the potential Vsub(f) is a potential well surrounded by a weaklyt penetrable barrier. Some applications of the theory to a particle in the field of two short-range potentials or in the field of a short-range and Coulomb centers are considered. Formulas are also obtained for the shifts and widths of the Landau levels and of the shallow level with an arbitrary moment which perturbs the Landau levels

  14. Influence of short range ordering and clustering on transport properties

    International Nuclear Information System (INIS)

    Vigier, G.; Pelletier, J.M.

    1982-01-01

    The influence of short range ordering and clustering phenomena on the electrical resistivity p and the thermopower S is investigated both theoretically and experimentally. According to the considered alloys either increases or decreases of transport properties may be observed when deviations from a random distribution of solute atoms occur. These observations are explained with a model based on free electrons and Born approximations the importance of the potential choice is underlined; two kinds of description of the structure factor are investigated. A good semiquantitative agreement is obtained between computed results and experimental observations

  15. Amorphous photonic crystals with only short-range order.

    Science.gov (United States)

    Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

    2013-10-04

    Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

    International Nuclear Information System (INIS)

    Perez, Danny

    2012-01-01

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

  17. Molecular dynamics of polarizable point dipole models for molten NaI. Comparison with first principles simulations

    Directory of Open Access Journals (Sweden)

    Trullàs J.

    2011-05-01

    Full Text Available Molecular dynamics simulations of molten NaI at 995 K have been carried out using polarizable ion models based on rigid ion pair potentials to which the anion induced dipole polarization is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and deformation short-range damping interactions that oppose the electrically induced dipole moments. The structure and self-diffusion results are compared with those obtained by Galamba and Costa Cabral using first principles Hellmann-Feynman molecular dynamics simulations and using classical molecular dynamics of a shell model which allows only the iodide polarization

  18. On the universality of the long-/short-range separation in multiconfigurational density-functional theory

    Science.gov (United States)

    Fromager, Emmanuel; Toulouse, Julien; Jensen, Hans Jørgen Aa.

    2007-02-01

    In many cases, the dynamic correlation can be calculated quite accurately and at a fairly low computational cost in Kohn-Sham density-functional theory (KS-DFT), using current standard approximate functionals. However, in general, KS-DFT does not treat static correlation effects (near degeneracy) adequately which, on the other hand, can be described in wave-function theory (WFT), for example, with a multiconfigurational self-consistent field (MCSCF) model. It is therefore of high interest to develop a hybrid model which combines the best of both WFT and DFT approaches. The merge of WFT and DFT can be achieved by splitting the two-electron interaction into long-range and short-range parts. The long-range part is then treated by WFT and the short-range part by DFT. In this work the authors consider the so-called "erf" long-range interaction erf(μr12)/r12, which is based on the standard error function, and where μ is a free parameter which controls the range of the long-/short-range decomposition. In order to formulate a general method, they propose a recipe for the definition of an optimal μopt parameter, which is independent of the approximate short-range functional and the approximate wave function, and they discuss its universality. Calculations on a test set consisting of He, Be, Ne, Mg, H2, N2, and H2O yield μopt≈0.4a.u.. A similar analysis on other types of test systems such as actinide compounds is currently in progress. Using the value of 0.4a.u. for μ, encouraging results are obtained with the hybrid MCSCF-DFT method for the dissociation energies of H2, N2, and H2O, with both short-range local-density approximation and PBE-type functionals.

  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. Rheology via nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    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

  1. The nuclear contacts and short range correlations in nuclei

    Science.gov (United States)

    Weiss, R.; Cruz-Torres, R.; Barnea, N.; Piasetzky, E.; Hen, O.

    2018-05-01

    Atomic nuclei are complex strongly interacting systems and their exact theoretical description is a long-standing challenge. An approximate description of nuclei can be achieved by separating its short and long range structure. This separation of scales stands at the heart of the nuclear shell model and effective field theories that describe the long-range structure of the nucleus using a mean-field approximation. We present here an effective description of the complementary short-range structure using contact terms and stylized two-body asymptotic wave functions. The possibility to extract the nuclear contacts from experimental data is presented. Regions in the two-body momentum distribution dominated by high-momentum, close-proximity, nucleon pairs are identified and compared to experimental data. The amount of short-range correlated (SRC) nucleon pairs is determined and compared to measurements. Non-combinatorial isospin symmetry for SRC pairs is identified. The obtained one-body momentum distributions indicate dominance of SRC pairs above the nuclear Fermi-momentum.

  2. Unsupervised learning in neural networks with short range synapses

    Science.gov (United States)

    Brunnet, L. G.; Agnes, E. J.; Mizusaki, B. E. P.; Erichsen, R., Jr.

    2013-01-01

    Different areas of the brain are involved in specific aspects of the information being processed both in learning and in memory formation. For example, the hippocampus is important in the consolidation of information from short-term memory to long-term memory, while emotional memory seems to be dealt by the amygdala. On the microscopic scale the underlying structures in these areas differ in the kind of neurons involved, in their connectivity, or in their clustering degree but, at this level, learning and memory are attributed to neuronal synapses mediated by longterm potentiation and long-term depression. In this work we explore the properties of a short range synaptic connection network, a nearest neighbor lattice composed mostly by excitatory neurons and a fraction of inhibitory ones. The mechanism of synaptic modification responsible for the emergence of memory is Spike-Timing-Dependent Plasticity (STDP), a Hebbian-like rule, where potentiation/depression is acquired when causal/non-causal spikes happen in a synapse involving two neurons. The system is intended to store and recognize memories associated to spatial external inputs presented as simple geometrical forms. The synaptic modifications are continuously applied to excitatory connections, including a homeostasis rule and STDP. In this work we explore the different scenarios under which a network with short range connections can accomplish the task of storing and recognizing simple connected patterns.

  3. Laser Controlled Molecular Orientation Dynamics

    International Nuclear Information System (INIS)

    Atabek, O.

    2004-01-01

    Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

  4. Molecular dynamics study of silver

    International Nuclear Information System (INIS)

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  5. Characterizing short-range vs. long-range spatial correlations in dislocation distributions

    Energy Technology Data Exchange (ETDEWEB)

    Chevy, Juliette, E-mail: juliette.chevy@gmail.com [Laboratoire de Glaciologie et Geophysique de l' Environnement-CNRS, 54 rue Moliere, 38402 St. Martin d' Heres (France)] [Laboratoire Science et Ingenierie des Materiaux et Procedes, Grenoble INP-CNRS-UJF, BP 75, 38402 St. Martin d' Heres Cedex (France); Fressengeas, Claude; Lebyodkin, Mikhail; Taupin, Vincent [Laboratoire de Physique et Mecanique des Materiaux, Universite Paul Verlaine-Metz/CNRS, Ile du Saulcy, 57045 Metz Cedex (France); Bastie, Pierre [Laboratoire de Spectrometrie Physique, BP 87, 38402 St. Martin d' Heres Cedex (France)] [Institut Laue Langevin, BP 156, 38042 Grenoble Cedex 9 (France); Duval, Paul [Laboratoire de Glaciologie et Geophysique de l' Environnement-CNRS, 54 rue Moliere, 38402 St. Martin d' Heres (France)

    2010-03-15

    Hard X-ray diffraction experiments have provided evidence of a strongly heterogeneous distribution of dislocation densities along the axis of cylindrical ice single crystals oriented for basal slip in torsion creep. The dislocation arrangements showed a complex scale-invariant character, which was analyzed by means of statistical and multifractal techniques. A trend to decreasing autocorrelation of the dislocation distribution was observed as deformation proceeds. At low strain levels, long-range spatial correlations control the distribution, but short-range correlations in relation with cross-slip progressively prevail when strain increases. This trend was reproduced by a model based on field dislocation dynamics, a theory accounting for both long-range elastic interactions and short-range interactions through transport of dislocation densities.

  6. Characterizing short-range vs. long-range spatial correlations in dislocation distributions

    International Nuclear Information System (INIS)

    Chevy, Juliette; Fressengeas, Claude; Lebyodkin, Mikhail; Taupin, Vincent; Bastie, Pierre; Duval, Paul

    2010-01-01

    Hard X-ray diffraction experiments have provided evidence of a strongly heterogeneous distribution of dislocation densities along the axis of cylindrical ice single crystals oriented for basal slip in torsion creep. The dislocation arrangements showed a complex scale-invariant character, which was analyzed by means of statistical and multifractal techniques. A trend to decreasing autocorrelation of the dislocation distribution was observed as deformation proceeds. At low strain levels, long-range spatial correlations control the distribution, but short-range correlations in relation with cross-slip progressively prevail when strain increases. This trend was reproduced by a model based on field dislocation dynamics, a theory accounting for both long-range elastic interactions and short-range interactions through transport of dislocation densities.

  7. Short range order in FeCo-X alloys

    International Nuclear Information System (INIS)

    Fultz, B.

    1988-01-01

    Moessbauer spectrometry was used to study the kinetics of chemical ordering in FeCo and in FeCo alloyed with ternary solutes. With respect to the binary FeCo alloy, the kinetics of B2 ordering were slowed when 2% of 4d- or 5d-series ternary solute atoms were present, but 3p- and 3d-series ternary solutes had little effect on ordering kinetics. The relaxation of order around the ternary solute atoms could be discerned in Moessbauer spectra, and it seems that the development of B2 short range order is influenced by structural relaxations around the ternary solute atoms. Different thermal treatments were shown to cause different relaxations of and correlations, suggesting that Moessbauer spectrometry can be used to identify different kinetic paths of ordering in ternary alloys. (orig.)

  8. Short-range disorder in pseudobinary ionic alloys

    International Nuclear Information System (INIS)

    Di Cicco, Andrea; Principi, Emiliano; Filipponi, Adriano

    2002-01-01

    The short-range distribution functions of the RbBr 1-x I x solid and molten ionic alloys have been accurately measured using multiple-edge refinement of the K-edge extended x-ray absorption fine structure spectra (EXAFS). The local structure is characterized by two well-defined first-neighbor peaks associated with the Rb-I and Rb-Br distributions, both for solid and liquid alloys. The distribution of distances in solid alloys gives experimental evidence to available theoretical models. In the liquid, the two distance distributions are found to be practically independent of the concentration x. The effect of different effective charge screening of the ions is observed in the molten systems for limiting concentrations

  9. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  10. A concurrent multiscale micromorphic molecular dynamics

    International Nuclear Information System (INIS)

    Li, Shaofan; Tong, Qi

    2015-01-01

    In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

  11. Color molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Hatsuda, Tetsuo

    2000-01-01

    We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

  12. Molecular dynamics of liquid crystals

    Science.gov (United States)

    Sarman, Sten

    1997-02-01

    We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.

  13. Hybrid gesture recognition system for short-range use

    Science.gov (United States)

    Minagawa, Akihiro; Fan, Wei; Katsuyama, Yutaka; Takebe, Hiroaki; Ozawa, Noriaki; Hotta, Yoshinobu; Sun, Jun

    2012-03-01

    In recent years, various gesture recognition systems have been studied for use in television and video games[1]. In such systems, motion areas ranging from 1 to 3 meters deep have been evaluated[2]. However, with the burgeoning popularity of small mobile displays, gesture recognition systems capable of operating at much shorter ranges have become necessary. The problems related to such systems are exacerbated by the fact that the camera's field of view is unknown to the user during operation, which imposes several restrictions on his/her actions. To overcome the restrictions generated from such mobile camera devices, and to create a more flexible gesture recognition interface, we propose a hybrid hand gesture system, in which two types of gesture recognition modules are prepared and with which the most appropriate recognition module is selected by a dedicated switching module. The two recognition modules of this system are shape analysis using a boosting approach (detection-based approach)[3] and motion analysis using image frame differences (motion-based approach)(for example, see[4]). We evaluated this system using sample users and classified the resulting errors into three categories: errors that depend on the recognition module, errors caused by incorrect module identification, and errors resulting from user actions. In this paper, we show the results of our investigations and explain the problems related to short-range gesture recognition systems.

  14. Folding of polymer chains with short-range binormal interactions

    International Nuclear Information System (INIS)

    Craig, A; Terentjev, E M

    2006-01-01

    We study the structure of chains which have anisotropic short-range contact interactions that depend on the alignment of the binormal vectors of chain segments. This represents a crude model of hydrogen bonding or 'stacking' interactions out of the plane of curvature. The polymers are treated as ribbon-like semi-flexible chains, where the plane of the ribbon is determined by the local binormal. We show that with dipole-dipole interactions between the binormals of contacting chain segments, mean-field theory predicts a first-order transition to a binormally aligned state. We describe the onset of this transition as a function of the temperature-dependent parameters that govern the chain stiffness and the strength of the binormal interaction, as well as the binormal alignment's coupling to chain collapse. We also examine a metastable state governing the folding kinetics. Finally, we discuss the possible mesoscopic structure of the aligned phase, and application of our model to secondary structure motifs like β-sheets and α-helices, as well as composite structures like β-(amyloid) fibrils

  15. Exploiting orbital effects for short-range extravehicular transfers

    Science.gov (United States)

    Williams, Trevor; Baughman, David

    The problem studied in this paper is that of using Simplified Aid for Extravehicular Activity (EVA) Rescue (SAFER) to carry out efficient short-range transfers from the payload bay of the Space Shuttle Orbiter to the vicinity of the underside of the vehicle, for instance for inspection and repair of thermal tiles or umbilical doors. Trajectories are shown to exist, for the shuttle flying noise forward and belly down, that take the astronaut to the vicinity of the underside with no thrusting after the initial push-off. However, these trajectories are too slow to be of practical interest, as they take roughly an hour to execute. Additionally, they are quite sensitive to errors in the initial push-off rates. To overcome both of these difficulties, trajectories are then studied which include a single in-flight impulse of small magnitude ( in the range 0.1 - 0.4 fps). For operational simplicity, this impulse is applied towards the Orbiter at the moment when the line-of -sight of the EVA crewmember is tangential to the underside of the vehicle. These trajectories are considerably faster than the non-impulsive ones: transit times of less than 10 minutes are achievable. Furthermore, the man-in-the-loop feedback scheme used for impulse timing greatly reduces the sensitivity to initial velocity errors. Finally, similar one-impulse trajectories are also shown to exist for the Orbiter in a gravity-gradient attitiude.

  16. Short range spread-spectrum radiolocation system and method

    Science.gov (United States)

    Smith, Stephen F.

    2003-04-29

    A short range radiolocation system and associated methods that allow the location of an item, such as equipment, containers, pallets, vehicles, or personnel, within a defined area. A small, battery powered, self-contained tag is provided to an item to be located. The tag includes a spread-spectrum transmitter that transmits a spread-spectrum code and identification information. A plurality of receivers positioned about the area receive signals from a transmitting tag. The position of the tag, and hence the item, is located by triangulation. The system employs three different ranging techniques for providing coarse, intermediate, and fine spatial position resolution. Coarse positioning information is provided by use of direct-sequence code phase transmitted as a spread-spectrum signal. Intermediate positioning information is provided by the use of a difference signal transmitted with the direct-sequence spread-spectrum code. Fine positioning information is provided by use of carrier phase measurements. An algorithm is employed to combine the three data sets to provide accurate location measurements.

  17. 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...

  18. Huge-scale molecular dynamics simulation of multibubble nuclei

    KAUST Repository

    Watanabe, Hiroshi

    2013-12-01

    We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.

  19. Short-range solar radiation forecasts over Sweden

    Directory of Open Access Journals (Sweden)

    T. Landelius

    2018-04-01

    Full Text Available In this article the performance for short-range solar radiation forecasts by the global deterministic and ensemble models from the European Centre for Medium-Range Weather Forecasts (ECMWF is compared with an ensemble of the regional mesoscale model HARMONIE-AROME used by the national meteorological services in Sweden, Norway and Finland. Note however that only the control members and the ensemble means are included in the comparison. The models resolution differs considerably with 18 km for the ECMWF ensemble, 9 km for the ECMWF deterministic model, and 2.5 km for the HARMONIE-AROME ensemble.The models share the same radiation code. It turns out that they all underestimate systematically the Direct Normal Irradiance (DNI for clear-sky conditions. Except for this shortcoming, the HARMONIE-AROME ensemble model shows the best agreement with the distribution of observed Global Horizontal Irradiance (GHI and DNI values. During mid-day the HARMONIE-AROME ensemble mean performs best. The control member of the HARMONIE-AROME ensemble also scores better than the global deterministic ECMWF model. This is an interesting result since mesoscale models have so far not shown good results when compared to the ECMWF models.Three days with clear, mixed and cloudy skies are used to illustrate the possible added value of a probabilistic forecast. It is shown that in these cases the mesoscale ensemble could provide decision support to a grid operator in terms of forecasts of both the amount of solar power and its probabilities.

  20. Characteristics of III-nitride based laser diode employed for short range underwater wireless optical communications

    Science.gov (United States)

    Xue, Bin; Liu, Zhe; Yang, Jie; Feng, Liangsen; Zhang, Ning; Wang, Junxi; Li, Jinmin

    2018-03-01

    An off-the-shelf green laser diode (LD) was measured to investigate its temperature dependent characteristics. Performance of the device was severely restricted by rising temperature in terms of increasing threshold current and decreasing modulation bandwidth. The observation reveals that dynamic characteristics of the LD is sensitive to temperature. Influence of light attenuation on the modulation bandwidth of the green LD was also studied. The impact of light attenuation on the modulation bandwidth of the LD in short and low turbid water channel was not obvious while slight difference in modulation bandwidth under same injection level was observed between water channel and free space even at short range.

  1. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

  2. 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 by th...

  3. Computational study of short-range interactions in bacteriochlorophyll aggregates

    Czech Academy of Sciences Publication Activity Database

    Alster, J.; Kabeláč, Martin; Tůma, R.; Pšenčík, J.; Burda, J. V.

    2012-01-01

    Roč. 998, SI (2012), s. 87-97 ISSN 2210-271X R&D Projects: GA AV ČR IAA400550808 Grant - others:GA ČR(CZ) GA206/09/0375; GA MŠk(CZ) ME10149 Program:GA Institutional support: RVO:61388963 Keywords : chlorosome * bacteriochlorophyll * molecular simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.139, year: 2012

  4. Intermediate- and short-range order in phosphorus-selenium glasses

    International Nuclear Information System (INIS)

    Bytchkov, Aleksei; Hennet, Louis; Price, David L.; Miloshova, Mariana; Bychkov, Eugene; Kohara, Shinji

    2011-01-01

    State-of-the-art neutron and x-ray diffraction measurements have been performed to provide a definitive picture of the intermediate- and short-range structures of P x Se 1-x glasses spanning two glass regions, x 0.025-0.54 and 0.64-0.84. Liquid P 4 Se 3 and amorphous red P and Se were also measured. Detailed information was obtained about the development with increasing phosphorous concentration of intermediate-range order on the length scale ∼6 A ring , based on the behavior of the first sharp diffraction peak. Attention is also paid to the feature in the structure factor at 7.5 A ring -1 , identified in earlier numerical simulations, provides further evidence of the existence of molecular units. The real-space transforms yield a reliable statistical picture of the changing short-range order as x increases, using the information about types and concentrations of local structural units provided by previous NMR measurements to interpret the trends observed.

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

    African Journals Online (AJOL)

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

  6. Chirality in molecular collision dynamics

    Science.gov (United States)

    Lombardi, Andrea; Palazzetti, Federico

    2018-02-01

    Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

  7. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  8. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  9. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  10. 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

  11. A novel nuclear dependence of nucleon–nucleon short-range correlations

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Hongkai [College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070 (China); Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Wang, Rong, E-mail: rwang@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Lanzhou University, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Huang, Yin [Lanzhou University, Lanzhou 730000 (China); Chen, Xurong [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2017-06-10

    A linear correlation is found between the magnitude of nucleon–nucleon short-range correlations and the nuclear binding energy per nucleon with pairing energy removed. By using this relation, the strengths of nucleon–nucleon short-range correlations of some unmeasured nuclei are predicted. Discussions on nucleon–nucleon pairing energy and nucleon–nucleon short-range correlations are made. The found nuclear dependence of nucleon–nucleon short-range correlations may shed some lights on the short-range structure of nucleus.

  12. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  13. A Short-Range Distance Sensor with Exceptional Linearity

    Science.gov (United States)

    Simmons, Steven; Youngquist, Robert

    2013-01-01

    A sensor has been demonstrated that can measure distance over a total range of about 300 microns to an accuracy of about 0.1 nm (resolution of about 0.01 nm). This represents an exceptionally large dynamic range of operation - over 1,000,000. The sensor is optical in nature, and requires the attachment of a mirror to the object whose distance is being measured. This work resulted from actively developing a white light interferometric system to be used to measure the depths of defects in the Space Shuttle Orbiter windows. The concept was then applied to measuring distance. The concept later expanded to include spectrometer calibration. In summary, broadband (i.e., white) light is launched into a Michelson interferometer, one mirror of which is fixed and one of which is attached to the object whose distance is to be measured. The light emerging from the interferometer has traveled one of two distances: either the distance to the fixed mirror and back, or the distance to the moving mirror and back. These two light beams mix and produce an interference pattern where some wavelengths interfere constructively and some destructively. Sending this light into a spectrometer allows this interference pattern to be analyzed, yielding the net distance difference between the two paths. The unique feature of this distance sensor is its ability to measure accurately distance over a dynamic range of more than one million, the ratio of its range (about 300 microns) to its accuracy (about 0.1 nanometer). Such a large linear operating range is rare and arises here because both amplitude and phase-matching algorithms contribute to the performance. The sensor is limited by the need to attach a mirror of some kind to the object being tracked, and by the fairly small total range, but the exceptional dynamic range should make it of interest.

  14. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  15. Pattern recognition in molecular dynamics. [FORTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

    1977-07-01

    An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

  16. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  17. Spherical harmonic expansion of short-range screened Coulomb interactions

    Energy Technology Data Exchange (ETDEWEB)

    Angyan, Janos G [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, UMR 7036, CNRS-Universite Henri Poincare, BP 239, F-54506 Vandoeuvre-les-Nancy (France); Gerber, Iann [Laboratoire de Cristallographie et de Modelisation des Materiaux Mineraux et Biologiques, UMR 7036, CNRS-Universite Henri Poincare, BP 239, F-54506 Vandoeuvre-les-Nancy (France); Marsman, Martijn [Institut fuer Materialphysik and Center for Computational Materials Science, Universitaet Wien, Sensengasse 8, A-1090, Vienna (Austria)

    2006-07-07

    Spherical harmonic expansions of the screened Coulomb interaction kernel involving the complementary error function are required in various problems in atomic, molecular and solid state physics, like for the evaluation of Ewald-type lattice sums or for range-separated hybrid density functionals. A general analytical expression is derived for the kernel, which is non-separable in the radial variables. With the help of series expansions a separable approximate form is proposed, which is in close analogy with the conventional multipole expansion of the Coulomb kernel in spherical harmonics. The convergence behaviour of these expansions is studied and illustrated by the electrostatic potential of an elementary charge distribution formed by products of Slater-type atomic orbitals.

  18. Short-ranged memory model with preferential growth

    Science.gov (United States)

    Schaigorodsky, Ana L.; Perotti, Juan I.; Almeira, Nahuel; Billoni, Orlando V.

    2018-02-01

    In this work we introduce a variant of the Yule-Simon model for preferential growth by incorporating a finite kernel to model the effects of bounded memory. We characterize the properties of the model combining analytical arguments with extensive numerical simulations. In particular, we analyze the lifetime and popularity distributions by mapping the model dynamics to corresponding Markov chains and branching processes, respectively. These distributions follow power laws with well-defined exponents that are within the range of the empirical data reported in ecologies. Interestingly, by varying the innovation rate, this simple out-of-equilibrium model exhibits many of the characteristics of a continuous phase transition and, around the critical point, it generates time series with power-law popularity, lifetime and interevent time distributions, and nontrivial temporal correlations, such as a bursty dynamics in analogy with the activity of solar flares. Our results suggest that an appropriate balance between innovation and oblivion rates could provide an explanatory framework for many of the properties commonly observed in many complex systems.

  19. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  20. Controlling Short-Range Interactions by Tuning Surface Chemistry in HDPE/Graphene Nanoribbon Nanocomposites.

    Science.gov (United States)

    Sadeghi, Soheil; Zehtab Yazdi, Alireza; Sundararaj, Uttandaraman

    2015-09-03

    Unique dispersion states of nanoparticles in polymeric matrices have the potential to create composites with enhanced mechanical, thermal, and electrical properties. The present work aims to determine the state of dispersion from the melt-state rheological behavior of nanocomposites based on carbon nanotube and graphene nanoribbon (GNR) nanomaterials. GNRs were synthesized from nitrogen-doped carbon nanotubes via a chemical route using potassium permanganate and some second acids. High-density polyethylene (HDPE)/GNR nanocomposite samples were then prepared through a solution mixing procedure. Different nanocomposite dispersion states were achieved using different GNR synthesis methods providing different surface chemistry, interparticle interactions, and internal compartments. Prolonged relaxation of flow induced molecular orientation was observed due to the presence of both carbon nanotubes and GNRs. Based on the results of this work, due to relatively weak interactions between the polymer and the nanofillers, it is expected that short-range interactions between nanofillers play the key role in the final dispersion state.

  1. Unitarity corrections to short-range order long-range rapidity correlations

    CERN Document Server

    Capella, A

    1978-01-01

    Although the effective hadronic forces have short range in rapidity space, one nevertheless expects long-range dynamical correlations induced by unitarity constraints. This paper contains a thorough discussion of long-range rapidity correlations in high-multiplicity events. In particular, the authors analyze in detail the forward- backward multiplicity correlations, measured recently in the whole CERN ISR energy range. They find from these data that the normalized variance of the number n of exchanged cut Pomerons, ((n/(n)-1)/sup 2/) , is most probably in the range 0.32 to 0.36. They show that such a number is obtained from Reggeon theory in the eikonal approximation. The authors also predict a very specific violation of local compensation of charge in multiparticle events: The violation should appear in the fourth-order zone correlation function and is absent in the second-order correlation function, the only one measured until now. (48 refs).

  2. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

    DEFF Research Database (Denmark)

    Hedegård, Erik D.; Olsen, Jógvan Magnus Haugaard; Knecht, Stefan

    2015-01-01

    . To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality......We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE......-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory...

  3. Wavelet Analysis for Molecular Dynamics

    Science.gov (United States)

    2015-06-01

    Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the

  4. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    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......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...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

  5. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  6. 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...

  7. Solvent-shared pairs of densely charged ions induce intense but short-range supra-additive slowdown of water rotation.

    Science.gov (United States)

    Vila Verde, Ana; Santer, Mark; Lipowsky, Reinhard

    2016-01-21

    The question "Can ions exert supra-additive effects on water dynamics?" has had several opposing answers from both simulation and experiment. We address this ongoing controversy by investigating water reorientation in aqueous solutions of two salts with large (magnesium sulfate) and small (cesium chloride) effects on water dynamics using molecular dynamics simulations and classical, polarizable models. The salt models are reparameterized to reproduce properties of both dilute and concentrated solutions. We demonstrate that water rotation in concentrated MgSO4 solutions is unexpectedly slow, in agreement with experiment, and that the slowdown is supra-additive: the observed slowdown is larger than that predicted by assuming that the resultant of the extra forces induced by the ions on the rotating water molecules tilts the free energy landscape associated with water rotation. Supra-additive slow down is very intense but short-range, and is strongly ion-specific: in contrast to the long-range picture initially proposed based on experiment, we find that intense supra-additivity is limited to water molecules directly bridging two ions in solvent-shared ion pair configuration; in contrast to a non-ion-specific origin to supra-additive effects proposed from simulations, we find that the magnitude of supra-additive slowdown strongly depends on the identity of the cations and anions. Supra-additive slowdown of water dynamics requires long-lived solvent-shared ion pairs; long-lived ion pairs should be typical for salts of multivalent ions. We discuss the origin of the apparent disagreement between the various studies on this topic and show that the short-range cooperative slowdown scenario proposed here resolves the existing controversy.

  8. Molecular dynamics and diffusion a compilation

    CERN Document Server

    Fisher, David

    2013-01-01

    The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

  9. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  10. Molecular dynamics modeling of polymer flammability

    International Nuclear Information System (INIS)

    Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

    1992-01-01

    Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

  11. First-principles molecular dynamics for metals

    International Nuclear Information System (INIS)

    Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

    1989-01-01

    A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

  12. 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.

  13. 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

  14. Nonadiabatic electron wavepacket dynamics behind molecular autoionization

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-01

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  15. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  16. Dynamic signature of molecular association in methanol

    International Nuclear Information System (INIS)

    Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

    2016-01-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  17. Introducing a new family of short-range potentials and their numerical solutions using the asymptotic iteration method

    Science.gov (United States)

    Assi, I. A.; Sous, A. J.

    2018-05-01

    The goal of this work is to derive a new class of short-range potentials that could have a wide range of physical applications, specially in molecular physics. The tridiagonal representation approach has been developed beyond its limitations to produce new potentials by requiring the representation of the Schrödinger wave operator to be multidiagonal and symmetric. This produces a family of Hulthén potentials that has a specific structure, as mentioned in the introduction. As an example, we have solved the nonrelativistic wave equation for the new four-parameter short-range screening potential numerically using the asymptotic iteration method, where we tabulated the eigenvalues for both s -wave and arbitrary l -wave cases in tables.

  18. Dependability investigation of wireless short range embedded systems: hardware platform oriented approach

    NARCIS (Netherlands)

    Senouci, B.; Kerkhoff, Hans G.; Annema, Anne J.; Bentum, Marinus Jan

    2015-01-01

    A new direction in short-range wireless applications has appeared in the form of high-speed data communication devices for distances of hundreds meters. Behind these embedded applications, a complex heterogeneous architecture is built. Moreover, these short range communications are introduced into

  19. Positional short-range order in the nematic phase of n BABAs

    Science.gov (United States)

    Usha Deniz, K.; Pepy, G.; Parette, G.; Keller, P.

    1991-10-01

    The positional short-range order, SRO ⊥, perpendicular to the nematic director n̂ has been studied in the fibre-type nematics, nBABAs, by neutron diffraction. SRO ⊥ is found to be dependent on other types of nematic short-range order but not on the orientational long-range order.

  20. Droplet spreading driven by van der Waals force: a molecular dynamics study

    KAUST Repository

    Wu, Congmin

    2010-07-07

    The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

  1. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  2. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  3. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  4. 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.)

  5. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  6. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  7. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  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. 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.

  10. Short-range airborne transmission of expiratory droplets between two people

    DEFF Research Database (Denmark)

    Liu, Li; Li, Yuguo; Nielsen, Peter Vilhelm

    2017-01-01

    , ventilation, and breathing mode. Under the specific set of conditions studied, we found a substantial increase in airborne exposure to droplet nuclei exhaled by the source manikin when a susceptible manikin is within about 1.5 m of the source manikin, referred to as the proximity effect. The threshold...... distance of about 1.5 m distinguishes the two basic transmission processes of droplets and droplet nuclei, that is, short-range modes and the long-range airborne route. The short-range modes include both the conventional large droplet route and the newly defined short-range airborne transmission. We thus...... reveal that transmission occurring in close proximity to the source patient includes both droplet-borne (large droplet) and short-range airborne routes, in addition to the direct deposition of large droplets on other body surfaces. The mechanisms of the droplet-borne and short-range airborne routes...

  11. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  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. Dynamical quenching of tunneling in molecular magnets

    International Nuclear Information System (INIS)

    José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

    2015-01-01

    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

  14. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    International Nuclear Information System (INIS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

  15. Structural study of liquids with strong short-range correlation in the atomic distribution

    International Nuclear Information System (INIS)

    Uzuki, Kenji

    1976-01-01

    Structure factors of liquids and amorphous solids having a relatively high degree of ordering in their short-range structures have been measured over a wide range of scattering vectors by means of the T-O-F neutron diffraction using epithermal pulsed neutrons generated by an electron linear accelerator. It has been shown in the case of liquid CS 2 that the size and shape of a molecule existing in the liquid phase are determined from the behaviour of the structure factor in the range of high scattering vectors, and that the structure factor in the region of low scattering vectors informs on inter-molecular orientational and center-center correlations in the liquid state. Moreover, based on highly resoluted radial distribution functions, a free rotating chain model has been discussed for chain molecules contained in liquid Se, and a splitting of the nearest neighbour Pd-Pd and Pd-Si correlation has been clearly found in the amorphous Pdsub(0.8) - Sisub(0.2) alloy. (orig./HK) [de

  16. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  17. Methods for studying short-range order in solid binary solutions

    International Nuclear Information System (INIS)

    Beranger, Gerard

    1969-12-01

    The short range order definition and its characteristic parameters are first recalled. The different methods to study the short range order are then examined: X ray diffusion, electrical resistivity, specific heat and thermoelectric power, neutron diffraction, electron spin resonance, study of thermodynamic and mechanical properties. The theory of the X ray diffraction effects due to short range order and the subsequent experimental method are emphasized. The principal results obtained from binary Systems, by the different experimental techniques, are reported and briefly discussed. The Au-Cu, Li-Mg, Au-Ni and Cu-Zn Systems are moreover described. (author) [fr

  18. Excited-state molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Pratt, S.T.

    1995-01-01

    This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

  19. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  20. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  1. Monte Carlo simulation of atomic short range order and cluster formation in two dimensional model alloys

    International Nuclear Information System (INIS)

    Rojas T, J.; Instituto Peruano de Energia Nuclear, Lima; Manrique C, E.; Torres T, E.

    2002-01-01

    Using monte Carlo simulation have been carried out an atomistic description of the structure and ordering processes in the system Cu-Au in a two-dimensional model. The ABV model of the alloy is a system of N atoms A and B, located in rigid lattice with some vacant sites. In the model we assume pair wise interactions between nearest neighbors with constant ordering energy J = 0,03 eV. The dynamics was introduced by means of a vacancy that exchanges of place with any atom of its neighbors. The simulations were carried out in a square lattice with 1024 and 4096 particles, using periodic boundary conditions to avoid border effects. We calculate the first two parameters of short range order of Warren-Cowley as function of the concentration and temperature. It was also studied the probabilities of formation of different atomic clusters that consist of 9 atoms as function of the concentration of the alloy and temperatures in a wide range of values. In some regions of temperature and concentration it was observed compositional and thermal polymorphism

  2. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  3. Molecular quantum dynamics. From theory to applications

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

    2014-09-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

  4. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  5. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  6. 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...

  7. Short Range Air Defense in Army Divisions: Do We Really Need It

    National Research Council Canada - National Science Library

    Anderson, Charles

    2000-01-01

    Ever since the Soviet threat collapsed, coupled with the demonstrated, overwhelming, capability of our air forces during numerous operations in the 1990s, the relevance of the Short Range Air Defense (SHORAD...

  8. Revision to dedicated short range communication roadside equipment specification - RSU 4.1.Bench Test Plan.

    Science.gov (United States)

    2017-04-28

    The document describes the overall process for evaluating Dedicated Short Range Communication (DSRC) Roadside Units (RSU) against USDOT RSU Specification 4.1 in preparation for field evaluation. The Test Cases contained in this document only evaluate...

  9. Extended Lagrangian Excited State Molecular Dynamics.

    Science.gov (United States)

    Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

    2018-02-13

    An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

  10. Magnetism and atomic short-range order in Ni-Rh alloys

    Science.gov (United States)

    Carnegie, D. W., Jr.; Claus, H.

    1984-07-01

    Low-field ac susceptibility measurements of Ni-Rh samples of various concentrations are presented. Giant effects of the metallurgical state on the magnetic ordering temperature are associated with changes in the degree of atomic short-range order. By careful control of this degree of short-range order, it is possible to demonstrate the existence of a spin-glass state in Ni-Rh alloys.

  11. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  12. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

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

  13. Temperature-dependent mechanical properties of single-layer molybdenum disulphide: Molecular dynamics nanoindentation simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Junhua, E-mail: junhua.zhao@uni-weimar.de [Jiangsu Province Key Laboratory of Advanced Manufacturing Equipment and Technology of Food, Jiangnan University, 214122 Wuxi (China); Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Jiang, Jin-Wu, E-mail: jwjiang5918@hotmail.com [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Rabczuk, Timon, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); School of Civil, Environmental and Architectural Engineering, Korea University, 136-701 Seoul (Korea, Republic of)

    2013-12-02

    The temperature-dependent mechanical properties of single-layer molybdenum disulphide (MoS{sub 2}) are obtained using molecular dynamics (MD) nanoindentation simulations. The Young's moduli, maximum load stress, and maximum loading strain decrease with increasing temperature from 4.2 K to 500 K. The obtained Young's moduli are in good agreement with those using our MD uniaxial tension simulations and the available experimental results. The tendency of maximum loading strain with different temperature is opposite with that of metal materials due to the short range Stillinger-Weber potentials in MoS{sub 2}. Furthermore, the indenter tip radius and fitting strain effect on the mechanical properties are also discussed.

  14. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  15. Short-ranged radial and tensor correlations in nuclear many-body systems

    International Nuclear Information System (INIS)

    Neff, T.; Feldmeier, H.

    2003-01-01

    The unitary correlation operator method (UCOM) is applied to realistic potentials. The effects of tensor correlations are investigated. The resulting phase shift equivalent correlated interactions are used in the no-core shell model for light nuclei and for mean-field calculations in the Fermionic Molecular Dynamics model for nuclei up to mass A=48. (orig.)

  16. Molecular Dynamics: New Frontier in Personalized Medicine.

    Science.gov (United States)

    Sneha, P; Doss, C George Priya

    2016-01-01

    The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

  17. Parallelization of quantum molecular dynamics simulation code

    International Nuclear Information System (INIS)

    Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

    1998-02-01

    A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

  18. Lipid Configurations from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

    2018-01-01

    of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...

  19. Molecular dynamics studies of actinide nitrides

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  20. Viscosity calculations at molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kirova, E M; Norman, G E

    2015-01-01

    Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)

  1. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  2. Molecular dynamics of surfactant protein C

    DEFF Research Database (Denmark)

    Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

    2006-01-01

    Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...

  3. Short-Range Prediction of Monsoon Precipitation by NCMRWF Regional Unified Model with Explicit Convection

    Science.gov (United States)

    Mamgain, Ashu; Rajagopal, E. N.; Mitra, A. K.; Webster, S.

    2018-03-01

    There are increasing efforts towards the prediction of high-impact weather systems and understanding of related dynamical and physical processes. High-resolution numerical model simulations can be used directly to model the impact at fine-scale details. Improvement in forecast accuracy can help in disaster management planning and execution. National Centre for Medium Range Weather Forecasting (NCMRWF) has implemented high-resolution regional unified modeling system with explicit convection embedded within coarser resolution global model with parameterized convection. The models configurations are based on UK Met Office unified seamless modeling system. Recent land use/land cover data (2012-2013) obtained from Indian Space Research Organisation (ISRO) are also used in model simulations. Results based on short-range forecast of both the global and regional models over India for a month indicate that convection-permitting simulations by the high-resolution regional model is able to reduce the dry bias over southern parts of West Coast and monsoon trough zone with more intense rainfall mainly towards northern parts of monsoon trough zone. Regional model with explicit convection has significantly improved the phase of the diurnal cycle of rainfall as compared to the global model. Results from two monsoon depression cases during study period show substantial improvement in details of rainfall pattern. Many categories in rainfall defined for operational forecast purposes by Indian forecasters are also well represented in case of convection-permitting high-resolution simulations. For the statistics of number of days within a range of rain categories between `No-Rain' and `Heavy Rain', the regional model is outperforming the global model in all the ranges. In the very heavy and extremely heavy categories, the regional simulations show overestimation of rainfall days. Global model with parameterized convection have tendency to overestimate the light rainfall days and

  4. Limited-area short-range ensemble predictions targeted for heavy rain in Europe

    Directory of Open Access Journals (Sweden)

    K. Sattler

    2005-01-01

    Full Text Available Inherent uncertainties in short-range quantitative precipitation forecasts (QPF from the high-resolution, limited-area numerical weather prediction model DMI-HIRLAM (LAM are addressed using two different approaches to creating a small ensemble of LAM simulations, with focus on prediction of extreme rainfall events over European river basins. The first ensemble type is designed to represent uncertainty in the atmospheric state of the initial condition and at the lateral LAM boundaries. The global ensemble prediction system (EPS from ECMWF serves as host model to the LAM and provides the state perturbations, from which a small set of significant members is selected. The significance is estimated on the basis of accumulated precipitation over a target area of interest, which contains the river basin(s under consideration. The selected members provide the initial and boundary data for the ensemble integration in the LAM. A second ensemble approach tries to address a portion of the model-inherent uncertainty responsible for errors in the forecasted precipitation field by utilising different parameterisation schemes for condensation and convection in the LAM. Three periods around historical heavy rain events that caused or contributed to disastrous river flooding in Europe are used to study the performance of the LAM ensemble designs. The three cases exhibit different dynamic and synoptic characteristics and provide an indication of the ensemble qualities in different weather situations. Precipitation analyses from the Deutsche Wetterdienst (DWD are used as the verifying reference and a comparison of daily rainfall amounts is referred to the respective river basins of the historical cases.

  5. Molecular dynamics in high electric fields

    International Nuclear Information System (INIS)

    Apostol, M.; Cune, L.C.

    2016-01-01

    Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

  6. Short-range/Long-range Integrated Target (SLIT) for Video Guidance Sensor Rendezvous and Docking

    Science.gov (United States)

    Roe, Fred D. (Inventor); Bryan, Thomas C. (Inventor)

    2009-01-01

    A laser target reflector assembly for mounting upon spacecraft having a long-range reflector array formed from a plurality of unfiltered light reflectors embedded in an array pattern upon a hemispherical reflector disposed upon a mounting plate. The reflector assembly also includes a short-range reflector array positioned upon the mounting body proximate to the long-range reflector array. The short-range reflector array includes three filtered light reflectors positioned upon extensions from the mounting body. The three filtered light reflectors retro-reflect substantially all incident light rays that are transmissive by their monochromatic filters and received by the three filtered light reflectors. In one embodiment the short-range reflector array is embedded within the hemispherical reflector,

  7. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  8. Double scattering of light from Biophotonic Nanostructures with short-range order

    Energy Technology Data Exchange (ETDEWEB)

    Noh, Heeso; Liew, Seng Fatt; Saranathan, Vinodkumar; Prum, Richard O.; Mochrie, Simon G.J.; Dufresne, Eric R.; Cao, Hui (Yale)

    2010-07-28

    We investigate the physical mechanism for color production by isotropic nanostructures with short-range order in bird feather barbs. While the primary peak in optical scattering spectra results from constructive interference of singly-scattered light, many species exhibit secondary peaks with distinct characteristic. Our experimental and numerical studies show that these secondary peaks result from double scattering of light by the correlated structures. Without an analog in periodic or random structures, such a phenomenon is unique for short-range ordered structures, and has been widely used by nature for non-iridescent structural coloration.

  9. Short-range wireless communication fundamentals of RF system design and application

    CERN Document Server

    Bensky, Alan

    2004-01-01

    The Complete "Tool Kit” for the Hottest Area in RF/Wireless Design!Short-range wireless-communications over distances of less than 100 meters-is the most rapidly growing segment of RF/wireless engineering. Alan Bensky is an internationally recognized expert in short-range wireless, and this new edition of his bestselling book is completely revised to cover the latest developments in this fast moving field.You'll find coverage of such cutting-edge topics as: architectural trends in RF/wireless integrated circuits compatibility and conflict issues between differen

  10. The effect of short-range spatial variability on soil sampling uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Perk, Marcel van der [Department of Physical Geography, Utrecht University, P.O. Box 80115, 3508 TC Utrecht (Netherlands)], E-mail: m.vanderperk@geo.uu.nl; De Zorzi, Paolo; Barbizzi, Sabrina; Belli, Maria [Agenzia per la Protezione dell' Ambiente e per i Servizi Tecnici (APAT), Servizio Laboratori, Misure ed Attivita di Campo, Via di Castel Romano, 100-00128 Roma (Italy); Fajgelj, Ales; Sansone, Umberto [International Atomic Energy Agency (IAEA), Agency' s Laboratories Seibersdorf, A-1400 Vienna (Austria); Jeran, Zvonka; Jacimovic, Radojko [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia)

    2008-11-15

    This paper aims to quantify the soil sampling uncertainty arising from the short-range spatial variability of elemental concentrations in the topsoils of agricultural, semi-natural, and contaminated environments. For the agricultural site, the relative standard sampling uncertainty ranges between 1% and 5.5%. For the semi-natural area, the sampling uncertainties are 2-4 times larger than in the agricultural area. The contaminated site exhibited significant short-range spatial variability in elemental composition, which resulted in sampling uncertainties of 20-30%.

  11. The effect of short-range spatial variability on soil sampling uncertainty.

    Science.gov (United States)

    Van der Perk, Marcel; de Zorzi, Paolo; Barbizzi, Sabrina; Belli, Maria; Fajgelj, Ales; Sansone, Umberto; Jeran, Zvonka; Jaćimović, Radojko

    2008-11-01

    This paper aims to quantify the soil sampling uncertainty arising from the short-range spatial variability of elemental concentrations in the topsoils of agricultural, semi-natural, and contaminated environments. For the agricultural site, the relative standard sampling uncertainty ranges between 1% and 5.5%. For the semi-natural area, the sampling uncertainties are 2-4 times larger than in the agricultural area. The contaminated site exhibited significant short-range spatial variability in elemental composition, which resulted in sampling uncertainties of 20-30%.

  12. 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

  13. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  14. Functional framework and hardware platform for dependability study in short range wireless embedded systems

    NARCIS (Netherlands)

    Senouci, B.; Annema, Anne J.; Bentum, Marinus Jan; Kerkhoff, Hans G.

    2011-01-01

    A new direction in short-range wireless applications has appeared in the form of high-speed data communication devices for distances of a few meters. Behind these embedded applications, a complex Hardware/Software architecture is built. Dependability is one of the major challenges in these systems.

  15. Neutron diffraction study on the medium and short-range order of ternary chalcogenide glasses

    Czech Academy of Sciences Publication Activity Database

    Neov, S.; Gerasimova, I.; Skordeva, E.; Arsova, D.; Pamukchieva, V.; Mikula, Pavol; Lukáš, Petr; Sonntag, R.

    1999-01-01

    Roč. 34, - (1999), s. 3669-3676 ISSN 0022-2461 R&D Projects: GA ČR GV202/97/K038 Keywords : neutron diffraction * short-range order * chalcogenide glasses Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.786, year: 1999

  16. EXAFS, Determination of Short Range Order and Local Structures in Materials

    NARCIS (Netherlands)

    Koningsberger, D.C.; Prins, R.

    1981-01-01

    Extended X-ray Absorption Fine Structure (EXAFS) is a powerful method of determining short range order and local structures in materials using X-ray photons produced by a synchrotron light source, or in-house by a high intensity rotating anode X-ray generator. The technique has provided valuable

  17. Status of the dedicated short-range communications technology and applications : report to Congress.

    Science.gov (United States)

    2015-07-01

    This report responds to a Congressional request for an assessment of the 5.9 Gigahertz (GHz) Dedicated Short Range : Communications (DSRC) in accordance with the requirements provided by Congress in the Moving Ahead for Progress in the : 21st Century...

  18. Investigations of multiphoton excitation and ionization in a short range potential

    International Nuclear Information System (INIS)

    Susskind, S.M.; Cowley, S.C.; Valeo, E.J.

    1989-02-01

    We introduce an approach to the study of excitation and ionization for a system with a short range potential. In particular, analytical and numerical results are presented for the multiphoton ionization rate, under strong field conditions, of an electron confined by a δ-function potential. 9 refs., 3 figs

  19. Investigations of multiphoton excitation and ionization in a short range potential

    Energy Technology Data Exchange (ETDEWEB)

    Susskind, S.M.; Cowley, S.C.; Valeo, E.J.

    1989-02-01

    We introduce an approach to the study of excitation and ionization for a system with a short range potential. In particular, analytical and numerical results are presented for the multiphoton ionization rate, under strong field conditions, of an electron confined by a delta-function potential. 9 refs., 3 figs.

  20. Fluid–fluid coexistence in colloidal systems with short-ranged strongly directional attraction

    NARCIS (Netherlands)

    Kern, N.; Frenkel, D.

    2003-01-01

    We present a systematic numerical study of the phase behavior of square-well fluids with a "patchy" short-ranged attraction. In particular, we study the effect of the size and number of attractive patches on the fluid–fluid coexistence. The model that we use is a generalization of the hard sphere

  1. Fluctuations in substitution type alloys and their analyses. Short-range order structures

    International Nuclear Information System (INIS)

    Iwasaki, Hiroshi; Ohshima, Ken-ichi

    2010-01-01

    This article is the fifth of the serial lecture, microstructures and fluctuations, in this magazine. The formula of X-ray diffuse scattering intensity was derived for binary alloys by introducing short-range order parameters. Diffuse scattering intensities for a single crystal Cu 3 Au were measured above critical temperature for ordering. The short-range parameters were obtained by a three-dimensional Fourier analysis. The long-range pair interaction between atoms was originated from the indirect screening interaction due to conduction electrons. A detailed study was made on short-range-order diffuse scattering from Cu 3 Au in the disordered state by electron diffraction. Fourfold splitting of the diffuse scattering was observed at 110 in the reciprocal lattice, and this result was attributed to the reflection of the form of the Fermi surface. The X-ray diffuse scattering intensity was measured at room temperature for disordered Cu-Pd alloys for the six composition of Pd. Twofold and fourfold splitting of diffuse scattering due to the short-range order (SRO) were observed at 100, 110 and equivalent positions respectively from alloys with more than 13.0at% Pd. The SRO parameters were determined from all the six alloys. For Cu-Pt alloys, the diffuse scattering originated from the correlation between Cu and Pt layers in direction was observed in addition to the one due to the reflection of the Fermi surface imaging. (author)

  2. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp; Tchipev, Nikola

    2012-01-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

  3. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  4. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  5. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  6. Nonequilibrium molecular dynamics: The first 25 years

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments

  7. Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Cedrix J. Dongmo Foumthuim

    2018-01-01

    Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

  8. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

    Science.gov (United States)

    Armen, Roger S; Chen, Jianhan; Brooks, Charles L

    2009-10-13

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

  9. Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system

    KAUST Repository

    Allsopp, Nicholas

    2012-04-01

    We report scaling results on the world\\'s largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the short-range atomic dynamics in structural glasses and amorphous materials. The code was able to scale up to 72 racks of an IBM BlueGene/P, with a measured 89% efficiency for a system with 100 billion particles. The code speed, with 0.13. s per iteration in the case of 1 billion particles, paves the way to the study of billion-body structural glasses with a resolution increase of two orders of magnitude with respect to the largest simulation ever reported. We demonstrate the effectiveness of our code by studying the liquid-glass transition of an exceptionally large system made by a binary mixture of 1 billion particles. © 2012.

  10. Molecular dynamics study of a nuclear waste glass matrix with plutonium

    International Nuclear Information System (INIS)

    Meis, C.; Delaye, J.M.; Ghaleb, D.

    1999-01-01

    Molecular dynamics simulation techniques were applied to model the incorporation of plutonium in the French nuclear waste glass matrix. Born-Mayer-Huggins analytical potentials were established to characterize short-range interactions between Pu-O and Pu-Pu pairs; the potentials were fitted to the structural properties of plutonium dioxide in the light of a recent experimental study showing that plutonium is found as Pu(IV) in the glass. The transferability of the established potentials to the glass structure is discussed, and the potential parameters are further refined by molecular dynamics simulations in an aluminoborosilicate glass to obtain mean Pu-O interatomic distances and first-neighbor coordination numbers matching the experimental values as closely as possible. Previously published Born-Mayer-Huggins potentials supplemented by Stillinger-Weber three-body terms were used for oxygen-cation and cation-cation interactions. The difficulties encountered in establishing a Pu-O potential that provides satisfactory results in both oxides and glasses are also discussed

  11. The molecular dynamics simulation of structure and transport properties of sheared super-cooled liquid metal

    International Nuclear Information System (INIS)

    Wang Li; Liu Xiangfa; Zhang Yanning; Yang Hua; Chen Ying; Bian Xiufang

    2003-01-01

    Much more attention has been paid to the microstructure of liquid metal under non-ordinary condition recently. In this Letter, the pair correlation function (PCF), together with internal energy of sheared super-cooled liquid Co as a function of temperature has been calculated by molecular dynamics simulation based upon the embedded atom method (EAM) and analyzed compared to that under normal condition. The finding indicates that there exist three obvious peaks of PCF for liquid Co; while as the shear stress is applied to the liquid, the first and second peaks of PCF become lower, the third peak disappeared. The concentric shell structure representing short-range order of liquid still exists, however, it is weakened by the addition of shear stress, leading to the increases of disordering degree of liquid metal. The curves of energy versus temperature suggest the higher crystalline temperature compared to that under normal condition at the same cooling rate. In addition, the viscosity of super-liquid Co is calculated by non-equilibrium molecular dynamics (NEMD)

  12. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  13. Molecular beam studies of reaction dynamics

    International Nuclear Information System (INIS)

    Lee, Yuan T.

    1991-03-01

    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

  14. A molecular dynamics approach to barrodiffusion

    Science.gov (United States)

    Cooley, James; Marciante, Mathieu; Murillo, Michael

    2016-10-01

    Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

  15. 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.

  16. Enhanced UWB Radio Channel Model for Short-Range Communication Scenarios Including User Dynamics

    DEFF Research Database (Denmark)

    Kovacs, Istvan Zsolt; Nguyen, Tuan Hung; Eggers, Patrick Claus F.

    2005-01-01

    channel model represents an enhancement of the existing IEEE 802.15.3a/4a PAN channel model, where antenna and user-proximity effects are not included. Our investigations showed that significant variations of the received wideband power and time-delay signal clustering are possible due the human body...

  17. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-01

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  18. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  19. The short range effective interaction and the spectra of calcium isotopes in (f-p) space

    International Nuclear Information System (INIS)

    Qing-ying, Z.; Shen-wu, L.; Jian-xin, W.

    1986-01-01

    In this work, the authors use a new type of extremely short range interaction, the double delta interaction (DDI) to calculate the low-lying spectra of calcium isotopes /sup 41/Ca through /sup 48/Ca. The configuration space (f-p) includes configurations ( f/sub 7/2//sup n/ ) and ( f/sub 7/2//sup n-1/2p/sub 3/2/). The calculated energies are compared with experimental data for 75 levels. For comparison, they also use usual modified surface delta interaction (MSDI) to calculate the same spectra aforementioned. It is clear that the results calculated with DDI are better than with MSDI. Therefore, in the short-range effective interaction the addition of body delta force to the modified surface delta force may improve the agreement with experiment. The authors believe that the conclusion will not be changed if one enlarges the shell model space

  20. Short-range order in amorphous thin films of indium selenides

    International Nuclear Information System (INIS)

    Zakharov, V.P.; Poltavtsev, Yu.G.; Sheremet, G.P.

    1982-01-01

    A structure of the short-range order and a character of interatomic interactions in indium selenides Insub(1-x)Sesub(x) with 0.333 <= x <= 0.75, obtained in the form of amorphous films 0.05-0.80 μm thick are studied using electron diffraction method. It is found out that mostly tetrahedrical coordination of nearest neighbours in the vicinity of indium atoms is characteristic for studied amorphous films, and coordination of selenium atoms is different. Amorphous film with x=0.75 posesses a considereably microheterogeneous structure of the short-range order, which is characterized by the presence of microunclusions of amorphous selenium and atoms of indium, octohedrically coordinated by selenium atoms

  1. Structure of the short-range atomic order of WO3 amorphous films

    International Nuclear Information System (INIS)

    Olevskij, S.S.; Sergeev, M.S.; Tolstikhina, A.L.; Avilov, A.S.; Shkornyakov, S.M.; Semiletov, S.A.

    1984-01-01

    To study the causes of electrochromism manifestation in thin tungsten oxide films, the structure of WO 3 amorphous films has been investigated. The films were obtained by three different methods: by W(CO) 6 tungsten carbonyl pyrolysis, by high-frequency ion-plasma sputtering of a target prepared by WO 3 powder sintering, and by WO 3 powder thermal evaporation. Monocrystalline wafers of silicon and sodium chloride were used as substrates. The structure of short-range order in WO 3 amorphous films varies versus, the method of preparation in compliance with the type of polyhedral elements, (WO 6 , WO 5 ) and with the character of their packing (contacts via edges or vertices). Manifestation of electroc ro mism in WO 3 films prepared by varions methods and having different structure of short-range order is supposed to be realized through various mechanisms. One cannot exclude a potential simultaneous effect of the two coloration mechanisms

  2. Study of the effect of short ranged ordering on the magnetism in FeCr alloys

    Energy Technology Data Exchange (ETDEWEB)

    Jena, Ambika Prasad, E-mail: apjena@bose.res.in [Department of Condensed Matter and Materials Science, S N Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake City, Kolkata 700098 (India); Sanyal, Biplab, E-mail: biplab.sanyal@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Mookerjee, Abhijit, E-mail: abhijit.mookerjee61@gmail.com [Department of Condensed Matter and Materials Science, S N Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake City, Kolkata 700098 (India)

    2014-01-15

    For the study of magnetism in systems where the local environment plays an important role, we propose a marriage between the Monte Carlo simulation and Zunger's special quasi-random structures. We apply this technique on disordered FeCr alloys and show that our estimates of the transition temperature is in good agreement with earlier experiments. - Highlights: • The magnetism in FeCr is sensitively depended on the ordering of the atoms : disordered or with short ranged ordering. • This work uses the SQS technique suggested by Zunger has been used to generate various degrees of short range ordering in FeCr. • The electronic structure and pair energies have been obatined from first principles ASR and Lichtenstein methods. • The effect of chemical ordering on magnetic ordering is studied in detail. • Only those situations where the chemical ordering is complete have been studied.

  3. Study of the effect of short ranged ordering on the magnetism in FeCr alloys

    International Nuclear Information System (INIS)

    Jena, Ambika Prasad; Sanyal, Biplab; Mookerjee, Abhijit

    2014-01-01

    For the study of magnetism in systems where the local environment plays an important role, we propose a marriage between the Monte Carlo simulation and Zunger's special quasi-random structures. We apply this technique on disordered FeCr alloys and show that our estimates of the transition temperature is in good agreement with earlier experiments. - Highlights: • The magnetism in FeCr is sensitively depended on the ordering of the atoms : disordered or with short ranged ordering. • This work uses the SQS technique suggested by Zunger has been used to generate various degrees of short range ordering in FeCr. • The electronic structure and pair energies have been obatined from first principles ASR and Lichtenstein methods. • The effect of chemical ordering on magnetic ordering is studied in detail. • Only those situations where the chemical ordering is complete have been studied

  4. Short-Range Noncontact Sensors for Healthcare and Other Emerging Applications: A Review

    Directory of Open Access Journals (Sweden)

    Changzhan Gu

    2016-07-01

    Full Text Available Short-range noncontact sensors are capable of remotely detecting the precise movements of the subjects or wirelessly estimating the distance from the sensor to the subject. They find wide applications in our day lives such as noncontact vital sign detection of heart beat and respiration, sleep monitoring, occupancy sensing, and gesture sensing. In recent years, short-range noncontact sensors are attracting more and more efforts from both academia and industry due to their vast applications. Compared to other radar architectures such as pulse radar and frequency-modulated continuous-wave (FMCW radar, Doppler radar is gaining more popularity in terms of system integration and low-power operation. This paper reviews the recent technical advances in Doppler radars for healthcare applications, including system hardware improvement, digital signal processing, and chip integration. This paper also discusses the hybrid FMCW-interferometry radars and the emerging applications and the future trends.

  5. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  6. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    International Nuclear Information System (INIS)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver

    2015-01-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom

  7. Neutrino-Nucleus Interactions and the Short-Range Structure of Nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Cavanna, F. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Palamara, O. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Schiavilla, R. [Old Dominion Univ., Norfolk, VA (United States); Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Soderberg, M. [Syracuse Univ., NY (United States); Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Wiringa, R. B. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-01-08

    Improvements in theoretical modeling of Short Range structures and phenomena, and comparisons with data, will require sustained collaboration between nuclear theorists and neutrino experimentalists. The extensive history of studying this area of nuclear physics in electron- and hadron-scattering experiments, coupled with the transformative capabilities of LArTPCs to identify neutrinos, will provide a ripe opportunity for new discoveries that will further our understanding of the nucleus.

  8. Determination of thermodynamical coefficients for Mo-W alloys according to short-range order parameters

    International Nuclear Information System (INIS)

    Erokhin, L.N.; Mokrov, A.P.; Shivrin, O.N.; Khanina, N.I.

    1986-01-01

    A method is proposed for determining thermodynamical coefficients according to short-range order parameters. The method approbation for Mo-W alloys has shown a good agreement between the thermodynamical and diffusion data. The Mo-W system in the concentration range under study is close to the ideal one. The calculated relative error of determination of interdiffusion coefficients in alloys of the Mo-W system does not exceed 16%

  9. Probing the short range behavior of nuclei with high PT photo- and electro-nuclear reactions

    International Nuclear Information System (INIS)

    Laget, J.M.

    1990-01-01

    The short range behavior of the nucleus and the use of the nucleus as a filter are studied. Special emphasis is given to photon and hadron induced reactions. The components of the nuclear wave function are described. The evidences of hard scattering processes in reactions induced by real photons as well as by hadrons on free nucleus are reviewed. The spin observables are also investigated. The perspectives opened by these studies in the nuclear environment are considered

  10. Short-range order of amorphous FeNiB alloy after neutron irradiation

    International Nuclear Information System (INIS)

    Miglierini, M.; Sitek, J.; Baluch, S.; Cirak, J.; Lipka, J.

    1990-01-01

    Transmission Moessbauer spectroscopy was used to study irradiation-induced changes in the short-range order of an amorphous Fe 80-x Ni x B 20 alloy. Neutron irradiation led to an increase of the width of a hyperfine field distribution implying atomic rearrangement towards disordering. Changes in a mean value of a HFD and Moessbauer line areas can be associated with a reorientation of spins due to radiation damage. (orig.)

  11. Short range correlations in the pion s-wave self-energy of pionic atoms

    OpenAIRE

    Salcedo, L. L.; Holinde, K.; Oset, E.; Schütz, C.

    1995-01-01

    We evaluate the contribution of second order terms to the pion-nucleus s-wave optical potential of pionic atoms generated by short range nuclear correlation. The corrections are sizeable because they involve the isoscalar s-wave $\\pi N$ amplitude for half off-shell situations where the amplitude is considerably larger than the on-shell one. In addition, the s-wave optical potential is reanalyzed by looking at all the different conventional contributions together lowest order, Pauli corrected ...

  12. Directional and short-range ordering kinetics in metallic alloys, crystalline and amorphous

    International Nuclear Information System (INIS)

    Hillairet, J.

    1985-01-01

    This presentation describes the methods (resistometric and anelastic) based on analysis of stress-induced directional ordering and short-range ordering and their application to the study of metallic alloys, crystalline and amorphous. It focuses on the determination of the atomic mobility and point defect properties. It discusses also the structural information which can be gained by Zener relaxation studies about the order-disorder transition and self-induced directional ordering phenomena

  13. Short-range order in InSb amorphized under ion bombardment

    International Nuclear Information System (INIS)

    Pavlov, P.V.; Tetel'baum, D.I.; Gerasimov, A.I.

    1979-01-01

    The investigation of short-range order is carried out in polycrystal InSb films, irradiated with Ne + ions with E=150 keV and with the 2x10 15 ion/cm 2 dose. The data are obtained testifying to the film amorphization, the cause of which is the defect storage but not the local melting. Stability of the obtained amorphous phase at the room temperature is noted

  14. Particle simulation algorithms with short-range forces in MHD and fluid flow

    International Nuclear Information System (INIS)

    Cable, S.; Tajima, T.; Umegaki, K.

    1992-07-01

    Attempts are made to develop numerical algorithms for handling fluid flows involving liquids and liquid-gas mixtures. In these types of systems, the short-range intermolecular interactions are important enough to significantly alter behavior predicted on the basis of standard fluid mechanics and magnetohydrodynamics alone. We have constructed a particle-in-cell (PIC) code for the purpose of studying the effects of these interactions. Of the algorithms considered, the one which has been successfully implemented is based on a MHD particle code developed by Brunel et al. In the version presented here, short range forces are included in particle motion by, first, calculating the forces between individual particles and then, to prevent aliasing, interpolating these forces to the computational grid points, then interpolating the forces back to the particles. The code has been used to model a simple two-fluid Rayleigh-Taylor instability. Limitations to the accuracy of the code exist at short wavelengths, where the effects of the short-range forces would be expected to be most pronounced

  15. Angular correlation between short-range. cap alpha. particles and. gamma. quanta

    Energy Technology Data Exchange (ETDEWEB)

    Kul' chitskii, L A; Latyshev, G D; Bulyginskii, D G

    1949-01-01

    Chang (Phys. Rev. 69, 60(1946); 70, 632(1946)) has found that the intensities of short-range ..cap alpha.. rays of Po and Ra are considerably higher than the values given by the Geiger-Nuttall law. This can be explained by assuming surface vibrations of ..cap alpha..-radioactive nuclei, which produce deformations and corresponding lowerings of the potential barrier in certain directions. In this case an angular correlation should exist between the short-range ..cap alpha.. ray and the accompanying ..gamma.. quantum. The authors checked this conclusion by applying the coincidence method to the ..cap alpha.. and ..gamma.. radiations of a mixture of RdTh (/sup 228/Th) and ThC (/sup 212/Bi). Maxima of coincidence numbers occur at angles 45 and 135 deg., with lesser maxima at 0 and 180 deg. Theoretical considerations show that in cases (like the one investigated) where the nuclear spin before and after the ..cap alpha.. and ..gamma.. emissions is zero, the angular correlations are uniquely determined whatever the deformation caused by the vibration; in other cases, the correlation depends on the kind of deformation. Therefore, it would be interesting to investigate the case of Pa, whose nuclear spin is not zero and the decay exhibits intensive groups of short-range ..cap alpha.. particles.

  16. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  17. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  18. How Dynamic Visualization Technology Can Support Molecular Reasoning

    Science.gov (United States)

    Levy, Dalit

    2013-01-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

  19. Short-Range Temporal Interactions in Sleep; Hippocampal Spike Avalanches Support a Large Milieu of Sequential Activity Including Replay.

    Directory of Open Access Journals (Sweden)

    J Matthew Mahoney

    Full Text Available Hippocampal neural systems consolidate multiple complex behaviors into memory. However, the temporal structure of neural firing supporting complex memory consolidation is unknown. Replay of hippocampal place cells during sleep supports the view that a simple repetitive behavior modifies sleep firing dynamics, but does not explain how multiple episodes could be integrated into associative networks for recollection during future cognition. Here we decode sequential firing structure within spike avalanches of all pyramidal cells recorded in sleeping rats after running in a circular track. We find that short sequences that combine into multiple long sequences capture the majority of the sequential structure during sleep, including replay of hippocampal place cells. The ensemble, however, is not optimized for maximally producing the behavior-enriched episode. Thus behavioral programming of sequential correlations occurs at the level of short-range interactions, not whole behavioral sequences and these short sequences are assembled into a large and complex milieu that could support complex memory consolidation.

  20. Molecular beam studies of adsorption dynamics

    International Nuclear Information System (INIS)

    Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

    1991-01-01

    We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential

  1. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  2. Molecular dynamics studies of displacement cascades

    International Nuclear Information System (INIS)

    Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.

    1990-02-01

    Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs

  3. A molecular dynamics simulation code ISIS

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-06-01

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

  4. Spin-diffusions and diffusive molecular dynamics

    Science.gov (United States)

    Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

    2017-12-01

    Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

  5. Modeling shockwave deformation via molecular dynamics

    International Nuclear Information System (INIS)

    Holian, B.L.

    1987-01-01

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

  6. A first-principles study of short range order in Cu-Zn

    International Nuclear Information System (INIS)

    Slutter, M.; Turchi, P.E.A.; Johnson, D.D.; Nicholson, D.M.; Stocks, G.M.; Pinski, F.J.

    1990-01-01

    Recently, measurements of short-range order (SRO) diffuse neutron scattering intensity have been performed on quenched Cu-Zn alloys with 22.4 to 31.1 atomic percent (a/o) Zn, and pair interactions were obtained by inverse Monte Carlo simulation. These results are compared to SRO intensities and effective pair interactions obtained from first-principles electronic structure calculations. The theoretical SRO intensities were calculated with the cluster variation method (CVM) in the tetrahedron-octahedron approximation with first-principles pain interactions as input. More generally, phase stability in the Cu-Zn alloy system is discussed, using ab-initio energetic properties

  7. Link Design Rules for Cost-Effective Short-Range Radio Over Multimode Fiber Systems

    DEFF Research Database (Denmark)

    Visani, Davide; Tartarini, Giovanni; Petersen, Martin Nordal

    2010-01-01

    Referring to short-range radio over multimode fiber links, we find out important guidelines for the realization of cost-effective intensity modulated directly detected systems. Since the quality of today's connectors is considerably higher than in the past, we demonstrate that two important...... parameters of the system are the finite detecting area of the photodiode and the laser frequency chirp. Furthemore, we show that the use of the central launch technique inherently determines a lower impact of modal noise fluctuations with respect to the offset launch one. This makes CL more convenient...

  8. Highly excited bound-state resonances of short-range inverse power-law potentials

    Energy Technology Data Exchange (ETDEWEB)

    Hod, Shahar [The Ruppin Academic Center, Emeq Hefer (Israel); The Hadassah Academic College, Jerusalem (Israel)

    2017-11-15

    We study analytically the radial Schroedinger equation with long-range attractive potentials whose asymptotic behaviors are dominated by inverse power-law tails of the form V(r) = -β{sub n}r{sup -n} with n > 2. In particular, assuming that the effective radial potential is characterized by a short-range infinitely repulsive core of radius R, we derive a compact analytical formula for the threshold energy E{sub l}{sup max} = E{sub l}{sup max}(n, β{sub n}, R), which characterizes the most weakly bound-state resonance (the most excited energy level) of the quantum system. (orig.)

  9. Short-range order and local conservation of quantum numbers in multiparticle production

    International Nuclear Information System (INIS)

    Le Bellac, M.

    1976-01-01

    These lectures discuss the implications of the hypotheses of short-range order (SRO) and local conservation of quantum numbers (LCQN) for multiple production of elementary particles at high energies. The consequences of SRO for semi-inclusive correlations and the distribution of rapidity gaps are derived, essentially in the framework of the cluster model. Then the experimental status of local conservation of charge and transverse momentum is reviewed. Finally, by making use of the unitarity relation, it is shown that LCQN has important consequences for the elastic amplitude. The derivation is given both in a model-independent way, and in specific multiperiheral models. (Author)

  10. Perturbation theory for short-range weakly-attractive potentials in one dimension

    Energy Technology Data Exchange (ETDEWEB)

    Amore, Paolo, E-mail: paolo.amore@gmail.com [Facultad de Ciencias, CUICBAS, Universidad de Colima, Bernal Díaz del Castillo 340, Colima, Colima (Mexico); Fernández, Francisco M., E-mail: fernande@quimica.unlp.edu.ar [INIFTA (UNLP, CONICET), Division Química Teórica, Blvd. 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2017-03-15

    We have obtained the perturbative expressions up to sixth order for the energy of the bound state in a one dimensional, arbitrarily weak, short range finite well, applying a method originally developed by Gat and Rosenstein Ref. [1]. The expressions up to fifth order reproduce the results already known in the literature, while the sixth order had not been calculated before. As an illustration of our formulas we have applied them to two exactly solvable problems and to a nontrivial problem.

  11. The Spectrum of Particles with Short-Ranged Interactions in a Harmonic Trap

    Directory of Open Access Journals (Sweden)

    Metsch B. Ch.

    2010-04-01

    Full Text Available The possibility to control short-ranged interactions of cold gases in optical traps by Feshbachresonances makes these systems ideal candidates to study universal scaling properties and Efimov physics. The spectrum of particles in a trap, idealised by a harmonic oscillator potential, in the zero range limit with 2- and 3-particle contact interactions is studied numerically. The Hamiltonian is regularised by restricting the oscillator basis and the coupling constants are tuned such that the ground state energies of the 2- and 3-particle sector are reproduced [1],[2]. Results for 2-, 3-, and 4 particle systems are presented and compared to exact results [3],[4].

  12. Study of the short-range 3He structure from the dd→3Hen reaction

    International Nuclear Information System (INIS)

    Ladygin, V.P.; Ladygina, N.V.

    1995-01-01

    An experiment on studying of the tensor analysing power C 0,NN,0,0 and spin correlation C N,N,0,0 due to the transverse polarization of both initial particles from the dd→ 3 Hen reaction has been proposed. Those polarization observables are very sensitive to the short-range 3 He structure. This experiment is proposed to be done at the LHE Accelerator Complex using both a polarized deuteron beam and a polarized deuterium target. 25 refs., 2 figs

  13. Influence of short range chemical order on density of states in α-ZrNi

    International Nuclear Information System (INIS)

    Duarte Junior, J.

    1986-01-01

    Calculations of the density of electronic states for amorphous alloys of ZrNi and ZrCu with different chemical order degrees, in order to verify the effect of chemical ordering on this property, are presented. The results obtained for ZrCu shown that the density of states at Fermi level do not vary significantly with the ordering. The results for ZrNi shown that the introduction of short range chemical order can decrease significantly the density of states at Fermi level, leading to better agreement with experimental results. (M.C.K.) [pt

  14. Measurement based scenario analysis of short-range distribution system planning

    DEFF Research Database (Denmark)

    Chen, Peiyuan; Bak-Jensen, Birgitte; Chen, Zhe

    2009-01-01

    This paper focuses on short-range distribution system planning using a probabilistic approach. Empirical probabilistic distributions of load demand and distributed generations are derived from the historical measurement data and incorporated into the system planning. Simulations with various...... feasible scenarios are performed based on a local distribution system at Støvring in Denmark. Simulation results provide more accurate and insightful information for the decision-maker when using the probabilistic analysis than using the worst-case analysis, so that a better planning can be achieved....

  15. EXAFS study of short range order in Fe-Zr amorphous alloys

    International Nuclear Information System (INIS)

    Fernandez-Gubieda, M.L.; Gorria, P.; Barandiaran, J.M.; Barquin, L.F.

    1995-01-01

    Room temperature X-ray absorption spectra on Fe K-edge have been performed in Fe 100-x-y Zr x B y and Fe 86 Zr 7 Cu 1 B 6 alloys (x=7, 7.7, 9; y=0, 2, 4, 6). Fe-Fe coordination number and interatomic distances do not change in any sample. However, small changes in the Fe-Zr short range order, which could explain the evolution of the magnetic properties, have been observed. (orig.)

  16. Numerical study of the glass-glass transition in short-ranged attractive colloids

    International Nuclear Information System (INIS)

    Zaccarelli, Emanuela; Sciortino, Francesco; Tartaglia, Piero

    2004-01-01

    We report extensive numerical simulations in the glass region for a simple model of short-ranged attractive colloids, the square well model. We investigate the behaviour of the density autocorrelation function and of the static structure factor in the region of temperatures and packing fractions where a glass-glass transition is expected according to theoretical predictions. We strengthen our observations by studying both waiting time and history dependence of the numerical results. We provide evidence supporting the possibility that activated bond-breaking processes destabilize the attractive glass, preventing the full observation of a sharp glass-glass kinetic transition

  17. Short Range Correlations in Nuclei at Large xbj through Inclusive Quasi-Elastic Electron Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Zhihong [Univ. of Virginia, Charlottesville, VA (United States)

    2013-12-01

    The experiment, E08-014, in Hall-A at Jefferson Lab aims to study the short-range correlations (SRC) which are necessary to explain the nuclear strength absent in the mean field theory. The cross sections for 2H, 3He, 4He, 12C, 40Ca and 48Ca, were measured via inclusive quasi-elastic electron scattering from these nuclei in a Q2 range between 0.8 and 2.8 (GeV/c)2 for x>1. The cross section ratios of heavy nuclei to 2H were extracted to study two-nucleon SRC for 1

  18. Study of an Ising model with competing long- and short-range interactions

    International Nuclear Information System (INIS)

    Loew, U.; Emery, V.J.; Fabricius, K.; Kivelson, S.A.

    1994-01-01

    A classical spin-one lattice gas model is used to study the competition between short-range ferromagnetic coupling and long-range antiferromagnetic Coulomb interactions. The model is a coarse-grained representation of frustrated phase separation in high-temperature superconductors. The ground states are determined for the complete range of parameters by using a combination of numerical and analytical techniques. The crossover between ferromagnetic and antiferromagnetic states proceeds via a rich structure of highly symmetric striped and checkerboard phases. There is no devil's staircase behavior because mixtures of stripes with different period phase separate

  19. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  20. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  1. Formation and transformation of a short range ordered iron carbonate precursor

    DEFF Research Database (Denmark)

    Dideriksen, Knud; Frandsen, Cathrine; Bovet, Nicolas

    2015-01-01

    (II) with varying pH produced broad peaks in X-ray diffraction and contained dominantly Fe and CO3 when probed with X-ray photoelectron spectroscopy. Reduced pair distribution function (PDF) analysis shows only peaks corresponding to interatomic distances below 15Å, reflecting a material with no long range...... structural order. Moreover, PDF peak positions differ from those for known iron carbonates and hydroxides. Mössbauer spectra also deviate from those expected for known iron carbonates and suggest a less crystalline structure. These data show that a previously unidentified iron carbonate precursor phase...... formed. Its coherent scattering domains determined from PDF analysis are slightly larger than for amorphous calcium carbonate, suggesting that the precursor could be nanocrystalline. Replica exchange molecular dynamics simulations of Fe-carbonate polynuclear complexes yield PDF peak positions that agree...

  2. 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)

  3. Distinct Short-Range Order Is Inherent to Small Amorphous Calcium Carbonate Clusters (<2 nm)

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Shengtong [Physical Chemistry, University of Konstanz, Universitätsstrasse 10 78457 Konstanz Germany; School of Chemical Engineering, State Key Laboratory of Chemical Engineering, Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road Shanghai 200237 P.R. China; Chevrier, Daniel M. [Department of Chemistry and Institute for Research in Materials, Dalhousie University, Halifax Nova Scotia B3H 4R2 Canada; Zhang, Peng [Department of Chemistry and Institute for Research in Materials, Dalhousie University, Halifax Nova Scotia B3H 4R2 Canada; Gebauer, Denis [Physical Chemistry, University of Konstanz, Universitätsstrasse 10 78457 Konstanz Germany; Cölfen, Helmut [Physical Chemistry, University of Konstanz, Universitätsstrasse 10 78457 Konstanz Germany

    2016-09-09

    Amorphous intermediate phases are vital precursors in the crystallization of many biogenic minerals. While inherent short-range orders have been found in amorphous calcium carbonates (ACCs) relating to different crystalline forms, it has never been clarified experimentally whether such orders already exist in very small clusters less than 2 nm in size. Here, we studied the stability and structure of 10,12-pentacosadiynoic acid (PCDA) protected ACC clusters with a core size of ca. 1.4 nm consisting of only seven CaCO3 units. Ligand concentration and structure are shown to be key factors in stabilizing the ACC clusters. More importantly, even in such small CaCO3 entities, a proto-calcite short-range order can be identified but with a relatively high degree of disorder that arises from the very small size of the CaCO3 core. Our findings support the notion of a structural link between prenucleation clusters, amorphous intermediates, and final crystalline polymorphs, which appears central to the understanding of polymorph selection.

  4. Short-range contacts govern the performance of industry-relevant battery cathodes

    Science.gov (United States)

    Morelly, Samantha L.; Alvarez, Nicolas J.; Tang, Maureen H.

    2018-05-01

    Fundamental understanding of how processing affects composite battery electrode structure and performance is still lacking, especially for industry-relevant electrodes with low fractions of inactive material. This work combines rheology, electronic conductivity measurements, and battery rate capability tests to prove that short-range electronic contacts are more important to cathode rate capability than either ion transport or long-range electronic conductivity. LiNi0.33Mn0.33Co0.33O2, carbon black, and polyvinylidene difluoride in 1-methyl-2-pyrrolidinone represent a typical commercial electrode with films. Improvements in battery rate capability at constant electrode porosity do not correlate to electronic conductivity, but rather show an optimum fraction of free carbon. Simple comparison of rate capability in electrodes with increased total carbon loading (3 wt%) shows improvement for all fractions of free carbon. These results clearly indicate that ion transport cannot be limiting and highlight the critical importance of short-range electronic contacts for controlling battery performance.

  5. CMOS Receiver Front-ends for Gigabit Short-Range Optical Communications

    CERN Document Server

    Aznar, Francisco; Calvo Lopez, Belén

    2013-01-01

    This book describes optical receiver solutions integrated in standard CMOS technology, attaining high-speed short-range transmission within cost-effective constraints.  These techniques support short reach applications, such as local area networks, fiber-to-the-home and multimedia systems in cars and homes. The authors show how to implement the optical front-end in the same technology as the subsequent digital circuitry, leading to integration of the entire receiver system in the same chip.  The presentation focuses on CMOS receiver design targeting gigabit transmission along a low-cost, standardized plastic optical fiber up to 50m in length.  This book includes a detailed study of CMOS optical receiver design – from building blocks to the system level. Reviews optical communications, including long-haul transmission systems and emerging applications focused on short-range; Explains necessary fundamentals, such as characteristics of a data signal, system requirements affecting receiver design and key par...

  6. Short range part of the NN interaction: Equivalent local potentials from quark exchange kernels

    International Nuclear Information System (INIS)

    Suzuk, Y.; Hecht, K.T.

    1983-01-01

    To focus on the nature of the short range part of the NN interaction, the intrinsically nonlocal interaction among the quark constituents of colorless nucleons is converted to an equivalent local potential using resonating group kernels which can be evaluated in analytic form. The WKB approximation based on the Wigner transform of the nonlocal kernels has been used to construct the equivalent potentials without recourse to the long range part of the NN interaction. The relative importance of the various components of the exchange kernels can be examined: The results indicate the importance of the color magnetic part of the exchange kernel for the repulsive part in the (ST) = (10), (01) channels, in particular since the energy dependence of the effective local potentials seems to be set by this term. Large cancellations of color Coulombic and quark confining contributions, together with the kinetic energy and norm exchange terms, indicate that the exact nature of the equivalent local potential may be sensitive to the details of the parametrization of the underlying quark-quark interaction. The equivalent local potentials show some of the characteristics of the phenomenological short range terms of the Paris potential

  7. Polyamorphism and substructure of short-range order in amorphous boron films

    International Nuclear Information System (INIS)

    Palatnik, L.S.; Nechitajlo, A.A.; Koz'ma, A.A.

    1981-01-01

    The structure and substructure of boron amorphous films are studied in detail. Amorphous condensate of Bsup(a) boron is built of the same (but only disorientedly located) 12 B icosahedrons as boron crystalline modifications: B 105 -equilibrium β-rhombic, metastable: B 50 -tetragonal, B 12 -α-rhombohedral Coordination number for Bsup(a) (Z 1 =6.4) is lower than in B 105 (Z 1 =6.6) but higher than in B 50 modification (Z 1 =6.1). In crystalline modifications B 105 , B 50 , B 12 coordination numbers ω in first coordination spheres of icosahedrons are equal to ν 105 =6+4.6=10.6; ν 50 =10+3=14; ν 12 =6 respectively. Both amorphous modifications of boron Bsub(1)sup(a) and Bsub(15)sup(a) are analogs to B 50 in respect of the short-range order of icosahedron location. The difference between them is in ''substructure'' of short-range order: part of boron atoms (approximately 12%) do not occupy the vertices (so that vacancies appear) and enter the emptinesses between icosahedrons. In other words, the structure B 50 is the model basis of both amorphous phases [ru

  8. Tensor-optimized antisymmetrized molecular dynamics as a successive variational method in nuclear many-body system

    Energy Technology Data Exchange (ETDEWEB)

    Myo, Takayuki, E-mail: takayuki.myo@oit.ac.jp [General Education, Faculty of Engineering, Osaka Institute of Technology, Osaka 535-8585 (Japan); Research Center for Nuclear Physics (RCNP), Osaka University, Ibaraki 567-0047 (Japan); Toki, Hiroshi [Research Center for Nuclear Physics (RCNP), Osaka University, Ibaraki 567-0047 (Japan); Ikeda, Kiyomi [RIKEN Nishina Center, Wako, Saitama 351-0198 (Japan); Horiuchi, Hisashi [Research Center for Nuclear Physics (RCNP), Osaka University, Ibaraki 567-0047 (Japan); Suhara, Tadahiro [Matsue College of Technology, Matsue 690-8518 (Japan)

    2017-06-10

    We study the tensor-optimized antisymmetrized molecular dynamics (TOAMD) as a successive variational method in many-body systems with strong interaction for nuclei. In TOAMD, the correlation functions for the tensor force and the short-range repulsion and their multiples are operated to the AMD state as the variational wave function. The total wave function is expressed as the sum of all the components and the variational space can be increased successively with the multiple correlation functions to achieve convergence. All the necessary matrix elements of many-body operators, consisting of the multiple correlation functions and the Hamiltonian, are expressed analytically using the Gaussian integral formula. In this paper we show the results of TOAMD with up to the double products of the correlation functions for the s-shell nuclei, {sup 3}H and {sup 4}He, using the nucleon–nucleon interaction AV8′. It is found that the energies and Hamiltonian components of two nuclei converge rapidly with respect to the multiple of correlation functions. This result indicates the efficiency of TOAMD for the power series expansion in terms of the tensor and short-range correlation functions.

  9. A molecular dynamics study of ambient and high pressure phases of silica: structure and enthalpy variation with molar volume.

    Science.gov (United States)

    Rajappa, Chitra; Sringeri, S Bhuvaneshwari; Subramanian, Yashonath; Gopalakrishnan, J

    2014-06-28

    Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, α-PbO2-type, and pyrite-type - for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase.

  10. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  11. Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

    National Research Council Canada - National Science Library

    Johnston, K

    1998-01-01

    .... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

  12. Molecular Dynamics and Bioactivity of a Novel Mutated Human ...

    African Journals Online (AJOL)

    Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...

  13. Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting

    National Research Council Canada - National Science Library

    Low, Tammy K

    2006-01-01

    .... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...

  14. A molecular dynamics calculation of solid phase of malonic acid ...

    Indian Academy of Sciences (India)

    Sathya S R R Perumal

    Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...

  15. Hybridization of tensor-optimized and high-momentum antisymmetrized molecular dynamics for light nuclei with bare interaction

    Science.gov (United States)

    Lyu, Mengjiao; Isaka, Masahiro; Myo, Takayuki; Toki, Hiroshi; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro; Yamada, Taiichi

    2018-01-01

    Many-body correlations play an essential role in the ab initio description of nuclei with nuclear bare interactions. We propose a new framework to describe light nuclei by the hybridization of the tensor-optimized antisymmetrized molecular dynamics (TOAMD) and the high-momentum AMD (HM-AMD), which we call "HM-TOAMD." In this framework, we describe the many-body correlations in terms of not only the correlation functions in TOAMD, but also the high-momentum pairs in the AMD wave function. With the bare nucleon-nucleon interaction AV8^', we sufficiently reproduce the energy and radius of the {^3}H nucleus in HM-TOAMD. The effects of tensor force and short-range repulsion in the bare interaction are nicely described in this new framework. We also discuss the convergence in calculation and flexibility of the model space for this new method.

  16. Next generation extended Lagrangian first principles molecular dynamics.

    Science.gov (United States)

    Niklasson, Anders M N

    2017-08-07

    Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

  17. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  18. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  19. A fermionic molecular dynamics technique to model nuclear matter

    International Nuclear Information System (INIS)

    Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

    2009-01-01

    Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

  20. Current-driven dynamics in molecular-scale devices

    International Nuclear Information System (INIS)

    Seideman, Tamar

    2003-01-01

    We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

  1. Molecular Dynamic Modeling and Simulation for Polymers

    National Research Council Canada - National Science Library

    Harrell, Anthony

    2003-01-01

    ... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...

  2. Molecular dynamics of a proguanil derivative

    African Journals Online (AJOL)

    pc

    Proguanil is a prophylactic antimalarial drug t .... presence of resistance to individual component. ... This is the mathematical ... predicting equilibrium structures of molecular systems ..... for the modeling and subsequent development of.

  3. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  4. Evidence for short range corelations from high Q2 (e,e') reactions

    International Nuclear Information System (INIS)

    Strikman, M.I.; Frankfurt, L.L.; Sargayan, M.M.

    1994-01-01

    For many years now short-range correlations (SRC) in nuclei have been considered as an essential feature of the nuclear wave function. At high energy (e,e') reactions, where Q 2 > 1 (GeV/c) 2 , x = Q 2 /2mq o > 1 and 1 GeV > q o > 300 ∼ 400 MeV the scattering from low momentum nucleons is kinematically suppressed and there the evidence of SRC expected to be more prominent. These reactions have been intensively investigated during the last decade or so at SLAC on both light and heavy nuclei. The above kinematics allows one to compute the cross section through the processes local in space. To explain this the authors analyse the representation of the cross section as a Fourier transform of the commutator of electromagnetic currents and see that the major contribution in the cross section is given by the region of integration

  5. Magnetic susceptibility as a method of investigation of short-range order in strongly nonstoichiometric carbides

    International Nuclear Information System (INIS)

    Nazarova, S.Z.; Gusev, A.I.

    2001-01-01

    Magnetic susceptibility in disordered and ordered carbides of transition metals (M = Ti, Zr, Hf, Nb, Ta) was studied, the results are generalized. It was ascertained that the change in carbide susceptibility induced by deviation from stoichiometry stems from specific features of electronic spectra of the compounds. The use of magnetic susceptibility for determining structural disorder-order transitions is discussed. It is shown that change in the contribution made by orbital paramagnetism, resulting from short-range order formation, is the reason of decrease in susceptibility of nonstoichiometric carbides during the ordering. Experimentally obtained data on susceptibility permitted evaluating short- and far-range order parameters in NbC y , TaC y , TiC y and HfC y carbides [ru

  6. Improving Short-Range Ensemble Kalman Storm Surge Forecasting Using Robust Adaptive Inflation

    KAUST Repository

    Altaf, Muhammad

    2013-08-01

    This paper presents a robust ensemble filtering methodology for storm surge forecasting based on the singular evolutive interpolated Kalman (SEIK) filter, which has been implemented in the framework of the H∞ filter. By design, an H∞ filter is more robust than the common Kalman filter in the sense that the estimation error in the H∞ filter has, in general, a finite growth rate with respect to the uncertainties in assimilation. The computational hydrodynamical model used in this study is the Advanced Circulation (ADCIRC) model. The authors assimilate data obtained from Hurricanes Katrina and Ike as test cases. The results clearly show that the H∞-based SEIK filter provides more accurate short-range forecasts of storm surge compared to recently reported data assimilation results resulting from the standard SEIK filter.

  7. Higher-order glass-transition singularities in systems with short-ranged attractive potentials

    International Nuclear Information System (INIS)

    Goetze, W; Sperl, M

    2003-01-01

    Within the mode-coupling theory for the evolution of structural relaxation, the A 4 -glass-transition singularities are identified for systems of particles interacting with a hard-sphere repulsion complemented by different short-ranged potentials: Baxter's singular potential regularized by a large-wavevector cut-off, a model for the Asakura-Oosawa depletion attraction, a triangular potential, a Yukawa attraction, and a square-well potential. The regular potentials yield critical packing fractions, critical Debye-Waller factors, and critical amplitudes very close to each other. The elastic moduli and the particle localization lengths for corresponding states of the Yukawa system and the square-well system may differ by up to 20 and 10%, respectively

  8. Mass dependence of short-range correlations in nuclei and the EMC effect

    Directory of Open Access Journals (Sweden)

    Cosyn Wim

    2014-03-01

    Full Text Available We sketch an approximate method to quantify the number of correlated pairs in any nucleus A. It is based on counting independent-particle model (IPM nucleon-nucleon pairs in a relative S-state with no radial excitation. We show that IPM pairs with those quantum numbers are most prone to short-range correlations and are at the origin of the high-momentum tail of the nuclear momentum distributions. Our method allows to compute the a2 ratios extracted from inclusive electron scattering. Furthermore, our results reproduce the observed linear correlation between the number of correlated pairs and the magnitude of the EMC effect. We show that the width of the pair center-ofmass distribution in exclusive two-nucleon knockout yields information on the quantum numbers of the pairs.

  9. The dependence of the nuclear charge form factor on short range correlations and surface fluctuation effects

    International Nuclear Information System (INIS)

    Massen, S. E.; Garistov, V. P.; Grypeos, M. E.

    1996-01-01

    The effects of nuclear surface fluctuations on harmonic oscillator elastic charge form factor of light nuclei are investigated, simultaneously approximating the short-range correlations through a Jastrow correlation factor. Inclusion of the surface fluctuation effects within this description, by truncating the cluster expansion at the two-body part, is found to improve somewhat the fit to the elastic charge form-factor of 16 O and 40 Ca. However, the convergence of the cluster expansion is expected to deteriorate. An additional finding is that surface-fluctuation correlations produce a drastic change in the asymptotic behaviour of the point-proton form-factor, which now falls off quite slowly (i.e. as const.q -4 ) at large values of the momentum transfer q

  10. Thermal algebraic-decay charge liquid driven by competing short-range Coulomb repulsion

    Science.gov (United States)

    Kaneko, Ryui; Nonomura, Yoshihiko; Kohno, Masanori

    2018-05-01

    We explore the possibility of a Berezinskii-Kosterlitz-Thouless-like critical phase for the charge degrees of freedom in the intermediate-temperature regime between the charge-ordered and disordered phases in two-dimensional systems with competing short-range Coulomb repulsion. As the simplest example, we investigate the extended Hubbard model with on-site and nearest-neighbor Coulomb interactions on a triangular lattice at half filling in the atomic limit by using a classical Monte Carlo method, and find a critical phase, characterized by algebraic decay of the charge correlation function, belonging to the universality class of the two-dimensional XY model with a Z6 anisotropy. Based on the results, we discuss possible conditions for the critical phase in materials.

  11. Ionization induced by strong electromagnetic field in low dimensional systems bound by short range forces

    Energy Technology Data Exchange (ETDEWEB)

    Eminov, P.A., E-mail: peminov@mail.ru [Moscow State University of Instrument Engineering and Computer Sciences, 20 Stromynka Street, Moscow 2107996 (Russian Federation); National Research University Higher School of Economics, 3/12 Bolshoy Trekhsvyatskiy pereulok, Moscow 109028 (Russian Federation)

    2013-10-01

    Ionization processes for a two dimensional quantum dot subjected to combined electrostatic and alternating electric fields of the same direction are studied using quantum mechanical methods. We derive analytical equations for the ionization probability in dependence on characteristic parameters of the system for both extreme cases of a constant electric field and of a linearly polarized electromagnetic wave. The ionization probabilities for a superposition of dc and low frequency ac electric fields of the same direction are calculated. The impulse distribution of ionization probability for a system bound by short range forces is found for a superposition of constant and alternating fields. The total probability for this process per unit of time is derived within exponential accuracy. For the first time the influence of alternating electric field on electron tunneling probability induced by an electrostatic field is studied taking into account the pre-exponential term.

  12. Age differences in visual search for compound patterns: long- versus short-range grouping.

    Science.gov (United States)

    Burack, J A; Enns, J T; Iarocci, G; Randolph, B

    2000-11-01

    Visual search for compound patterns was examined in observers aged 6, 8, 10, and 22 years. The main question was whether age-related improvement in search rate (response time slope over number of items) was different for patterns defined by short- versus long-range spatial relations. Perceptual access to each type of relation was varied by using elements of same contrast (easy to access) or mixed contrast (hard to access). The results showed large improvements with age in search rate for long-range targets; search rate for short-range targets was fairly constant across age. This pattern held regardless of whether perceptual access to a target was easy or hard, supporting the hypothesis that different processes are involved in perceptual grouping at these two levels. The results also point to important links between ontogenic and microgenic change in perception (H. Werner, 1948, 1957).

  13. Structure factor of polymers interacting via a short range repulsive potential: Application to hairy wormlike micelles

    International Nuclear Information System (INIS)

    Massiera, Gladys; Ramos, Laurence; Ligoure, Christian; Pitard, Estelle

    2003-01-01

    We use the random phase approximation to compute the structure factor S(q) of a solution of chains interacting through a soft and short range repulsive potential V. Above a threshold polymer concentration, whose magnitude is essentially controlled by the range of the potential, S(q) exhibits a peak whose position depends on the concentration. We take advantage of the close analogy between polymers and wormlike micelles and apply our model, using a Gaussian function for V, to quantitatively analyze experimental small angle neutron scattering profiles of solutions of hairy wormlike micelles. These samples, which consist in surfactant self-assembled flexible cylinders decorated by amphiphilic copolymer, provide indeed an appropriate experimental model system to study the structure of sterically interacting polymer solutions

  14. Interlayer exchange coupling in Er|Tb superlattices mediated by short range incommensurate Er order

    International Nuclear Information System (INIS)

    Pfuhl, E; Brueckel, T; Voigt, J; Mattauch, S; Korolkov, D

    2010-01-01

    We study the magnetic correlations in Er|Tb superlattices by means of off-specular scattering of polarized neutrons. We show here the co-existence of inhomogeneous magnetic states: i) ferromagnetic order of moments within the Tb layers below 230 K (FM), correlation length of about 10 bilayer, ii) an incommensurate modulated magnetic order, restricted to single Er layers and iii) antiferromagnetic coupling of ferromagnetic layers below 70K (AFC). Polarised off-specular neutron scattering under grazing incidence reveals that i) magnetic fluctuations appear when the sample is cooled below 70 K, ii) these fluctuations lead to AFC, when the sample is cooled to 10 K, which iii) persists, when the sample is subsequently heated up to 45 K, while the order is not present during the cooling cycle. Also the short range incommensurate order changes accordingly, implying that the magnetic order in the Er layers mediates the interlayer coupling between ferromagnetic Tb layers.

  15. Short-range correlations in an extended time-dependent mean-field theory

    International Nuclear Information System (INIS)

    Madler, P.

    1982-01-01

    A generalization is performed of the time-dependent mean-field theory by an explicit inclusion of strong short-range correlations on a level of microscopic reversibility relating them to realistic nucleon-nucleon forces. Invoking a least action principle for correlated trial wave functions, equations of motion for the correlation functions and the single-particle model wave function are derived in lowest order of the FAHT cluster expansion. Higher order effects as well as long-range correlations are consider only to the extent to which they contribute to the mean field via a readjusted phenomenological effective two-body interaction. The corresponding correlated stationary problem is investigated and appropriate initial conditions to describe a heavy ion reaction are proposed. The singleparticle density matrix is evaluated

  16. A New Theoretical Analysis of the Effects of Short Range Correlations in Inclusive Lepton Scattering

    Science.gov (United States)

    Benedetta Mezzetti, Chiara; Ciofi Degli Atti, Claudio

    2009-05-01

    Recently, evidence of short range correlations (SRC) has been provided by experimental data on inclusive lepton A(e, e')X scattering by the observation of a scaling behavior of the ratios of the cross sections on heavy nuclei to those on the deuteron and ^3He. Other attempts to get information on SRC rely on the concept of Y-scaling, whose interest has been renewed by new Jlab data. A new approach to Y-scaling, relying on the definition of a new relativistic scaling variable which incorporates the momentum dependence of the excitation energy of the (A - 1) system is presented, with the resulting scaling function being closely related to the longitudinal momentum distributions. Taking into account final state interaction effects, the new analysis of experimental data on nuclei, ranging from ^3He to Nuclear Matter, provides unique information on the nucleon momentum distributions and confirms the analysis in terms of cross section ratios.

  17. Short-range structure and thermal properties of lead tellurite glasses

    Science.gov (United States)

    Hirdesh, Kaur, Amarjot; Khanna, Atul; Gonzàlez, Fernando

    2017-05-01

    PbO-TeO2 glasses having composition: xPbO-(100 - x)TeO2 (x = 10, 15 and 20 mol%) were prepared by melt quenching and characterized by X-ray diffraction, density measurements, differential scanning calorimetry and Raman spectroscopy. Glass density increases from 5.89 to 6.22 g cm-3 with increase in PbO concentration from 10 to 20 mol%, due to the replacement of TeO2 by heavier PbO. DSC studies found that glass transition temperature (Tg) decreases from a value of 295°C to 281°C. Raman studies found that glass short-range structure consists of TeO4 and TeO3 structural units and that PbO modifies the network by the structural transformation: TeO4 to TeO3.

  18. Short-range structure and thermal properties of barium tellurite glasses

    Science.gov (United States)

    Kaur, Amarjot; Khanna, Atul; Gonzàlez, Fernando

    2017-05-01

    BaO-TeO2 glasses containing 10 to 20 BaO mol% were prepared and characterized by X-ray diffraction, density measurements, differential scanning calorimetry and Raman spectroscopy. Glass density decreases with increase in BaO concentration from 10 to 20 mol%, due to replacement of heavier TeO2 by lighter BaO, however glass transition temperature (Tg) increases significantly from a value of 318°C to 327°C due to increase in average single bond enthalpy of the tellurite network. Raman studies found that glass short-range structure consists of TeO4 and TeO3 structural units and BaO modifies the network by producing the structural transformation: TeO4→ TeO3.

  19. Improving Short-Range Ensemble Kalman Storm Surge Forecasting Using Robust Adaptive Inflation

    KAUST Repository

    Altaf, Muhammad; Butler, T.; Luo, X.; Dawson, C.; Mayo, T.; Hoteit, Ibrahim

    2013-01-01

    This paper presents a robust ensemble filtering methodology for storm surge forecasting based on the singular evolutive interpolated Kalman (SEIK) filter, which has been implemented in the framework of the H∞ filter. By design, an H∞ filter is more robust than the common Kalman filter in the sense that the estimation error in the H∞ filter has, in general, a finite growth rate with respect to the uncertainties in assimilation. The computational hydrodynamical model used in this study is the Advanced Circulation (ADCIRC) model. The authors assimilate data obtained from Hurricanes Katrina and Ike as test cases. The results clearly show that the H∞-based SEIK filter provides more accurate short-range forecasts of storm surge compared to recently reported data assimilation results resulting from the standard SEIK filter.

  20. Utilizing Context in Location-Aware Short-Range Wireless Communication

    Directory of Open Access Journals (Sweden)

    Vesa A. Korhonen

    2010-01-01

    Full Text Available We discuss how a short-range wireless communication service implemented for modern mobile communication devices can provide additional value for both the consumer and the service/product provider. When used as an information search tool, such systems allow services and products being promoted at the location they are available. For the customer, it may provide a “digitally augmented vision”, an enhanced view to the current environment. With data filtering and search rules, this may provide a self-manageable context, where the user's own personal environment and preferences to the features available in the current surroundings cooperate with a direct connection to the web-based social media. A preliminary design for such service is provided. The conclusion is that the method can generate additional revenue to the company and please the customers' buying process. In addition to the marketing, the principles described here are also applicable to other forms of human interaction.

  1. 79 GHz UWB automotive short range radar – Spectrum allocation and technology trends

    Directory of Open Access Journals (Sweden)

    H.-L. Bloecher

    2009-05-01

    Full Text Available Automotive UWB (Ultra-Wideband short range radar (SSR is on the market as a key technology for novel comfort and safety systems. SiGe based 79 GHz UWB SRR will be a definite candidate for the long term substitution of the 24 GHz UWB SRR. This paper will give an overview of the finished BMBF joint project KOKON and the recently started successing project RoCC, which concentrate on the development of this technology and sensor demonstrators. In both projects, the responsibilities of Daimler AG deal with application based sensor specification, test and evaluation of realized sensor demonstrators. Recent UWB SRR frequency regulation approaches and activitites will be introduced. Furthermore, some first results of Daimler activities within RoCC will be presented, dealing with the packaging and operation of these sensors within the complex car environment.

  2. Short-range wakefields generated in the blowout regime of plasma-wakefield acceleration

    Science.gov (United States)

    Stupakov, G.

    2018-04-01

    In the past, calculation of wakefields generated by an electron bunch propagating in a plasma has been carried out in linear approximation, where the plasma perturbation can be assumed small and plasma equations of motion linearized. This approximation breaks down in the blowout regime where a high-density electron driver expels plasma electrons from its path and creates a cavity void of electrons in its wake. In this paper, we develop a technique that allows us to calculate short-range longitudinal and transverse wakes generated by a witness bunch being accelerated inside the cavity. Our results can be used for studies of the beam loading and the hosing instability of the witness bunch in plasma-wakefield and laser-wakefield acceleration.

  3. Multi-channel, passive, short-range anti-aircraft defence system

    Science.gov (United States)

    Gapiński, Daniel; Krzysztofik, Izabela; Koruba, Zbigniew

    2018-01-01

    The paper presents a novel method for tracking several air targets simultaneously. The developed concept concerns a multi-channel, passive, short-range anti-aircraft defence system based on the programmed selection of air targets and an algorithm of simultaneous synchronisation of several modified optical scanning seekers. The above system is supposed to facilitate simultaneous firing of several self-guided infrared rocket missiles at many different air targets. From the available information, it appears that, currently, there are no passive self-guided seekers that fulfil such tasks. This paper contains theoretical discussions and simulations of simultaneous detection and tracking of many air targets by mutually integrated seekers of several rocket missiles. The results of computer simulation research have been presented in a graphical form.

  4. Direct separation of short range order in intermixed nanocrystalline and amorphous phases

    International Nuclear Information System (INIS)

    Frenkel, Anatoly I.; Kolobov, Alexander V.; Robinson, Ian K.; Cross, Julie O.; Maeda, Yoshihito; Bouldin, Charles E.

    2002-01-01

    Diffraction anomalous fine-structure (DAFS) and extended x-ray absorption fine-structure (EXAFS) measurements were combined to determine short range order (SRO) about a single atomic type in a sample of mixed amorphous and nanocrystalline phases of germanium. EXAFS yields information about the SRO of all Ge atoms in the sample, while DAFS determines the SRO of only the ordered fraction. We determine that the first-shell distance distribution is bimodal; the nanocrystalline distance is the same as the bulk crystal, to within 0.01(2) A ring , but the mean amorphous Ge-Ge bond length is expanded by 0.076(19) Angstrom. This approach can be applied to many systems of mixed amorphous and nanocrystalline phases

  5. An Empirical Path-Loss Model for Wireless Channels in Indoor Short-Range Office Environment

    Directory of Open Access Journals (Sweden)

    Ye Wang

    2012-01-01

    Full Text Available A novel empirical path-loss model for wireless indoor short-range office environment at 4.3–7.3 GHz band is presented. The model is developed based on the experimental datum sampled in 30 office rooms in both line of sight (LOS and non-LOS (NLOS scenarios. The model is characterized as the path loss to distance with a Gaussian random variable X due to the shadow fading by using linear regression. The path-loss exponent n is fitted by the frequency using power function and modeled as a frequency-dependent Gaussian variable as the standard deviation σ of X. The presented works should be available for the research of wireless channel characteristics under universal indoor short-distance environments in the Internet of Things (IOT.

  6. Contribution of silicon recombination properties in resolution of short-range particle detectors

    International Nuclear Information System (INIS)

    Verbitskaya, E.M.; Eremin, V.K.; Malyarenko, A.M.; Strokan, N.B.; Sukhanov, V.L.

    1987-01-01

    Tracks of short-range particles represent dense clusters of electron-hole pairs 2-4 μm in diameter and 20-30 μm long. Thus, conditions for charge carrier transport in microscopic Si volume are discovered at registration of each particle. Statistical distribution by the specimen square of the main parameter - lifetime of charge carriers (τ) is disclosed as a result of particle chaotic hitting the detector. Analytical description for the shape of the spectral line of the detector is found in the assumption of Gauss distribution τ. The function is applied to the analysis of detector spectra with maximum energy resolution, for which contributions to the shape of the line of the fundamental factors and nonperfection of Si or of the detector structure as a whole are comparable. Excess fluctuations of α-particle energy transformation to the charge of electron-hole pairs are found relatively to adopted values

  7. Contribution of silicon recombination properties in resolution of short-range particle detectors

    Energy Technology Data Exchange (ETDEWEB)

    Verbitskaya, E M; Eremin, V K; Malyarenko, A M; Strokan, N B; Sukhanov, V L

    1987-10-01

    Tracks of short-range particles represent dense clusters of electron-hole pairs 2-4 ..mu..m in diameter and 20-30 ..mu..m long. Thus, conditions for charge carrier transport in microscopic Si volume are discovered at registration of each particle. Statistical distribution by the specimen square of the main parameter - lifetime of charge carriers (tau) is disclosed as a result of particle chaotic hitting the detector. Analytical description for the shape of the spectral line of the detector is found in the assumption of Gauss distribution tau. The function is applied to the analysis of detector spectra with maximum energy resolution, for which contributions to the shape of the line of the fundamental factors and nonperfection of Si or of the detector structure as a whole are comparable. Excess fluctuations of ..cap alpha..-particle energy transformation to the charge of electron-hole pairs are found relatively to adopted values.

  8. Dependence of Coulomb Sum Rule on the Short Range Correlation by Using Av18 Potential

    Science.gov (United States)

    Modarres, M.; Moeini, H.; Moshfegh, H. R.

    The Coulomb sum rule (CSR) and structure factor are calculated for inelastic electron scattering from nuclear matter at zero and finite temperature in the nonrelativistic limit. The effect of short-range correlation (SRC) is presented by using lowest order constrained variational (LOCV) method and the Argonne Av18 and Δ-Reid soft-core potentials. The effects of different potentials as well as temperature are investigated. It is found that the nonrelativistic version of Bjorken scaling approximately sets in at the momentum transfer of about 1.1 to 1.2 GeV/c and the increase of temperature makes it to decrease. While different potentials do not significantly change CSR, the SRC improves the Coulomb sum rule and we get reasonably close results to both experimental data and others theoretical predictions.

  9. n-p Short-Range Correlations from (p,2p+n) Measurements

    Science.gov (United States)

    Tang, A.; Watson, J. W.; Aclander, J.; Alster, J.; Asryan, G.; Averichev, Y.; Barton, D.; Baturin, V.; Bukhtoyarova, N.; Carroll, A.; Gushue, S.; Heppelmann, S.; Leksanov, A.; Makdisi, Y.; Malki, A.; Minina, E.; Navon, I.; Nicholson, H.; Ogawa, A.; Panebratsev, Yu.; Piasetzky, E.; Schetkovsky, A.; Shimanskiy, S.; Zhalov, D.

    2003-01-01

    We studied the 12C(p,2p+n) reaction at beam momenta of 5.9, 8.0, and 9.0 GeV/c. For quasielastic (p,2p) events pf, the momentum of the knocked-out proton before the reaction, was compared (event by event) with pn, the coincident neutron momentum. For |pn|>kF=0.220 GeV/c (the Fermi momentum) a strong back-to-back directional correlation between pf and pn was observed, indicative of short-range n-p correlations. From pn and pf we constructed the distributions of c.m. and relative motion in the longitudinal direction for correlated pairs. We also determined that 49±13% of events with |pf|>kF had directionally correlated neutrons with |pn|>kF.

  10. Observation of short range three-particle correlations in e+e- annihilations at LEP energies

    CERN Document Server

    Abreu, P; Adye, T; Agasi, E; Ajinenko, I; Aleksan, Roy; Alekseev, G D; Allport, P P; Almehed, S; Alvsvaag, S J; Amaldi, Ugo; Amato, S; Andreazza, A; Andrieux, M L; Antilogus, P; Apel, W D; Arnoud, Y; Augustin, J E; Augustinus, A; Baillon, Paul; Bambade, P; Barate, R; Barbiellini, Guido; Bardin, Dimitri Yuri; Barker, G J; Baroncelli, A; Barrio, J A; Bartl, Walter; Barão, F; Bates, M J; Battaglia, Marco; Baubillier, M; Baudot, J; Becks, K H; Begalli, M; Beillière, P; Belokopytov, Yu A; Belous, K S; Benvenuti, Alberto C; Berggren, M; Bertrand, D; Bianchi, F; Bigi, M; Bilenky, S M; Billoir, P; Bloch, D; Blume, M; Blyth, S; Bocci, V; Bolognese, T; Bonesini, M; Bonivento, W; Booth, P S L; Borisov, G; Bosio, C; Bosworth, S; Botner, O; Bouquet, B; Bourdarios, C; Bowcock, T J V; Bozzo, M; Branchini, P; Brand, K D; Brenner, R A; Bricman, C; Brillault, L; Brown, R C A; Brunet, J M; Brückman, P; Bugge, L; Buran, T; Buys, A; Bärring, O; Caccia, M; Calvi, M; Camacho-Rozas, A J; Camporesi, T; Canale, V; Canepa, M; Cankocak, K; Cao, F; Carena, F; Carrilho, P; Carroll, L; Caso, Carlo; Castillo-Gimenez, M V; Cattai, A; Cavallo, F R; Cerrito, L; Chabaud, V; Charpentier, P; Chaussard, L; Chauveau, J; Checchia, P; Chelkov, G A; Chierici, R; Chochula, P; Chorowicz, V; Cindro, V; Collins, P; Contreras, J L; Contri, R; Cortina, E; Cosme, G; Cossutti, F; Crawley, H B; Crennell, D J; Crosetti, G; Cuevas-Maestro, J; Czellar, S; D'Almagne, B; Da Silva, W; Dahl-Jensen, Erik; Dahm, J; Dam, M; Damgaard, G; Daum, A; Dauncey, P D; Davenport, Martyn; De Angelis, A; De Boeck, H; De Brabandere, S; De Clercq, C; De Lotto, B; De Min, A; De Paula, L S; De Saint-Jean, C; Defoix, C; Della Ricca, G; Delpierre, P A; Demaria, N; Di Ciaccio, Lucia; Dijkstra, H; Djama, F; Dolbeau, J; Doroba, K; Dracos, M; Drees, J; Drees, K A; Dris, M; Dufour, Y; Dupont, F; Dönszelmann, M; Edsall, D M; Ehret, R; Eigen, G; Ekelöf, T J C; Ekspong, Gösta; Elsing, M; Engel, J P; Ershaidat, N; Erzen, B; Espirito-Santo, M C; Falk, E; Fassouliotis, D; Feindt, Michael; Fenyuk, A; Ferrer, A; Filippas-Tassos, A; Firestone, A; Fischer, P A; Fokitis, E; Fontanelli, F; Formenti, F; Franek, B J; Frenkiel, P; Fries, D E C; Frodesen, A G; Frühwirth, R; Fulda-Quenzer, F; Fuster, J A; Föth, H; Fürstenau, H; Galloni, A; Gamba, D; Gandelman, M; García, C; García, J; Gaspar, C; Gasparini, U; Gavillet, P; Gazis, E N; Gelé, D; Gerber, J P; Gibbs, M; Gillespie, D; Gokieli, R; Golob, B; Gopal, Gian P; Gorn, L; Gracco, Valerio; Graziani, E; Grosdidier, G; Gunnarsson, P; Guy, J; Guz, Yu; Górski, M; Günther, M; Haedinger, U; Hahn, F; Hahn, M; Hahn, S; Hajduk, Z; Hallgren, A; Hamacher, K; Hao, W; Harris, F J; Hedberg, V; Henriques, R P; Hernández, J J; Herquet, P; Herr, H; Hessing, T L; Higón, E; Hilke, Hans Jürgen; Hill, T S; Holmgren, S O; Holt, P J; Holthuizen, D J; Houlden, M A; Huet, K; Hultqvist, K; Ioannou, P; Jackson, J N; Jacobsson, R; Jalocha, P; Janik, R; Jarlskog, G; Jarry, P; Jean-Marie, B; Johansson, E K; Joram, Christian; Juillot, P; Jönsson, L B; Jönsson, P E; Kaiser, M; Kalmus, George Ernest; Kapusta, F; Karlsson, M; Karvelas, E; Katargin, A; Katsanevas, S; Katsoufis, E C; Keränen, R; Khomenko, B A; Khovanskii, N N; King, B J; Kjaer, N J; Klein, H; Klovning, A; Kluit, P M; Kokkinias, P; Koratzinos, M; Kostyukhin, V; Kourkoumelis, C; Kramer, P H; Krammer, Manfred; Kreuter, C; Kronkvist, I J; Krumshtein, Z; Krupinski, W; Królikowski, J; Kubinec, P; Kucewicz, W; Kurvinen, K L; Kuznetsov, O; Köhne, J H; Köne, B; La Vaissière, C de; Lacasta, C; Laktineh, I; Lamblot, S; Lamsa, J; Lanceri, L; Lane, D W; Langefeld, P; Lapin, V; Last, I; Laugier, J P; Lauhakangas, R; Leder, Gerhard; Ledroit, F; Lefébure, V; Legan, C K; Leitner, R; Lemoigne, Y; Lemonne, J; Lenzen, Georg; Lepeltier, V; Lesiak, T; Liko, D; Lindner, R; Lipniacka, A; Lippi, I; Lokajícek, M; Loken, J G; Loukas, D; Lutz, P; Lyons, L; López, J M; López-Aguera, M A; López-Fernandez, A; Lörstad, B; MacNaughton, J N; Maehlum, G; Maio, A; Malychev, V; Mandl, F; Marco, J; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Maron, T; Martí i García, S; Martínez-Rivero, C; Martínez-Vidal, F; Maréchal, B; Matorras, F; Matteuzzi, C; Matthiae, Giorgio; Mazzucato, M; McCubbin, M L; McKay, R; McNulty, R; Medbo, J; Meroni, C; Meyer, W T; Michelotto, M; Migliore, E; Mirabito, L; Mitaroff, Winfried A; Mjörnmark, U; Moa, T; Monge, M R; Morettini, P; Mundim, L M; Murray, W J; Muryn, B; Myagkov, A; Myatt, Gerald; Mönig, K; Møller, R; Müller, H; Naraghi, F; Navarria, Francesco Luigi; Navas, S; Negri, P; Neumann, W; Neumeister, N; Nicolaidou, R; Nielsen, B S; Nieuwenhuizen, M; Nikolaenko, V; Niss, P; Nomerotski, A; Normand, Ainsley; Némécek, S; Oberschulte-Beckmann, W; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, Risto; Ouraou, A; Paganini, P; Paganoni, M; Pagès, P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Passeri, A; Pegoraro, M; Peralta, L; Pernegger, H; Pernicka, Manfred; Perrotta, A; Petridou, C; Petrolini, A; Phillips, H T; Piana, G; Pierre, F; Pimenta, M; Plaszczynski, S; Podobrin, O; Pol, M E; Polok, G; Poropat, P; Pozdnyakov, V; Prest, M; Privitera, P; Pukhaeva, N; Pullia, Antonio; Radojicic, D; Ragazzi, S; Rahmani, H; Rames, J; Ratoff, P N; Read, A L; Reale, M; Rebecchi, P; Redaelli, N G; Regler, Meinhard; Reid, D; Renton, P B; Resvanis, L K; Richard, F; Richardson, J; Rinaudo, G; Ripp, I; Romero, A; Roncagliolo, I; Ronchese, P; Roos, L; Rosenberg, E I; Rosso, E; Roudeau, Patrick; Rovelli, T; Ruhlmann-Kleider, V; Ruiz, A; Rídky, J; Rückstuhl, W; Saarikko, H; Sacquin, Yu; Sadovskii, A; Sajot, G; Salt, J; Sannino, M; Schneider, H; Schyns, M A E; Sciolla, G; Scuri, F; Sedykh, Yu; Segar, A M; Seitz, A; Sekulin, R L; Shellard, R C; Siccama, I; Siegrist, P; Simonetti, S; Simonetto, F; Sissakian, A N; Sitár, B; Skaali, T B; Smadja, G; Smirnov, N; Smirnova, O G; Smith, G R; Sokolov, A; Sosnowski, R; Souza-Santos, D; Spassoff, Tz; Spiriti, E; Squarcia, S; Stanescu, C; Stapnes, Steinar; Stavitski, I; Stepaniak, K; Stichelbaut, F; Stocchi, A; Strauss, J; Strub, R; Stugu, B; Stäck, H; Szczekowski, M; Szeptycka, M; Sánchez, J; Tabarelli de Fatis, T; Tavernet, J P; Tilquin, A; Timmermans, J; Tkatchev, L G; Todorov, T; Toet, D Z; Tomaradze, A G; Tomé, B; Tortora, L; Tranströmer, G; Treille, D; Trischuk, W; Tristram, G; Trombini, A; Troncon, C; Tsirou, A L; Turluer, M L; Tyapkin, I A; Tyndel, M; Tzamarias, S; Ullaland, O; Valenti, G; Vallazza, E; Van Eldik, J; Van der Velde, C; Vassilopoulos, N; Vegni, G; Ventura, L; Venus, W A; Verbeure, F; Verlato, M; Vertogradov, L S; Vilanova, D; Vincent, P; Vitale, L; Vlasov, E; Vodopyanov, A S; Vrba, V; Wahlen, H; Walck, C; Wehr, A; Weierstall, M; Weilhammer, Peter; Wetherell, Alan M; Wicke, D; Wickens, J H; Wielers, M; Wilkinson, G R; Williams, W S C; Winter, M; Witek, M; Woschnagg, K; Yip, K; Yushchenko, O P; Zach, F; Zacharatou-Jarlskog, C; Zaitsev, A; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zevgolatakos, E; Zimin, N I; Zito, M; Zontar, D; Zuberi, R; Zucchelli, G C; Zumerle, G; de Boer, Wim; van Apeldoorn, G W; van Dam, P; Åsman, B; Österberg, K; Überschär, B; Überschär, S

    1995-01-01

    \\def\\tpc{three-particle correlation} \\def\\twopc{two-particle correlation} Measurements are presented of short range three-particle correlations in e^+ e^- annihilations at LEP using data collected by the DELPHI detector. %The jet structure is studied using three-particle correlation functions. At small values of the four-momentum difference, strong three-particle correlations are observed for like-sign (+++ and ---) and for unlike-sign (++- and +--) pion combinations which are not a consequence of two-particle correlations. A possible explanation of the observed effects in like-sign combinations is the existence of higher order Bose-Einstein interference, which significantly changes the particle distributions in jets.

  11. Pseudorotational dynamics of small molecular species

    International Nuclear Information System (INIS)

    Hagelberg, F.

    2002-01-01

    The electron nuclear dynamics (END) theory was designed to provide a full description of the dynamic development of the electronic system. It is independent of any potential energy surface constructions. The dynamic behavior of molecules close to the threshold of dissociation was the objective of this study. Thus, simulations based on END theory were performed with the aim to extend the current understanding of the dynamic features of pseudorotational into a non-adiabatic regime. Electron dynamics of triatomic species (H 3 + and Li 3 + ) in terms of electronic angular momentum expectation values were characterized. Finally, it is shown that the expansion coefficients which carry the information about the excitation content of the electronic system at any stage of the motional process can be calculated. (nevyjel)

  12. Searching for Short Range Correlations Using (e,e'NN) Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Bin [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2003-02-01

    Electron induced two nucleon knockout reactions (e,e'pp) and (e,e'np) were performed for 3He, 4He, and 12C nuclei with incident energies of 2.261 GeV and 4.461 GeV using the CLAS detector at Jefferson Lab. Events with missing momenta lower than the Fermi level and missing energies smaller than the pion threshold were studied. The residual system was assumed to be a spectator and the process was considered as a quasi-free knockout of an NN pair. The data showed that the initial momentum extends up to 800 MeV/c with considerable strength. The cross sections for 3He(e,e'pp)n were compared to the calculations of J.M. Laget. It was found that the final state interactions (FSI) and the meson exchange currents (MEC) dominate the cross sections and the short range properties of the NN pair were substantially undermined. However, the node of the S state wave function of the pp pair at around 400 MeV/c initial momentum starts to be recognizable in the 4.461 GeV data. The data and the theory suggest that with higher momentum transfers, especially in the region xBj > 1, the competing processes such as FSI and MEC will be less important and the detailed study of the short-range properties of nucleons inside nuclei will be more desirable.

  13. Air defense planning for an area with the use of very short range air defense sets

    Directory of Open Access Journals (Sweden)

    Tadeusz Pietkiewicz

    2017-12-01

    Full Text Available This paper presents a heuristic method of planning the deployment of very short-range anti-air missile and artillery sets (VSHORAD around an area (‘protected area’ in order to protect it. A function dependent on the distance between the earliest feasible points of destroying targets and the centre of the protected area was taken as an objective function. This is a different indicator from those commonly used in the literature, and based on the likelihood of a defense zone penetration by means of an air attack (MAA: the kill probability of the MAA and the probability of area losses. The model constraints resulted directly from the restrictions imposed by real air defense systems and the nature of the area being defended. This paper assumes that the VSHORAD system operates as a part of a general, superordinate air defense command and control system based on the idea of network-centric warfare, which provides the VSHORAD system with a recognized air picture, air defense plans, and combat mission specifications. The presented method has been implemented. The final part of the paper presents the computational results. Keywords: optimal planning, air defense system, area installation protection, deployment of very short range anti-air missile and artillery sets (VSHORAD

  14. Effects of short range ΔN interaction on observables of the πNN system

    International Nuclear Information System (INIS)

    Alexandrou, C.; Blankleider, B.

    1990-01-01

    The inadequacy of standard few-body approaches in describing the πNN system has motivated searches for the responsible missing mechanism. In the case of πd scattering, it has recently been asserted that an additional short range ΔN interaction can account for essentially all the discrepancies between a few-body calculation and experimental data. This conclusion, however, has been based on calculations where a phenomenological ΔN interaction is added only in Born term to background few-body amplitudes. In the present work we investigate the effect of including such a ΔN interaction to all orders within a unitary few-body calculation of the πNN system. Besides testing the validity of adding the ΔN interaction in Born term in πd scattering, our fully coupled approach also enables us to see the influence of the same ΔN interaction on the processes NN→πd and NN→NN. For πd elastic scattering, we find that the higher order ΔN interaction terms can have as much influence on πd observables as the lowest order contribution alone. Moreover, we find that the higher order contributions tend to cancel the effect obtained by adding the ΔN interaction in Born term only. The effect of the same ΔN interaction on NN→πd and NN→NN appears to be as significant as in πd→πd, suggesting that future investigations of the short range ΔN interaction should be done in the context of the fully coupled πNN system

  15. Very-short range forecasting system for 2018 Pyeonchang Winter Olympic and Paralympic games

    Science.gov (United States)

    Nam, Ji-Eun; Park, Kyungjeen; Kim, Minyou; Kim, Changhwan; Joo, Sangwon

    2016-04-01

    The 23rd Olympic Winter and the 13th Paralympic Winter Games will be held in Pyeongchang, Republic of Korea respectively from 9 to 25 February 2018 and from 9 to 18 February 2018. The Korea Meteorological Administration (KMA) and the National Institute for Meteorological Science (NIMS) have the responsibility to provide weather information for the management of the Games and the safety of the public. NIMS will carry out a Forecast Demonstration Project (FDP) and a Research and Development Project (RDP) which will be called ICE-POP 2018. These projects will focus on intensive observation campaigns to understand severe winter weathers over the Pyeongchang region, and the research results from the RDP will be used to improve the accuracy of nowcasting and very short-range forecast systems during the Games. To support these projects, NIMS developed Very-short range Data Assimilation and Prediction System (VDAPS), which is run in real time with 1 hour cycling interval and up to 12 hour forecasts. The domain is covering Korean Peninsular and surrounding seas with 1.5km horizontal resolution. AWS, windprofiler, buoy, sonde, aircraft, scatwinds, and radar radial winds are assimilated by 3DVAR on 3km resolution inner domain. The rain rate is converted into latent heat and initialized via nudging. The visibility data are also assimilated with the addition of aerosol control variable. The experiments results show the improvement in rainfall over south sea of Korean peninsula. In order to reduce excessive rainfalls during first 2 hours due to the reduced cycling interval, the data assimilation algorithm is optimized.

  16. Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

    NARCIS (Netherlands)

    Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

    2007-01-01

    This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

  17. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  18. Molecular dynamics simulations of quasi-brittle crack development in iron

    Energy Technology Data Exchange (ETDEWEB)

    Borodin, V.A., E-mail: borodin@dni.polin.kiae.su [Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe (Germany); NRC Kurchatov Institute, Kurchatov Sq. 1, 123182 Moscow (Russian Federation); Vladimirov, P.V., E-mail: Pavel.Vladimirov@kit.edu [Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe (Germany)

    2011-08-31

    The paper presents the results of molecular dynamics (MD) simulations of three-dimensional kinetics of micro-crack propagation in alpha-iron and the accompanying lattice transformations at the crack tips. We show that crack initiation on {l_brace}0 0 1{r_brace} planes in iron is preceded with the emission of compact slip bands from the pre-crack tips, in agreement with the predictions of the earlier quasi-two-dimensional simulations. The application of Voronoi decomposition technique for atomic short-range order processing has allowed us to clarify the kinetics of structural transformations at the tips of nucleating and propagating cracks for three most common systems of crack propagation in iron. It is demonstrated that the compact slip bands emanating from the crack tips not only accompany crack nucleation, but remain an essential feature of the crack propagation on {l_brace}0 0 1{r_brace} planes. Due to the strong coupling between the crack tip and slip band propagation, the crack propagation can be limited by slip band interaction with microstructural obstacles, abundantly created in ferritic-martensitic steels in radiation environment of nuclear facilities.

  19. 369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

    Energy Technology Data Exchange (ETDEWEB)

    Swaminarayan, Sriram [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Kadau, Kai [Los Alamos National Laboratory; Fossum, Gordon C [IBM CORPORATION

    2008-01-01

    The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.

  20. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  1. Ab initio molecular dynamics in a finite homogeneous electric field.

    Science.gov (United States)

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  2. How Confinement-Induced Structures Alter the Contribution of Hydrodynamic and Short-Ranged Repulsion Forces to the Viscosity of Colloidal Suspensions

    Directory of Open Access Journals (Sweden)

    Meera Ramaswamy

    2017-10-01

    Full Text Available Confined systems ranging from the atomic to the granular are ubiquitous in nature. Experiments and simulations of such atomic and granular systems have shown a complex relationship between the microstructural arrangements under confinement, the short-ranged particle stresses, and flow fields. Understanding the same correlation between structure and rheology in the colloidal regime is important due to the significance of such suspensions in industrial applications. Moreover, colloidal suspensions exhibit a wide range of structures under confinement that could considerably modify such force balances and the resulting viscosity. Here, we use a combination of experiments and simulations to elucidate how confinement-induced structures alter the relative contributions of hydrodynamic and short-range repulsive forces to produce up to a tenfold change in the viscosity. In the experiments we use a custom-built confocal rheoscope to image the particle configurations of a colloidal suspension while simultaneously measuring its stress response. We find that as the gap decreases below 15 particle diameters, the viscosity first decreases from its bulk value, shows fluctuations with the gap, and then sharply increases for gaps below 3 particle diameters. These trends in the viscosity are shown to strongly correlate with the suspension microstructure. Further, we compare our experimental results to those from two different simulations techniques, which enables us to determine the relative contributions of hydrodynamic and short-range repulsive stresses to the suspension rheology. The first method uses the lubrication approximation to find the hydrodynamic stress and includes a short-range repulsive force between the particles while the second is a Stokesian dynamics simulation that calculates the full hydrodynamic stress in the suspension. We find that the decrease in the viscosity at moderate confinements has a significant contribution from both the

  3. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  4. Dynamics of molecular superrotors in an external magnetic field

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Valery

    2015-08-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  5. Dynamics of molecular superrotors in an external magnetic field

    International Nuclear Information System (INIS)

    Korobenko, Aleksey; Milner, Valery

    2015-01-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

  6. Molecular dynamics with deterministic and stochastic numerical methods

    CERN Document Server

    Leimkuhler, Ben

    2015-01-01

    This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

  7. Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Chengzhen Sun; Bofeng Bai

    2017-01-01

    Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

  8. First principles molecular dynamics without self-consistent field optimization

    International Nuclear Information System (INIS)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-01

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

  9. Will high-resolution global ocean models benefit coupled predictions on short-range to climate timescales?

    Science.gov (United States)

    Hewitt, Helene T.; Bell, Michael J.; Chassignet, Eric P.; Czaja, Arnaud; Ferreira, David; Griffies, Stephen M.; Hyder, Pat; McClean, Julie L.; New, Adrian L.; Roberts, Malcolm J.

    2017-12-01

    As the importance of the ocean in the weather and climate system is increasingly recognised, operational systems are now moving towards coupled prediction not only for seasonal to climate timescales but also for short-range forecasts. A three-way tension exists between the allocation of computing resources to refine model resolution, the expansion of model complexity/capability, and the increase of ensemble size. Here we review evidence for the benefits of increased ocean resolution in global coupled models, where the ocean component explicitly represents transient mesoscale eddies and narrow boundary currents. We consider lessons learned from forced ocean/sea-ice simulations; from studies concerning the SST resolution required to impact atmospheric simulations; and from coupled predictions. Impacts of the mesoscale ocean in western boundary current regions on the large-scale atmospheric state have been identified. Understanding of air-sea feedback in western boundary currents is modifying our view of the dynamics in these key regions. It remains unclear whether variability associated with open ocean mesoscale eddies is equally important to the large-scale atmospheric state. We include a discussion of what processes can presently be parameterised in coupled models with coarse resolution non-eddying ocean models, and where parameterizations may fall short. We discuss the benefits of resolution and identify gaps in the current literature that leave important questions unanswered.

  10. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  11. Study of short range order in alloy of glassy metals and effect of neutron irradiation on them

    International Nuclear Information System (INIS)

    Habibi, S.; Banaee, N.; Salman, M.; Gupta, A.; Principi, G.

    2000-04-01

    In this paper, we have studied a series of glassy metals with composition Fe 78-x Ni x Si 8 B 14 with x=0, 15, 25,38,53, 58. We have used Moessbauer spectroscopy to get information about short range order and local structure in these alloys. The specimens are exposed to neutron irradiation to perturb local structure and their short range order. The hyperfine parameters obtained from spectra before and after n-irradiation and are compared

  12. Short range order of Mg-Cd-alloys during the transition from the solid to the molten state

    International Nuclear Information System (INIS)

    Boos, A.; Steeb, S.

    1977-01-01

    Recently a method was published for the determination of short range order parameters in binary melts and also a method for the determination of the concentration of different structures which form such a melt. These methods are used in the present work to evaluate the atomic structure of Mg-Cd-melts and to reval the changes in short range order during the melting process. (orig.) [de

  13. The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps

    Directory of Open Access Journals (Sweden)

    Leanda D. Mason

    2018-05-01

    Full Text Available Ecological traps attract biota to low-quality habitats. Landscape traps are zones caught in a vortex of spiralling degradation. Here, we demonstrate how short-range endemic (SRE traits may make such taxa vulnerable to ecological and landscape traps. Three SRE species of mygalomorph spider were used in this study: Idiommata blackwalli, Idiosoma sigillatum and an undescribed Aganippe sp. Mygalomorphs can be long-lived (>43 years and select sites for permanent burrows in their early dispersal phase. Spiderlings from two species, I. blackwalli (n = 20 and Aganippe sp. (n = 50, demonstrated choice for microhabitats under experimental conditions, that correspond to where adults typically occur in situ. An invasive veldt grass microhabitat was selected almost exclusively by spiderlings of I. sigillatum. At present, habitat dominated by veldt grass in Perth, Western Australia, has lower prey diversity and abundance than undisturbed habitats and therefore may act as an ecological trap for this species. Furthermore, as a homogenising force, veldt grass can spread to form a landscape trap in naturally heterogeneous ecosystems. Selection of specialised microhabitats of SREs may explain high extinction rates in old, stable landscapes undergoing (human-induced rapid change.

  14. Objectives for next generation of practical short-range atmospheric dispersion models

    International Nuclear Information System (INIS)

    Olesen, H.R.; Mikkelsen, T.

    1992-01-01

    The proceedings contains papers from the workshop ''Objectives for Next Generation of Practical Short-Range Atmospheric Dispersion Models''. They deal with two types of models, namely models for regulatory purposes and models for real-time applications. The workshop was the result of an action started in 1991 for increased cooperation and harmonization within atmospheric dispersion modelling. The focus of the workshop was on the management of model development and the definition of model objectives, rather than on detailed model contents. It was the intention to identify actions that can be taken in order to improve the development and use of atmospheric dispersion models. The papers in the proceedings deal with various topics within the broad spectrum of matters related to up-to-date practical models, such as their scientific basis, requirements for model input and output, meteorological preprocessing, standardisation within modelling, electronic information exchange as a potentially useful tool, model evaluation and data bases for model evaluation. In addition to the papers, the proceedings contain summaries of the discussions at the workshop. These summaries point to a number of recommended actions which can be taken in order to improve ''modelling culture''. (AB)

  15. Evidence for short range corelations from high Q{sup 2} (e,e{prime}) reactions

    Energy Technology Data Exchange (ETDEWEB)

    Strikman, M.I. [Pennsylvania State Univ., University Park, PA (United States); Frankfurt, L.L.; Sargayan, M.M. [Tel Aviv Univ. (Iceland)] [and others

    1994-04-01

    For many years now short-range correlations (SRC) in nuclei have been considered as an essential feature of the nuclear wave function. At high energy (e,e{prime}) reactions, where Q{sup 2} > 1 (GeV/c){sup 2}, x = Q{sup 2}/2mq{sub o} > 1 and 1 GeV > q{sub o}> 300 {approximately} 400 MeV the scattering from low momentum nucleons is kinematically suppressed and there the evidence of SRC expected to be more prominent. These reactions have been intensively investigated during the last decade or so at SLAC on both light and heavy nuclei. The above kinematics allows one to compute the cross section through the processes local in space. To explain this the authors analyse the representation of the cross section as a Fourier transform of the commutator of electromagnetic currents and see that the major contribution in the cross section is given by the region of integration.

  16. On the skill of various ensemble spread estimators for probabilistic short range wind forecasting

    Science.gov (United States)

    Kann, A.

    2012-05-01

    A variety of applications ranging from civil protection associated with severe weather to economical interests are heavily dependent on meteorological information. For example, a precise planning of the energy supply with a high share of renewables requires detailed meteorological information on high temporal and spatial resolution. With respect to wind power, detailed analyses and forecasts of wind speed are of crucial interest for the energy management. Although the applicability and the current skill of state-of-the-art probabilistic short range forecasts has increased during the last years, ensemble systems still show systematic deficiencies which limit its practical use. This paper presents methods to improve the ensemble skill of 10-m wind speed forecasts by combining deterministic information from a nowcasting system on very high horizontal resolution with uncertainty estimates from a limited area ensemble system. It is shown for a one month validation period that a statistical post-processing procedure (a modified non-homogeneous Gaussian regression) adds further skill to the probabilistic forecasts, especially beyond the nowcasting range after +6 h.

  17. Dissipative NEGF methodology to treat short range Coulomb interaction: Current through a 1D nanostructure.

    Science.gov (United States)

    Martinez, Antonio; Barker, John R; Di Prieto, Riccardo

    2018-06-13

    A methodology describing Coulomb blockade in the Non-equilibrium Green Function formalism is presented. We carried out ballistic and dissipative simulations through a 1D quantum dot using an Einstein phonon model. Inelastic phonons with different energies have been considered. The methodology incorporates the short-range Coulomb interaction between two electrons through the use of a two-particle Green's function. Unlike previous work, the quantum dot has spatial resolution i.e. it is not just parameterized by the energy level and coupling constants of the dot. Our method intends to describe the effect of electron localization while maintaining an open boundary or extended wave function. The formalism conserves the current through the nanostructure. A simple 1D model is used to explain the increase of mobility in semi-crystalline polymers as a function of the electron concentration. The mechanism suggested is based on the lifting of energy levels into the transmission window as a result of the local electron-electron repulsion inside a crystalline domain. The results are aligned with recent experimental findings. Finally, as a proof of concept, we present a simulation of a low temperature resonant structure showing the stability diagram in the Coulomb blockade regime. . © 2018 IOP Publishing Ltd.

  18. Short-range order clustering in BCC Fe-Mn alloys induced by severe plastic deformation

    Science.gov (United States)

    Shabashov, V. A.; Kozlov, K. A.; Sagaradze, V. V.; Nikolaev, A. L.; Lyashkov, K. A.; Semyonkin, V. A.; Voronin, V. I.

    2018-03-01

    The effect of severe plastic deformation, namely, high-pressure torsion (HPT) at different temperatures and ball milling (BM) at different time intervals, has been investigated by means of Mössbauer spectroscopy in Fe100-xMnx (x = 4.1, 6.8, 9) alloys. Deformation affects the short-range clustering (SRC) in BCC lattice. Two processes occur: destruction of SRC by moving dislocations and enhancement of the SRC by migration of non-equilibrium defects. Destruction of SRC prevails during HPT at 80-293 K; whereas enhancement of SRC dominates at 473-573 K. BM starts enhancing the SRC formation at as low as 293 K due to local heating at impacts. The efficiency of HPT in terms of enhancing SRC increases with increasing temperature. The authors suppose that at low temperatures, a significant fraction of vacancies are excluded from enhancing SRC because of formation of mobile bi- and tri-vacancies having low efficiency of enhancing SRC as compared to that of mono vacancies. Milling of BCC Fe100-xMnx alloys stabilises the BCC phase with respect to α → γ transition at subsequent isothermal annealing because of a high degree of work hardening and formation of composition inhomogeneity.

  19. Probing short-range correlations in asymmetric nuclei with quasi-free pair knockout reactions

    Science.gov (United States)

    Stevens, Sam; Ryckebusch, Jan; Cosyn, Wim; Waets, Andreas

    2018-02-01

    Short-range correlations (SRC) in asymmetric nuclei with an unusual neutron-to-proton ratio can be studied with quasi-free two-nucleon knockout processes following the collision between accelerated ions and a proton target. We derive an approximate factorized cross section for those SRC-driven p (A ,p‧N1N2) reactions. Our reaction model hinges on the factorization properties of SRC-driven A (e ,e‧N1N2) reactions for which strong indications are found in theory-experiment comparisons. In order to put our model to the test we compare its predictions with results of 12C (p ,p‧ pn) measurements conducted at Brookhaven National Laboratory (BNL) and find a fair agreement. The model can also reproduce characteristic features of SRC-driven two-nucleon knockout reactions, like back-to-back emission of the correlated nucleons. We study the asymmetry dependence of nuclear SRC by providing predictions for the ratio of proton-proton to proton-neutron knockout cross sections for the carbon isotopes 9-15C thereby covering neutron excess values (N - Z) / Z between -0.5 and +0.5.

  20. Current research efforts at JILA to test the equivalence principle at short ranges

    International Nuclear Information System (INIS)

    Faller, J.E.; Niebauer, T.M.; McHugh, M.P.; Van Baak, D.A.

    1988-01-01

    We are presently engaged in three different experiments to search for a possible breakdown of the equivalence principle at short ranges. The first of these experiments, which has been completed, is our so-called Galilean test in which the differential free-fall of two objects of differing composition was measured using laser interferometry. We observed that the differential acceleration of two test bodies was less than 5 parts in 10 billion. This experiment set new limits on a suggested baryon dependent ''Fifth Force'' at ranges longer than 1 km. With a second experiment, we are investigating substance dependent interactions primarily for ranges up to 10 meters using a fluid supported torsion balance; this apparatus has been built and is now undergoing laboratory tests. Finally, a proposal has been made to measure the gravitational signal associated with the changing water level at a large pumped storage facility in Ludington, Michigan. Measuring the gravitational signal above and below the pond will yield the value of the gravitational constant, G, at ranges from 10-100 m. These measurements will serve as an independent check on other geophysical measurements of G

  1. Performance analysis of dedicated short range communications technology and overview of the practicability for developing countries

    Directory of Open Access Journals (Sweden)

    Vandana Bassoo

    2015-12-01

    Full Text Available Vehicular communication is a widely researched field and aims at developing technologies that may complement systems such as the advanced driver assistance systems. It is therefore important to analyse and infer on the performance of vehicular technologies for different driving and on-road criteria. This study considers the dedicated short range communications technology and more precisely the IEEE 802.11p standard for a performance and practicability analysis. There is also the proposal of a new classification scheme for typical driving conditions, which includes the main categories of Emergency and Safety scenarios while sub-classifications of Critical and Preventive Safety also exist. The scheme is used to build up scenarios as well as related equations relevant to developing countries for practical network simulation. The results obtained indicate that the relative speed of nodes is a determining factor in the overall performance and effectiveness of wireless vehicular communication systems. Moreover, delay values of low order were observed while an effective communication range of about 800 m was calculated for highway scenarios. The research thus indicates suitability of the system for an active use in collision avoidance even though independent factors such as climatic conditions and driver behaviour may affect its effectiveness in critical situations.

  2. Short-range ferromagnetism in alloy ribbons of Fe-Cr-Si-Nb-(Ag, Cu)

    Energy Technology Data Exchange (ETDEWEB)

    THANH, P. Q.; HOA, N. Q.; CHAU, N. [Vietnam National University, Hanoi (Viet Nam); HUU, C. X. [Danang University of Technology, Danang (Viet Nam); NGO, D. T. [Technical University of Denmark, Kgs. Lyngby (Denmark); PHAN, T. L. [Chungbuk National University, Cheongju (Korea, Republic of)

    2014-04-15

    We have studied the magnetic properties of two amorphous alloy ribbons Fe{sub 72}Cr{sub 6}Si{sub 4}Nb{sub 5}B{sub 12}Ag{sub 1} (FCSNB-Ag) and Fe{sub 72}Cr{sub 6}Si{sub 4}Nb{sub 5}B{sub 12}Cu{sub 1} (FCSNB-Cu), prepared by using a melt-spinning technique. Magnetization (M) measurements for various temperatures (T) and magnetic fields (H) indicate that ferromagnetic-paramagnetic (FM-PM) phase transitions take place in FCSNB-Ag and FCSNB-Cu at Curie temperatures (T{sub C} ) of about 308.3 K and 322.5 K, respectively. Analyses of M - H data at different temperatures in the vicinity of the FM-PM phase transition based on the modified Arrott plot method and scaling hypothesis yielded the exponent values of β = 0.369 ± 0.005, γ = 1.359 ± 0.005 and δ = 4.7 ± 0.1 for FCSNB-Ag, and β = 0.376 ± 0.002, γ = 1.315 ± 0.006 and δ = 4.5 ± 0.1 for FCSNB-Cu. Compared with the values from theoretical models, these values are close to those expected for the 3D Heisenberg model, demonstrating the existence of short-range FM order in the amorphous alloy ribbons.

  3. Experimental Searches for Exotic Short-Range Forces Using Mechanical Oscillators

    Science.gov (United States)

    Weisman, Evan

    Experimental searches for forces beyond gravity and electromagnetism at short range have attracted a great deal of attention over the last decade. In this thesis I describe the test mass development for two new experiments searching for forces below 1 mm. Both modify a previous experiment that used 1 kHz mechanical oscillators as test masses with a stiff conducting shield between them to suppress backgrounds, a promising technique for probing exceptionally small distances at the limit of instrumental thermal noise. To further reduce thermal noise, one experiment will use plated silicon test masses at cryogenic temperatures. The other experiment, which searches for spin-dependent interactions, will apply the spin-polarizable material Dy3Fe5O 12 to the test mass surfaces. This material exhibits orbital compensation of the magnetism associated with its intrinsic electron spin, minimizing magnetic backgrounds. Several plated silicon test mass prototypes were fabricated using photolithography (useful in both experiments), and spin-dependent materials were synthesized with a simple chemical recipe. Both silicon and spin-dependent test masses demonstrate the mechanical and magnetic properties necessary for sensitive experiments. I also describe sensitivity calculations of another proposed spin-dependent experiment, based on a modified search for the electron electric dipole moment, which show unprecedented sensitivity to exotic monopole-dipole forces. Inspired by a finite element model, a study attempting to maximize detector quality factor versus geometry is also presented, with experimental results so far not explained by the model.

  4. Meta-heuristic CRPS minimization for the calibration of short-range probabilistic forecasts

    Science.gov (United States)

    Mohammadi, Seyedeh Atefeh; Rahmani, Morteza; Azadi, Majid

    2016-08-01

    This paper deals with the probabilistic short-range temperature forecasts over synoptic meteorological stations across Iran using non-homogeneous Gaussian regression (NGR). NGR creates a Gaussian forecast probability density function (PDF) from the ensemble output. The mean of the normal predictive PDF is a bias-corrected weighted average of the ensemble members and its variance is a linear function of the raw ensemble variance. The coefficients for the mean and variance are estimated by minimizing the continuous ranked probability score (CRPS) during a training period. CRPS is a scoring rule for distributional forecasts. In the paper of Gneiting et al. (Mon Weather Rev 133:1098-1118, 2005), Broyden-Fletcher-Goldfarb-Shanno (BFGS) method is used to minimize the CRPS. Since BFGS is a conventional optimization method with its own limitations, we suggest using the particle swarm optimization (PSO), a robust meta-heuristic method, to minimize the CRPS. The ensemble prediction system used in this study consists of nine different configurations of the weather research and forecasting model for 48-h forecasts of temperature during autumn and winter 2011 and 2012. The probabilistic forecasts were evaluated using several common verification scores including Brier score, attribute diagram and rank histogram. Results show that both BFGS and PSO find the optimal solution and show the same evaluation scores, but PSO can do this with a feasible random first guess and much less computational complexity.

  5. Two-dimensional quasistatic stationary short range surface plasmons in flat nanoprisms.

    Science.gov (United States)

    Nelayah, J; Kociak, M; Stéphan, O; Geuquet, N; Henrard, L; García de Abajo, F J; Pastoriza-Santos, I; Liz-Marzán, L M; Colliex, C

    2010-03-10

    We report on the nanometer scale spectral imaging of surface plasmons within individual silver triangular nanoprisms by electron energy loss spectroscopy and on related discrete dipole approximation simulations. A dependence of the energy and intensity of the three detected modes as function of the edge length is clearly identified both experimentally and with simulations. We show that for experimentally available prisms (edge lengths ca. 70 to 300 nm) the energies and intensities of the different modes show a monotonic dependence as function of the aspect ratio of the prisms. For shorter or longer prisms, deviations to this behavior are identified thanks to simulations. These modes have symmetric charge distribution and result from the strong coupling of the upper and lower triangular surfaces. They also form a standing wave in the in-plane direction and are identified as quasistatic short range surface plasmons of different orders as emphasized within a continuum dielectric model. This model explains in simple terms the measured and simulated energy and intensity changes as function of geometric parameters. By providing a unified vision of surface plasmons in platelets, such a model should be useful for engineering of the optical properties of metallic nanoplatelets.

  6. Interplay between short-range correlated disorder and Coulomb interaction in nodal-line semimetals

    Science.gov (United States)

    Wang, Yuxuan; Nandkishore, Rahul M.

    2017-09-01

    In nodal-line semimetals, Coulomb interactions and short-range correlated disorder are both marginal perturbations to the clean noninteracting Hamiltonian. We analyze their interplay using a weak-coupling renormalization group approach. In the clean case, the Coulomb interaction has been found to be marginally irrelevant, leading to Fermi liquid behavior. We extend the analysis to incorporate the effects of disorder. The nodal line structure gives rise to kinematical constraints similar to that for a two-dimensional Fermi surface, which plays a crucial role in the one-loop renormalization of the disorder couplings. For a twofold degenerate nodal loop (Weyl loop), we show that disorder flows to strong coupling along a unique fixed trajectory in the space of symmetry inequivalent disorder couplings. Along this fixed trajectory, all symmetry inequivalent disorder strengths become equal. For a fourfold degenerate nodal loop (Dirac loop), disorder also flows to strong coupling, however, the strengths of symmetry inequivalent disorder couplings remain different. We show that feedback from disorder reverses the sign of the beta function for the Coulomb interaction, causing the Coulomb interaction to flow to strong coupling as well. However, the Coulomb interaction flows to strong coupling asymptotically more slowly than disorder. Extrapolating our results to strong coupling, we conjecture that at low energies nodal line semimetals should be described by a noninteracting nonlinear sigma model. We discuss the relation of our results with possible many-body localization at zero temperatures in such materials.

  7. Short-range order studies in nonstoichiometric transition metal carbides and nitrides by neutron diffuse scattering

    International Nuclear Information System (INIS)

    Priem, Thierry

    1988-01-01

    Short-range order in non-stoichiometric transition metal carbides and nitrides (TiN 0.82 , TiC 0.64 , TiC 0.76 , NbC 0.73 and NbC 0.83 ) was investigated by thermal neutron diffuse scattering on G4-4 (L.L.B - Saclay) and D10 (I.L.L. Grenoble) spectrometers. From experimental measurements, we have found that metalloid vacancies (carbon or nitrogen) prefer the f.c.c. third neighbour positions. Ordering interaction energies were calculated within the Ising model framework by three approximations: mean field (Clapp and Moss formula), Monte-Carlo simulation, Cluster variation Method. The energies obtained by the two latter methods are very close, and in qualitative agreement with theoretical values calculated from the band structure. Theoretical phase diagrams were calculated from these ordering energies for TiN x and TiC x ; three ordered structures were predicted, corresponding to compositions Ti 6 N 5 Ti 2 C and Ti 3 C 2 . On the other hand, atomic displacements are induced by vacancies. The metal first neighbours were found to move away from a vacancy, whereas the second neighbours move close to it. Near neighbour atomic displacements were theoretically determined by the lattice statics formalism with results in good agreement with experiment. (author) [fr

  8. A UHF RFID system with on-chip-antenna tag for short range communication

    International Nuclear Information System (INIS)

    Peng Qi; Zhang Chun; Zhao Xijin; Wang Zhihua

    2015-01-01

    A UHF RF identification system based on the 0.18 μm CMOS process has been developed for short range and harsh size requirement applications, which is composed of a fully integrated tag and a special reader. The whole tag chip with the antenna takes up an area of 0.36 mm 2 , which is smaller than other reported tags with an on-chip antenna (OCA) using the standard CMOS process. A self-defined protocol is proposed to reduce the power consumption, and minimize the size of the tag. The specialized SOC reader system consists of the RF transceiver, digital baseband, MCU and host interface. Its power consumption is about 500 mW. Measurement results show that the system's reading range is 2 mm with 20 dBm reader output power. With an inductive antenna printed on a paper substrate around the OCA tag, the reading range can be extended from several centimeters to meters, depending on the shape and size of the inductive antenna. (paper)

  9. Influence of retardation effects on photodisintegration of a quantum system bound by short-range forces

    International Nuclear Information System (INIS)

    Preobrazhenskii, M.A.; Golovinskii, P.A.

    1996-01-01

    Expressions for cross sections for multiphonon disintegration of quantum systems bound by short-range forces are obtained in the plane-wave approximation taking into account retardation effects. It is shown that, in the region of nonrelativistic energies, their contribution is factored, and the resulting universal factor is expressed for an arbitrary degree of process nonlinearity n in terms of elementary functions. Arguments of functions are determined only by the mode ω, the radiation spectrum width β, and the bound-state energy of a system. The dependence of the contribution of retardation effects on ω, β, and n is studied in detail. Analytical expressions for cross sections for multiquantum disintegration in the first nonvanishing order with respect to correlation interaction, which exactly take into account retardation effects, are obtained. It is shown that for two-quantum processes, the contribution of correlation effects is expressed in terms of a function representing an extension of dipole polarizability, whereas for n>2, it can be described in the dipole approximation

  10. Demonstration of micro-projection enabled short-range communication system for 5G.

    Science.gov (United States)

    Chou, Hsi-Hsir; Tsai, Cheng-Yu

    2016-06-13

    A liquid crystal on silicon (LCoS) based polarization modulated image (PMI) system architecture using red-, green- and blue-based light-emitting diodes (LEDs), which offers simultaneous micro-projection and high-speed data transmission at nearly a gigabit, serving as an alternative short-range communication (SRC) approach for personal communication device (PCD) application in 5G, is proposed and experimentally demonstrated. In order to make the proposed system architecture transparent to the future possible wireless data modulation format, baseband modulation schemes such as multilevel pulse amplitude modulation (M-PAM), M-ary phase shift keying modulation (M-PSK) and M-ary quadrature amplitude modulation (M-QAM) which can be further employed by more advanced multicarrier modulation schemes (such as DMT, OFDM and CAP) were used to investigate the highest possible data transmission rate of the proposed system architecture. The results demonstrated that an aggregative data transmission rate of 892 Mb/s and 900 Mb/s at a BER of 10^(-3) can be achieved by using 16-QAM baseband modulation scheme when data transmission were performed with and without micro-projection simultaneously.

  11. Large magnetoelectric coupling in magnetically short-range ordered Bi₅Ti₃FeO₁₅ film.

    Science.gov (United States)

    Zhao, Hongyang; Kimura, Hideo; Cheng, Zhenxiang; Osada, Minoru; Wang, Jianli; Wang, Xiaolin; Dou, Shixue; Liu, Yan; Yu, Jianding; Matsumoto, Takao; Tohei, Tetsuya; Shibata, Naoya; Ikuhara, Yuichi

    2014-06-11

    Multiferroic materials, which offer the possibility of manipulating the magnetic state by an electric field or vice versa, are of great current interest. However, single-phase materials with such cross-coupling properties at room temperature exist rarely in nature; new design of nano-engineered thin films with a strong magneto-electric coupling is a fundamental challenge. Here we demonstrate a robust room-temperature magneto-electric coupling in a bismuth-layer-structured ferroelectric Bi₅Ti₃FeO₁₅ with high ferroelectric Curie temperature of ~1000 K. Bi₅Ti₃FeO₁₅ thin films grown by pulsed laser deposition are single-phase layered perovskit with nearly (00l)-orientation. Room-temperature multiferroic behavior is demonstrated by a large modulation in magneto-polarization and magneto-dielectric responses. Local structural characterizations by transmission electron microscopy and Mössbauer spectroscopy reveal the existence of Fe-rich nanodomains, which cause a short-range magnetic ordering at ~620 K. In Bi₅Ti₃FeO₁₅ with a stable ferroelectric order, the spin canting of magnetic-ion-based nanodomains via the Dzyaloshinskii-Moriya interaction might yield a robust magneto-electric coupling of ~400 mV/Oe·cm even at room temperature.

  12. Short-Range-Order for fcc-based Binary Alloys Revisited from Microscopic Geometry

    Science.gov (United States)

    Yuge, Koretaka

    2018-04-01

    Short-range order (SRO) in disordered alloys is typically interpreted as competition between chemical effect of negative (or positive) energy gain by mixing constituent elements and geometric effects comes from difference in effective atomic radius. Although we have a number of theoretical approaches to quantitatively estimate SRO at given temperatures, it is still unclear to systematically understand trends in SRO for binary alloys in terms of geometric character, e.g., effective atomic radius for constituents. Since chemical effect plays significant role on SRO, it has been believed that purely geometric character cannot capture the SRO trends. Despite these considerations, based on the density functional theory (DFT) calculations on fcc-based 28 equiatomic binary alloys, we find that while conventional Goldschmidt or DFT-based atomic radius for constituents have no significant correlation with SRO, atomic radius for specially selected structure, constructed purely from information about underlying lattice, can successfully capture the magnitude of SRO. These facts strongly indicate that purely geometric information of the system plays central role to determine characteristic disordered structure.

  13. Electronic structure of disordered binary alloys with short range correlation in Bethe lattice

    International Nuclear Information System (INIS)

    Moreno, I.F.

    1987-01-01

    The determination of the electronic structure of a disordered material along the tight-binding model when applied to a Bethe lattice. The diagonal as well as off-diagonal disorder, are considered. The coordination number on the Bethe is fixed lattice to four (Z=4) that occurs in most compound semiconductors. The main proposal was to study the conditions under which a relatively simple model of a disordered material, i.e, a binary alloy, could account for the basic properties of transport or more specifically for the electronic states in such systems. By using a parametrization of the pair probability the behaviour of the electronic density of states (DOS) for different values of the short range order parameter, σ, which makes possible to treat the segregated, random and alternating cases, was analysed. In solving the problem via the Green function technique in the Wannier representation a linear chain of atoms was considered and using the solution of such a 1-D system the problem of the Bethe lattice which is constructed using such renormalized chains as elements, was solved. The results indicate that the obtained DOS are strongly dependent on the correlation assumed for the occupancy in the lattice. (author) [pt

  14. Short-range second order screened exchange correction to RPA correlation energies

    Science.gov (United States)

    Beuerle, Matthias; Ochsenfeld, Christian

    2017-11-01

    Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors. Therefore a variety of schemes have been devised to include exchange in the calculation of RPA correlation energies in order to correct this shortcoming. One of the most popular RPA plus exchange schemes is the second order screened exchange (SOSEX) correction. RPA + SOSEX delivers more accurate absolute correlation energies and also improves upon RPA for non-isogyric processes. On the other hand, RPA + SOSEX barrier heights are worse than those obtained from plain RPA calculations. To combine the benefits of RPA correlation energies and the SOSEX correction, we introduce a short-range RPA + SOSEX correction. Proof of concept calculations and benchmarks showing the advantages of our method are presented.

  15. Short-range order analysis and some physical properties of InxSe1-x glasses

    International Nuclear Information System (INIS)

    El-Kabany, N.

    2012-01-01

    Bulk In x Se 1-x (with x=5-25 at%) glasses were prepared using the melt-quench technique. Short range order(SRO) was examined by the X-ray diffraction using Cu(k α ) radiation in the wave vector interval 0.28≤k≤6.5 A 0-1 .The SRO parameters have been obtained from the radial distribution function. The inter-atomic distance obtained from the first and second peak are r 1 =0.263 and r 2 =0.460 nm, which is equivalent In-Se and Se-Se bond length. The fundamental structural unit for the studied glasses is In 2 Se 3 pyramid. Using the differential scanning calorimetry (DSC), the crystallization mechanism of In x Se 1-x chalcogenide glass has been studied. The glass transition activation energy (E g ) is 289±0.3 kj/mol.There is a correlation amongst the glass forming ability, bond strength and the number of lone pair electrons. The utility of the Gibbs-Di Marzio relation was achieved by estimating T g theoretically.

  16. Measurement of transparency ratios for protons from short-range correlated pairs

    Science.gov (United States)

    Hen, O.; Hakobyan, H.; Shneor, R.; Piasetzky, E.; Weinstein, L. B.; Brooks, W. K.; May-Tal Beck, S.; Gilad, S.; Korover, I.; Beck, A.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anefalos Pereira, S.; Arrington, J. R.; Baghdasaryan, H.; Ball, J.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Bono, J.; Boiarinov, S.; Briscoe, W. J.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fleming, J. A.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Griffioen, K. A.; Guo, L.; Hafidi, K.; Harrison, N.; Heddle, D.; Hicks, K.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jo, H. S.; Joo, K.; Keller, D.; Khandaker, M.; Khetarpal, P.; Kim, A.; Klein, F. J.; Koirala, S.; Kubarovsky, A.; Kubarovsky, V.; Kuhn, S. E.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Martinez, D.; Mayer, M.; McKinnon, B.; Mineeva, T.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munevar, E.; Munoz Camacho, C.; Mustapha, B.; Nadel-Turonski, P.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Park, S.; Pasyuk, E.; Phelps, E.; Phillips, J. J.; Pisano, S.; Pivnyuk, N.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Raue, B. A.; Rimal, D.; Ripani, M.; Ritchie, B. G.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Schott, D.; Schumacher, R. A.; Seraydaryan, H.; Sharabian, Y. G.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S. S.; Stepanyan, S.; Strauch, S.; Taiuti, M.; Tang, W.; Taylor, C. E.; Tian, Ye; Tkachenko, S.; Ungaro, M.; Vernarsky, B.; Vlassov, A.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Wood, M. H.; Zachariou, N.; Zana, L.; Zhang, J.; Zheng, X.; Zonta, I.

    2013-05-01

    Nuclear transparency, Tp (A), is a measure of the average probability for a struck proton to escape the nucleus without significant re-interaction. Previously, nuclear transparencies were extracted for quasi-elastic A (e ,e‧ p) knockout of protons with momentum below the Fermi momentum, where the spectral functions are well known. In this Letter we extract a novel observable, the transparency ratio, Tp (A) /Tp(12 C), for knockout of high-missing-momentum protons from the breakup of short-range correlated pairs (2N-SRC) in Al, Fe and Pb nuclei relative to C. The ratios were measured at momentum transfer Q2 ⩾ 1.5(GeV /c) 2 and xB ⩾ 1.2 where the reaction is expected to be dominated by electron scattering from 2N-SRC. The transparency ratios of the knocked-out protons coming from 2N-SRC breakup are 20-30% lower than those of previous results for low missing momentum. They agree with Glauber calculations and agree with renormalization of the previously published transparencies as proposed by recent theoretical investigations. The new transparencies scale as A - 1 / 3, which is consistent with dominance of scattering from nucleons at the nuclear surface.

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

    Science.gov (United States)

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

    2013-11-07

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

  18. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  19. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  20. Dynamic molecular oxygen production in cometary comae

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P.

    2017-05-01

    Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

  1. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  2. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  3. AceCloud: Molecular Dynamics Simulations in the Cloud.

    Science.gov (United States)

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  4. State-to-state dynamics of molecular energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  5. Chain networking revealed by molecular dynamics simulation

    Science.gov (United States)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  6. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  7. Short-Range-Order Mineral Physical Protection On Black Carbon Stabilization

    Science.gov (United States)

    Liang, B.; Weng, Y. T.; Wang, C. C.; Song, Y. F.; Lehmann, J.; Wang, C. H.

    2015-12-01

    Soil organic matter is one of the largest reservoirs in global carbon cycle, and black carbon (BC) represents a chemical resistant component. Black C plays an important role in global climate change. Generally considered recalcitrant due to high aromaticity, the reactive surface and functional groups of BC are crucial for carbon sequestration in soils. Mineral sorption and physical protection is an important mechanism for BC long term stabilization and sequestration in environments. Previous studies on mineral protection of BC were limited to analysis techniques in two-dimensions, for example, by SEM, TEM, and NanoSIMS. Little is known about the scope of organo-mineral association, the in-situ distribution and forms of minerals, and the ultimate interplay of BC and minerals. The aim of this study is to investigate the three-dimensional interaction of organic C and minerals in submicron scale using synchrotron-based Transmission X-ray Microcopy (TXM) and Fourier-Transform Infrared Spectroscopy (FTIR). Abundant poorly-crystallined nano-minerals particles were observed. These short-range-order (SRO) minerals also aggregate into clusters and sheets, and form envelops-like structures on the surface of BC. On top of large surface contact area, the intimate interplay between BC and minerals reinforces the stability of both organic C and minerals, resulting from chemical bonding through cation bridging and ligand exchange. The mineral protection enhances BC stabilization and sequestration and lowers its bioavailability in environment. The results suggest that mineral physical protection for BC sequestration may be more important than previous understanding.

  8. 2D fluorescence spectra measurement of six kinds of bioagents simulants by short range Lidar

    Science.gov (United States)

    Sanpedro, Man

    2018-02-01

    Pantoea agglomerans (Pan), Staphylococcus aureus (Sta), Bacillus globigii (BG) and Escherichia coli (EH), these four kinds of bioagents simulants of were cultured and then their growth curves were measured, the generation time was 0.99h, 0.835h, 1.07h and 1.909h, respectively. A small short range fluorescence lidar working at wavelengths of 266nm and 355nm was designed and used to measure the two-dimensional fluorescence spectra of bioagents simulants in the amino acid segment and NADH segment, respectively. In a controllable fluorescence measurement chamber, the two-dimensional fluorescence spectra of vegetative liquid bacterial aerosols as well as BSA and OVA, two protein toxinic simulants were measured with a resolution of 4nm. The two-dimensional fluorescence spectral shape of Pan, Sta, EH and BG, BSA and OVA were consistent with the standard fluorescent component tryptophan in the amino acid band with FWHM of 60nm, but the central wavelength of the fluorescence spectra of these simulants blue/purple shifted obviously as affected by the external biochemical environment, concentration and ratio of different bacterial internal fluorophores, so the energy level between the excited state and the ground state of the fluorescence molecule increased. Differently, weak NADH fluorescence spectra with 100nm FWHM inside the four vegetative bacteria aerosols were detected, but Rayleigh scattering, Raman scattering contribution of water, nitrogen in the fluorescence spectra could not be effectively extracted. The second - order derivative fluorescence spectra of four simulants showed that the high - order processing and recognition of the fluorescence spectra was feasible.

  9. Fungal biomineralization of montmorillonite and goethite to short-range-ordered minerals

    Science.gov (United States)

    Li, Huan; Hu, Shuijin; Polizzotto, Matthew L.; Chang, Xiaoli; Shen, Qirong; Ran, Wei; Yu, Guanghui

    2016-10-01

    Highly reactive nano-scale minerals, e.g., short-range-ordered minerals (SROs) and other nanoparticles, play an important role in soil carbon (C) retention. Yet, the mechanisms that govern biomineralization from bulk minerals to highly reactive nano-scale minerals remain largely unexplored, which critically hinders our efforts toward managing nano-scale minerals for soil C retention. Here we report the results from a study that explores structural changes during Aspergillus fumigatus Z5 transformation of montmorillonite and goethite to SROs. We examined the morphology and structure of nano-scale minerals, using high-resolution transmission electron microscopy, time-resolved solid-state 27Al and 29Si NMR, and Fe K-edge X-ray absorption fine structure spectroscopy combined with two dimensional correlation spectroscopy (2D COS) analysis. Our results showed that after a 48-h cultivation of montmorillonite and goethite with Z5, new biogenic intracellular and extracellular reactive nano-scale minerals with a size of 3-5 nm became abundant. Analysis of 2D COS further suggested that montmorillonite and goethite were the precursors of the dominant biogenic nano-scale minerals. Carbon 1s near edge X-ray absorption fine structure (NEXAFS) spectra and their deconvolution results demonstrated that during fungus Z5 growth, carboxylic C (288.4-289.1 eV) was the dominant organic group, accounting for approximately 34% and 59% in the medium and aggregates, respectively. This result suggested that high percentage of the production of organic acids during the growth of Z5 was the driving factor for structural changes during biomineralization. This is, to the best of our knowledge, the first report of the structural characterization of nano-scale minerals by 2D COS, highlighting its potential to elucidate biomineralization pathways and thus identify the precursors of nano-scale minerals.

  10. Short-range structure of barium tellurite glasses and its correlation with stress-optic response

    Science.gov (United States)

    Kaur, Amarjot; Khanna, Atul; Fábián, Margit

    2018-06-01

    The atomic parameters of metal ion-oxygen speciation such as bond-lengths and nearest neighbor distances for Ba-O, Te-O and O-O pairs, co-ordination numbers and bond angle distributions for O-Ba-O, O-Te-O and O-O-O linkages are determined by neutron diffraction and Reverse Monte Carlo simulations on the series of xBaO-(100-x)TeO2 glasses containing 10, 15 and 20 mol% BaO. The glass network depolymerizes and the average Te-O co-ordination number decreases from 3.60 ± 0.02 to 3.48 ± 0.02 with increase in BaO concentration. Te-O bond lengths are in the range: 1.97 ± 0.01–1.92 ± 0.01 Å. Ba2+ is mostly in octahedral coordination and the Ba-O bond lengths are in the range: 2.73 ± 0.01 to 2.76 ± 0.03 Å. Te-O co-ordination number is also determined by Raman spectroscopy and it shows good agreement with the neutron data. The short-range structural properties i.e. metal ion coordination number (Nc) and bond lengths (d) were correlated with the stress-optic response. The bonding characteristic, Br values were determined from the structural data of xBaO-(100-x)TeO2 glasses and were used to predict the stress-induced birefringence properties.

  11. Short-range and long-range forces in quantum theory: selected topics

    International Nuclear Information System (INIS)

    Hiller, J.R.

    1980-01-01

    Short-range forces (SRF) are encountered when the effects of the parity-violating (PV) weak neutral current are considered in atomic systems. We consider these and other SRF that are associated with operators that contain delta functions. Identities which convert a delta-function matrix element to that of a global operator are reviewed. Past and possible future applications of such identities are described. It has been found that use of these identities can substantially improve the results obtained with less accurate wave functions. We present a further application to the hyperfine structure of the ground state of lithium where we again find that results are improved by the use of an identity. A long-range force (LRF) is here defined to be one that is associated with a potential V(r) that is asymptotically of the form lambda r - 1 (r 0 /r)/sup N-1/. We use a dispersion-theoretic approach to study LRF between hadrons due to two-glucon exchange within the framework of quantum chromodynamics. Such an LRF is usually related to the presence of a spectrum of physical states that extends to zero mass. A speculative scheme put forward by Feinberg and Sucher is used to avoid requiring the existence of massless gluons as observable particles. Semi-quantitative expressions for the two-glucon exchange potential between hadrons and, in particular, between two nucleons are obtained. Limits on two-gluon corrections to πp forward scattering dispersion relations are used to provide an upper bound for lambda, the coupling constant in the nucleon-nucleon potential. For N greater than or equal to 7, expected on heuristic grounds, we obtain the bound lambda less than or equal to 10 6 , which is very weak; gluon effects as treated here do not lead to significant effects in the dispersion-theoretic analysis of πp scattering

  12. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  13. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-01-01

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition

  14. Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

    Czech Academy of Sciences Publication Activity Database

    Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

    2015-01-01

    Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

  15. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

    1991-01-01

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  16. Theory of multiexciton dynamics in molecular chains

    Science.gov (United States)

    Wang, Luxia; May, Volkhard

    2016-11-01

    Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.

  17. Photoionization dynamics of excited molecular states

    International Nuclear Information System (INIS)

    Dehmer, J.L.; O'Halloran, M.A.; Tomkins, F.S.; Dehmer, P.M.; Pratt, S.T.

    1987-01-01

    Resonance Enhanced Multiphoton Ionization (REMPI) utilizes tunable dye lasers to ionize an atom or molecule by first preparing an excited state by multiphoton absorption and then ionizing that state before it can decay. This process is highly selective with respect to both the initial and resonant intermediate states of the target, and it can be extremely sensitive. In addition, the products of the REMPI process can be detected as needed by analyzing the resulting electrons, ions, fluorescence, or by additional REMPI. This points to a number of opportunities for exploring excited state physics and chemistry at the quantum-state-specific level. Here we will first give a brief overview of the large variety of experimental approaches to excited state phenomena made possible by REMPI. Then we will examine in more detail, recent studies of the three photon resonant, four photon (3 + 1) ionization of H 2 via the C 'PI/sup u/ state. Strong non-Franck-Condon behavior in the photoelectron spectra of this nominally simple Rydberg state has led to the examination of a variety of dynamical mechanisms. Of these, the role of doubly excited autoionizing states now seems decisive. Progress on photoelectron studies of autoionizing states in H 2 , excited in a (2 + 1) REMPI process via the E, F 1 Σ/sub g/ + will also be briefly discussed. 26 refs., 7 figs

  18. Dynamical photo-induced electronic properties of molecular junctions

    Science.gov (United States)

    Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

    2018-03-01

    Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

  19. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

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

  20. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  1. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  2. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  3. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  4. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  5. Molecular dynamics study of the silica-water-SDA interactions

    NARCIS (Netherlands)

    Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.

    2009-01-01

    In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species

  6. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NARCIS (Netherlands)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-01-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers

  7. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  8. Toluene model for molecular dynamics simulations in the ranges 298

    NARCIS (Netherlands)

    Fioroni, M.; Vogt, D.

    2004-01-01

    An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons

  9. Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics

    NARCIS (Netherlands)

    Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de

    1997-01-01

    The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.

  10. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  11. 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

  12. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  13. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  14. Molecular dynamics study on the relaxation properties of bilayered ...

    Indian Academy of Sciences (India)

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  15. Metal cluster fission: jellium model and Molecular dynamics simulations

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...

  16. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

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

  17. Free energy from molecular dynamics with multiple constraints

    NARCIS (Netherlands)

    den Otter, Wouter K.; Briels, Willem J.

    2000-01-01

    In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

  18. 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.

  19. Interplay of long-range and short-range Coulomb interactions in an Anderson-Mott insulator

    Science.gov (United States)

    Baćani, Mirko; Novak, Mario; Orbanić, Filip; Prša, Krunoslav; Kokanović, Ivan; Babić, Dinko

    2017-07-01

    In this paper, we tackle the complexity of coexisting disorder and Coulomb electron-electron interactions (CEEIs) in solids by addressing a strongly disordered system with intricate CEEIs and a screening that changes both with charge carrier doping level Q and temperature T . We report on an experimental comparative study of the T dependencies of the electrical conductivity σ and magnetic susceptibility χ of polyaniline pellets doped with dodecylbenzenesulfonic acid over a wide range. This material is special within the class of doped polyaniline by exhibiting in the electronic transport a crossover between a low-T variable range hopping (VRH) and a high-T nearest-neighbor hopping (NNH) well below room temperature. Moreover, there is evidence of a soft Coulomb gap ΔC in the disorder band, which implies the existence of a long-range CEEI. Simultaneously, there is an onsite CEEI manifested as a Hubbard gap U and originating in the electronic structure of doped polyaniline, which consists of localized electron states with dynamically varying occupancy. Therefore, our samples represent an Anderson-Mott insulator in which long-range and short-range CEEIs coexist. The main result of the study is the presence of a crossover between low- and high-T regimes not only in σ (T ) but also in χ (T ) , the crossover temperature T* being essentially the same for both observables over the entire doping range. The relatively large electron localization length along the polymer chains results in U being small, between 12 and 20 meV for the high and low Q , respectively. Therefore, the thermal energy at T* is sufficiently large to lead to an effective closing of the Hubbard gap and the consequent appearance of NNH in the electronic transport within the disorder band. ΔC is considerably larger than U , decreasing from 190 to 30 meV as Q increases, and plays the role of an activation energy in the NNH.

  20. Chiral approach to nuclear matter: Role of explicit short-range NN-terms

    International Nuclear Information System (INIS)

    Fritsch, S.; Kaiser, N.

    2004-01-01

    We extend a recent chiral approach to nuclear matter by including the most general (momentum-independent) NN-contact interaction. Iterating this two-parameter contact vertex with itself and with one-pion exchange the emerging energy per particle exhausts all terms possible up to and including fourth order in the small momentum expansion. Two (isospin-dependent) cut-offs Λ 0,1 are introduced to regularize the (linear) divergences of some three-loop in-medium diagrams. The equation of state of pure neutron matter, anti E n (k n ), can be reproduced very well up to quite high neutron densities of ρ n =0.5 fm -3 by adjusting the strength of a repulsive nn-contact interaction. Binding and saturation of isospin-symmetric nuclear matter is a generic feature of our perturbative calculation. Fixing the maximum binding energy per particle to - anti E(k f0 )=15.3 MeV we find that any possible equilibrium density ρ 0 lies below ρ 0 max =0.191 fm -3 . The additional constraint from the neutron matter equation of state leads however to a somewhat too low saturation density of ρ 0 =0.134 fm -3 . We also investigate the effects of the NN-contact interaction on the complex single-particle potential U(p,k f )+iW(p,k f ). We find that the effective nucleon mass at the Fermi surface is bounded from below by M * (k f0 ) ≥1.4 M. This property keeps the critical temperature of the liquid-gas phase transition at somewhat too high values T c ≥21 MeV. The downward bending of the asymmetry energy A(k f ) above nuclear-matter saturation density is a generic feature of the approximation to fourth order. We furthermore investigate the effects of the NN-contact interaction on the (vector-∇ρ) 2 -term in the nuclear energy density functional E[ρ,τ]. Altogether, there is within this complete fourth-order calculation no ''magic'' set of adjustable short-range parameters with which one could reproduce simultaneously and accurately all semi-empirical properties of nuclear matter. In

  1. Research of Short-range Missile Motion in Terms of Different Wind Loads

    Directory of Open Access Journals (Sweden)

    A. N. Klishin

    2015-01-01

    Full Text Available When modeling the aircraft motion it is advisable to choose a particular model of the Earth, depending both on the task and on the required accuracy of calculation. The article describes various models of the Earth, such as the flat Earth with a plane-parallel field of gravity, spherical and non-rotating Earth with a plane-parallel field of gravity, spherical and non-rotating Earth with a central gravitational field, spherical and non-rotating Earth, taking into account the polar flattening of the Earth, spherical Earth based compression and polar daily rotation. The article also considers the influence of these models on the motion of the selected aircraft.To date, there is technical equipment to provide highly accurate description of the Earthshape, gravitational field, etc. The improved accuracy of the Earth model description results in more correct description of the trajectory and motion parameters of a ballistic missile. However, for short ranges (10-20 km this accuracy is not essential, and, furthermore, it increases time of calculation. Therefore, there is a problem of choosing the optimal description of the Earth parameters.The motion in the model of the Earth, which takes into account a daily rotation of the planet and polar flattening, is discussed in more detail, and the geographical latitude impact on coordinates of the points of fall of a ballistic missile is analyzed on the basis of obtained graphs.The article individually considers a problem of the wind effect on the aircraft motion and defines dependences of the missile motion on the parameters of different wind loads, such as wind speed and height of its action.A mathematical model of the missile motion was built and numerically integrated, using the Runge-Kutta 4th order method, for implementation and subsequent analysis.Based on the analysis of the calculation results in the abovementioned models of the Earth, differences in impact of these models on the parameters of the

  2. Multiscale equation-free algorithms for molecular dynamics

    Science.gov (United States)

    Abi Mansour, Andrew

    Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

  3. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

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

  4. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  5. Implementation of surface hopping molecular dynamics using semiempirical methods

    International Nuclear Information System (INIS)

    Fabiano, E.; Keal, T.W.; Thiel, W.

    2008-01-01

    A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

  6. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  7. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    Directory of Open Access Journals (Sweden)

    Dirk-Sören Lühmann

    2015-08-01

    Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  8. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

    2015-04-21

    Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

  9. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik; Szepessy, Anders

    2010-01-01

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  10. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  11. Molecular electron recollision dynamics in intense circularly polarized laser pulses

    Science.gov (United States)

    Bandrauk, André D.; Yuan, Kai-Jun

    2018-04-01

    Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

  12. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    Science.gov (United States)

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  13. Impacts of Amazonia biomass burning aerosols assessed from short-range weather forecasts

    Directory of Open Access Journals (Sweden)

    S. R. Kolusu

    2015-11-01

    Full Text Available The direct radiative impacts of biomass burning aerosols (BBA on meteorology are investigated using short-range forecasts from the Met Office Unified Model (MetUM over South America during the South American Biomass Burning Analysis (SAMBBA. The impacts are evaluated using a set of three simulations: (i no aerosols, (ii with monthly mean aerosol climatologies and (iii with prognostic aerosols modelled using the Coupled Large-scale Aerosol Simulator for Studies In Climate (CLASSIC scheme. Comparison with observations show that the prognostic CLASSIC scheme provides the best representation of BBA. The impacts of BBA are quantified over central and southern Amazonia from the first and second day of 2-day forecasts during 14 September–3 October 2012. On average, during the first day of the forecast, including prognostic BBA reduces the clear-sky net radiation at the surface by 15 ± 1 W m−2 and reduces net top-of-atmosphere (TOA radiation by 8 ± 1 W m−2, with a direct atmospheric warming of 7 ± 1 W m−2. BBA-induced reductions in all-sky radiation are smaller in magnitude: 9.0 ± 1 W m−2 at the surface and 4.0 ± 1 W m−2 at TOA. In this modelling study the BBA therefore exert an overall cooling influence on the Earth–atmosphere system, although some levels of the atmosphere are directly warmed by the absorption of solar radiation. Due to the reduction of net radiative flux at the surface, the mean 2 m air temperature is reduced by around 0.1 ± 0.02 °C. The BBA also cools the boundary layer (BL but warms air above by around 0.2 °C due to the absorption of shortwave radiation. The overall impact is to reduce the BL depth by around 19 ± 8 m. These differences in heating lead to a more anticyclonic circulation at 700 hPa, with winds changing by around 0.6 m s−1. Inclusion of climatological or prognostic BBA in the MetUM makes a small but significant improvement in forecasts of temperature and relative humidity, but improvements were

  14. Short Range-Ordered Minerals: Insight into Aqueous Alteration Processes on Mars

    Science.gov (United States)

    Ming, Douglas W.; Morris, R. V.; Golden, D. C.

    2011-01-01

    Short range-ordered (SRO) aluminosilicates (e.g., allophane) and nanophase ferric oxides (npOx) are common SRO minerals derived during aqueous alteration of basaltic materials. NpOx refers to poorly crystalline or amorphous alteration products that can be any combination of superparamagnetic hematite and/or goethite, akaganeite, schwertmannite, ferrihydrite, iddingsite, and nanometer-sized ferric oxide particles that pigment palagonitic tephra. Nearly 30 years ago, SRO phases were suggested as alteration phases on Mars based on similar spectral properties for altered basaltic tephra on the slopes of Mauna Kea in Hawaii and Martian bright regions measured by Earth-based telescopes. Detailed characterization of altered basaltic tephra on Mauna Kea have identified a variety of alteration phases including allophane, npOx, hisingerite, jarosite, alunite, hematite, goethite, ferrihydrite, halloysite, kaolinite, smectite, and zeolites. The presence of npOx and other Fe-bearing minerals (jarosite, hematite, goethite) was confirmed by the M ssbauer Spectrometer onboard the Mars Exploration Rovers. Although the presence of allophane has not been definitely identified on Mars robotic missions, chemical analysis by the Spirit and Opportunity rovers and thermal infrared spectral orbital measurements suggest the presence of allophane or allophane-like phases on Mars. SRO phases form under a variety of environmental conditions on Earth ranging from cold and arid to warm and humid, including hydrothermal conditions. The formation of SRO aluminosilicates such as allophane (and crystalline halloysite) from basaltic material is controlled by several key factors including activity of water, extent of leaching, Si activity in solution, and available Al. Generally, a low leaching index (e.g., wet-dry cycles) and slightly acidic to alkaline conditions are necessary. NpOx generally form under aqueous oxidative weathering conditions, although thermal oxidative alteration may occasional be

  15. Short range order and phase separation in Ti-rich Ti-Al alloys

    International Nuclear Information System (INIS)

    Liew, H.J.

    1999-01-01

    of the reaction over a range of scales, from the atomic level on which order occurs through to large scale precipitates. Ti-15at%Al displays a phase separation mechanism involving both ordering and chemical phase decomposition which occurs in a time and temperature range that is readily accessible experimentally. Hence this alloy is an appropriate model system on which to conduct fundamental investigations into a complex decomposition mechanism and its kinetics. Both experimental and modelling results show that short range order develops rapidly in the alloy, and is followed by the formation and growth of congruent long range ordered regions of DO 19 structure. At a later stage composition variations form and increase in amplitude through a spinodal mechanism. From these findings, it cannot be ruled out that the observed decomposition sequence is due solely to the kinetics of ordering being more rapid than those of chemical phase separation. However, there are some indications which suggest that a thermodynamic criterion is operating, such that the onset of chemical phase separation occurs only after ordering has been achieved to some extent. The observed mechanism is fully consistent in appearance with the class of reactions known as conditional spinodals. (author)

  16. Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

    Science.gov (United States)

    Cooke, Ben; Schmidler, Scott C

    2008-10-28

    We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

  17. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  18. MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  19. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  20. Molecular dynamics of TBP and DBP studied by neutron transmission

    International Nuclear Information System (INIS)

    Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.

    1984-04-01

    Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt

  1. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    International Nuclear Information System (INIS)

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-01-01

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  2. Control of strength and stability of emulsion-gels by a combination of long- and short-range interactions

    NARCIS (Netherlands)

    Blijdenstein, T.B.J.; Hendriks, W.P.G.; Linden, van der E.; Vliet, van T.; Aken, van G.A.

    2003-01-01

    This paper discusses the change in phase behavior and mechanical properties of oil-in-water emulsion gels brought about by variation of long- and short-range attractive interactions. The model system studied consisted of oil droplets stabilized by the protein -lactoglobulin (-lg). A long-range

  3. On-chip patch antenna on InP substrate for short-range wireless communication at 140 GHz

    DEFF Research Database (Denmark)

    Dong, Yunfeng; Johansen, Tom Keinicke; Zhurbenko, Vitaliy

    2017-01-01

    This paper presents the design of an on-chip patch antenna on indium phosphide (InP) substrate for short-range wireless communication at 140 GHz. The antenna shows a simulated gain of 5.3 dBi with 23% bandwidth at 140 GHz and it can be used for either direct chip-to-chip communication or chip...

  4. Two-nucleon electromagnetic current in chiral effective field theory: One-pion exchange and short-range contributions

    International Nuclear Information System (INIS)

    Koelling, S.; Epelbaum, E.; Krebs, H.; Meissner, U.-G.

    2011-01-01

    We derive the leading one-loop contribution to the one-pion exchange and short-range two-nucleon electromagnetic current operator in the framework of chiral effective field theory. The derivation is carried out using the method of unitary transformation. Explicit results for the current and charge densities are given in momentum and coordinate space.

  5. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    National Research Council Canada - National Science Library

    Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy

    2006-01-01

    .... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...

  6. On the universality of the long-/short-range separation in multiconfigurational density-functional theory

    DEFF Research Database (Denmark)

    Fromager, Emmanuel; Toulouse, Julien; Jensen, Hans Jørgen Aagaard

    2007-01-01

    In many cases, the dynamic correlation can be calculated quite accurately and at a fairly low computational cost in Kohn-Sham density-functional theory (KS-DFT), using current standard approximate functionals. However, in general, KS-DFT does not treat static correlation effects (near degeneracy...

  7. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  8. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  9. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  10. Microscopic study of nuclear 'pasta' by quantum molecular dynamics

    International Nuclear Information System (INIS)

    Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

    2002-01-01

    Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)

  11. Nonlinear dynamics of zigzag molecular chains (in Russian)

    DEFF Research Database (Denmark)

    Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

    1999-01-01

    models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...

  12. The chaos and order in nuclear molecular dynamics

    International Nuclear Information System (INIS)

    Srokowski, T.

    1995-01-01

    The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs

  13. Statistical ensembles and molecular dynamics studies of anisotropic solids. II

    International Nuclear Information System (INIS)

    Ray, J.R.; Rahman, A.

    1985-01-01

    We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities

  14. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  15. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)

    2007-02-14

    We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

  16. Fermionic molecular dynamics for ground states and collisions of nuclei

    International Nuclear Information System (INIS)

    Feldmeier, H.; Bieler, K.; Schnack, J.

    1994-08-01

    The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)

  17. Fermionic molecular dynamics for colliding and decaying nuclei

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    1993-11-01

    Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

  18. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  19. Optical spectra and lattice dynamics of molecular crystals

    CERN Document Server

    Zhizhin, GN

    1995-01-01

    The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

  20. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Christian Mücksch

    Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  1. Stereochemical errors and their implications for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Freddolino Peter L

    2011-05-01

    Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

  2. Ultrafast dissociation: An unexpected tool for probing molecular dynamics

    International Nuclear Information System (INIS)

    Morin, Paul; Miron, Catalin

    2012-01-01

    Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

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

    KAUST Repository

    Yoon, Seyoon; Monteiro, Paulo J.M.

    2013-01-01

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

  4. High-temperature annealing of graphite: A molecular dynamics study

    Science.gov (United States)

    Petersen, Andrew; Gillette, Victor

    2018-05-01

    A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  6. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  7. Incorporation of quantum statistical features in molecular dynamics

    International Nuclear Information System (INIS)

    Ohnishi, Akira; Randrup, J.

    1995-01-01

    We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)

  8. Molecular Dynamics Simulations of Tensile Behavior of Copper

    OpenAIRE

    Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

    2014-01-01

    Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...

  9. Automated processing of data generated by molecular dynamics

    International Nuclear Information System (INIS)

    Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima

    2008-01-01

    A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)

  10. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

    OpenAIRE

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-01-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...

  11. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    International Nuclear Information System (INIS)

    Swygenhoven, H. van; Caro, A.

    1997-01-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs

  12. Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Science.gov (United States)

    Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

    2009-01-01

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337

  13. Molecular dynamics simulation of cascade damage in gold

    International Nuclear Information System (INIS)

    Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.

    1997-01-01

    High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists

  14. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  15. Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses

    International Nuclear Information System (INIS)

    Rudenko, A; Feuerstein, B; Zrost, K; Jesus, V L B de; Ergler, T; Dimopoulou, C; Schroeter, C D; Moshammer, R; Ullrich, J

    2005-01-01

    We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape

  16. 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...

  17. Molecular dynamics simulation of bubble nucleation in explosive boiling

    International Nuclear Information System (INIS)

    Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang

    2009-01-01

    Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)

  18. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    International Nuclear Information System (INIS)

    Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

    2015-01-01

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

  19. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2017-07-01

    Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.

  20. Kinetic arrest and glass-glass transition in short-ranged attractive colloids

    International Nuclear Information System (INIS)

    Sztucki, M.; Narayanan, T.; Belina, G.; Moussaied, A.; Pignon, F.; Hoekstra, H.

    2006-01-01

    A thermally reversible repulsive hard-sphere to sticky-sphere transition was studied in a model colloidal system over a wide volume fraction range. The static microstructure was obtained from high resolution small angle x-ray scattering, the colloid dynamics was probed by dynamic x-ray and light scattering, and supplementary mechanical properties were derived from bulk rheology. At low concentration, the system shows features of gas-liquid type phase separation. The bulk phase separation is presumably interrupted by a gelation transition at the intermediate volume fraction range. At high volume fractions, fluid-attractive glass and repulsive glass-attractive glass transitions are observed. It is shown that the volume fraction of the particles can be reliably deduced from the absolute scattered intensity. The static structure factor is modeled in terms of an attractive square-well potential, using the leading order series expansion of Percus-Yevick approximation. The ensemble-averaged intermediate scattering function shows different levels of frozen components in the attractive and repulsive glassy states. The observed static and dynamic behavior are consistent with the predictions of a mode-coupling theory and numerical simulations for a square-well attractive system

  1. Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  2. Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

    Science.gov (United States)

    Lehmann, Kevin K.

    2003-03-01

    Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

  3. Excitation dynamics and relaxation in a molecular heterodimer

    International Nuclear Information System (INIS)

    Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

    2012-01-01

    Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

  4. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

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

    2015-04-01

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

  5. Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

    Energy Technology Data Exchange (ETDEWEB)

    Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

    2017-04-04

    The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

  6. Electron-nuclear corellations for photoinduced dynamics in molecular dimers

    Science.gov (United States)

    Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

    2003-03-01

    Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

  7. High-energy X-ray study of short range order and phase transformations in titanium-vanadium

    International Nuclear Information System (INIS)

    Ramsteiner, I.B.

    2005-01-01

    This work presents a study of configurational correlations and phase transformations in the binary alloy Ti-V, using high-energy X-ray diffraction. The experiments have been performed at the European Synchrotron Radiation Facility (ESRF) in Grenoble. The high-energy (60-100 keV) technique developed recently allows in-situ measurements on bulk material in transmission geometry. The first part of the thesis discusses multiple scattering effects which might occur with this method. These effects are experimentally verified and discussed. Special emphasis is put on the questions, whether they affect the results obtained with this method, and how they can be avoided. Understanding alloys on the most fundamental level requires knowledge about the atomic interaction potentials. Competing with entropy, these potentials determine the configurational short range order in a disordered alloy, which generates together with static and dynamic distortions the diffuse scattering. The thesis presents measurements and calculations of the diffuse scattering patterns of Ti-V. The calculations, taking into account configurational correlations, static distortions induced by atomic size mismatch and thermal diffuse scattering, agree with the experimental data. Structural transformations in Ti-V are carefully characterized using high-energy x-ray diffraction in combination with the complementary transmission electron microscopy (TEM). While the first technique allows to study the phenomena in-situ and time-resolved, TEM yields real space images and chemical information about the phases. Ti-V near the equiatomic composition is a beta-Ti-alloy. The body centered cubic beta phase is retained at room temperature by fast quenching. Aging the material below the phase transformation temperature, however, leads to the precipitation of hexagonal alpha titanium. Another transformation process confusing earlier works is identified as TiC formation from carbon impurities in the material. In addition

  8. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

    NARCIS (Netherlands)

    van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  9. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

    NARCIS (Netherlands)

    van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  11. Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

    Science.gov (United States)

    Hu, Hao; Liu, Haiyan

    2013-05-30

    Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

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

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  13. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Ould-Kaddour, F.; Barrat, J.L.

    1991-05-01

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  14. Molecular dynamics of coalescence and collisions of silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)

    2014-12-15

    We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.

  15. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  16. Molecular dynamics of coalescence and collisions of silver nanoparticles

    International Nuclear Information System (INIS)

    Guevara-Chapa, Enrique; Mejía-Rosales, Sergio

    2014-01-01

    We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy

  17. Liquid-vapor coexistence by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Baranyai, Andras; Cummings, Peter T.

    2000-01-01

    We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

  18. The classical and quantum dynamics of molecular spins on graphene

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

  19. Investigation of Multiconfigurational Short-Range Density Functional Theory for Electronic Excitations in Organic Molecules

    DEFF Research Database (Denmark)

    Hubert, Mickaël; Hedegård, Erik D.; Jensen, Hans Jørgen Aa

    2016-01-01

    -srDFT for a selected benchmark set of electronic excitations of organic molecules, covering the most common types of organic chromophores. This investigation confirms the expectation that the MC-srDFT method is accurate for a broad range of excitations and comparable to accurate wave function methods such as CASPT2......Computational methods that can accurately and effectively predict all types of electronic excitations for any molecular system are missing in the toolbox of the computational chemist. Although various Kohn-Sham density-functional methods (KS-DFT) fulfill this aim in some cases, they become...... and double excitations have been promising, it is nevertheless important that the accuracy of MC-srDFT is at least comparable to the best KS-DFT methods also for organic molecules that are typically of single-reference character. In this paper we therefore systematically investigate the performance of MC...

  20. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

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

    Directory of Open Access Journals (Sweden)

    Elena ePapaleo

    2015-05-01

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

  2. Accelerated molecular dynamics methods: introduction and recent developments

    International Nuclear Information System (INIS)

    Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) (10, 19, 23) to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  3. Accelerated molecular dynamics methods: introduction and recent developments

    Energy Technology Data Exchange (ETDEWEB)

    Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  4. Short-Range Correlated Magnetic Core-Shell CrO₂/Cr₂O₃ Nanorods: Experimental Observations and Theoretical Considerations.

    Science.gov (United States)

    Gandhi, Ashish C; Li, Tai-Yue; Chan, Ting Shan; Wu, Sheng Yun

    2018-05-09

    With the evolution of synthesis and the critical characterization of core-shell nanostructures, short-range magnetic correlation is of prime interest in employing their properties to develop novel devices and widespread applications. In this regard, a novel approach of the magnetic core-shell saturated magnetization (CSSM) cylinder model solely based on the contribution of saturated magnetization in one-dimensional CrO₂/Cr₂O₃ core-shell nanorods (NRs) has been developed and applied for the determination of core-diameter and shell-thickness. The nanosized effect leads to a short-range magnetic correlation of ferromagnetic core-CrO₂ extracted from CSSM, which can be explained using finite size scaling method. The outcome of this study is important in terms of utilizing magnetic properties for the critical characterization of core-shell nanomagnetic materials.

  5. Changes in structure of the short-range order of the InP melt when heated

    International Nuclear Information System (INIS)

    Glazov, V.M.; Dovletov, K.; Nashel'skij, A.Ya.; Mamedov, M.M.

    1977-01-01

    An investigation of the temperature dependence of the InP viscosity has indicated an ''after-melting'' effect similar to that observed in other A 3 V 5 compounds having a sphalerite structure. The termodynamic parameters of the viscous flow of indium phosphide melt have been calculated, and a suggestion has been made on the loosening of the short-range order structure of the melt during the period preceding solidification. With the similarity in the behaviour of InP and of A 3 Sb compound melts as a basis, a suggestion has been put forward that the influence of the thermal dissociation upon the character of the changes in the short-range order structure directly after transition from the solid to the liquid phase is negligible

  6. Properties of short-range and long-range correlation energy density functionals from electron-electron coalescence

    International Nuclear Information System (INIS)

    Gori-Giorgi, Paola; Savin, Andreas

    2006-01-01

    The combination of density-functional theory with other approaches to the many-electron problem through the separation of the electron-electron interaction into a short-range and a long-range contribution is a promising method, which is raising more and more interest in recent years. In this work some properties of the corresponding correlation energy functionals are derived by studying the electron-electron coalescence condition for a modified (long-range-only) interaction. A general relation for the on-top (zero electron-electron distance) pair density is derived, and its usefulness is discussed with some examples. For the special case of the uniform electron gas, a simple parametrization of the on-top pair density for a long-range only interaction is presented and supported by calculations within the ''extended Overhauser model.'' The results of this work can be used to build self-interaction corrected short-range correlation energy functionals

  7. Correlation of optical energy gap with the nearest neighbour short range order in amorphous V2O5 films

    International Nuclear Information System (INIS)

    Dhawan, Sahil; Vedeshwar, Agnikumar G; Tandon, R P

    2011-01-01

    The optical and structural properties of well characterized vacuum-evaporated amorphous V 2 O 5 films were studied in the thickness range 5-500 nm. The structural analyses show that V-O, O-O and V-V nearest neighbour distances defining the short range order vary nonlinearly with film thickness. The optical absorption shows thickness-dependent energy gap (E g ) and the nonlinear behaviour of thickness-dependent E g is similar to that of nearest neighbour distance with film thickness. The E g correlates linearly very well with all the three nearest neighbour distances. The variation of E g with film thickness is attributed to the residual stress in the film which causes the changes in short range order. The change in E g corresponding to the change in V-O distance was found to be 35 eV nm -1 . This change is almost three times of that with V-V distance.

  8. SHORT-RANGE WAKEFIELD IN A FLAT PILLBOX CAVITY GENERATED BY A SUB-RELATIVISTIC BEAM BUNCH

    International Nuclear Information System (INIS)

    WANG, H.; PALMER, R.B.; GALLARDO, J.

    2001-01-01

    The short-range wakefield between two parallel conducting plates generated by a sub-relativistic beam bunch has been solved analytically by the image charge method in time domain. Comparing with the traditional modal analysis in frequency domain, this algorithm simplifies the mathematics and reveals in greater details the physics of electromagnetic field generation, propagation, reflection and causality. The calculated results have an excellent agreement with MAFIA and ABC1 simulations in all range of beam velocities

  9. Investigation into short-range order, electric conductivity and optical absorption edge of indium selenide thin amorphous films

    International Nuclear Information System (INIS)

    Bilyj, M.N.; Didyk, G.V.; Stetsiv, Ya.I.; Yurechko, R.Ya.

    1980-01-01

    Thin amorphous films of InSe have been obtained by the method of discrete vacuum evaporation of about 10 -2 Pa. The short-range order is investigated according to the radial distribution curves. The temperature and film thickness are shown to affect the character of conductivity. The width of the forbidden band determined by the fundamental absorption edge is found to depend on the time of film annealing

  10. Electron irradiation effect on short-range ordering in Cu-Al and Ag-Al alloys

    International Nuclear Information System (INIS)

    Kulish, N.P.; Mel'nikova, N.A.; Petrenko, P.V.; Ryabishchuk, A.L.; Tatarov, A.A.

    1990-01-01

    Method of X-ray diffuse scattering is used to study short-range order variation in Cu-Al and Ag-Al alloys under radiation effect and the following heat treatment. Irradiation was carried out at -40 deg C by 1.6 MeV electrons, fluence of 5x10 7 cm -2 and 0.5 MeV gamma-rays, the dose being 10 7 pH

  11. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  12. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  13. Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

    Science.gov (United States)

    Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

    1999-06-01

    Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.

  14. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  15. 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

  16. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

    NARCIS (Netherlands)

    Risselada, H. Jelger; Marrink, Siewert J.

    2009-01-01

    The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high

  17. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

    NARCIS (Netherlands)

    Marrink, SJ; Mark, AE

    2003-01-01

    Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

  18. Reaction Ensemble Molecular Dynamics: Direct Simulation of the Dynamic Equilibrium Properties of Chemically Reacting Mixtures

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.

    2004-01-01

    Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004

  19. Short-Range Prediction of the Zone of Moving Vehicles in Arterial Networks

    Directory of Open Access Journals (Sweden)

    Rouzbeh Forouzandeh Jonaghani

    2018-01-01

    Full Text Available In many moving object databases, future locations of vehicles in arterial networks are predicted. While most of studies apply the frequent behavior of historical trajectories or vehicles’ recent kinematics as the basis of predictions, consideration of the dynamics of the intersections is mostly neglected. Signalized intersections make vehicles experience different delays, which vary from zero to some minutes based on the traffic state at intersections. In the absence of traffic signal information (red and green times of traffic signal phases, the queue lengths, approaching traffic volume, turning volumes to each intersection leg, etc., the experienced delays in traffic signals are random variables. In this paper, we model the probability distribution function (PDF and cumulative distribution function (CDF of the delay for any point in the arterial networks based on a spatiotemporal model of the queue at the intersection. The probability of the presence of a vehicle in a zone is determined based on the modeled probability function of the delay. A comparison between the results of the proposed method and a well-known kinematic-based method indicates a significant improvement in the precisions of the predictions.

  20. Physical properties of Cu nanoparticles: A molecular dynamics study

    International Nuclear Information System (INIS)

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

    2014-01-01

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