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In ab initio molecular dynamics, whenever information about the potential energy surface is needed for integrating the equations of motion, it is computed 'on the fly' using electronic structure calculations. For Born-Oppenheimer methods, the electronic structure calculations are converged, whereas in the extended Lagrangian approach the electronic structure is propagated along with the nuclei. Some recent advances for both approaches are discussed.

International Nuclear Information System (INIS)

In this thesis, a new ab-initio method for molecular dynamics within the framework of density functional theory was developed and implemented. It is strongly related to the projector-augmented-wave method (PAW) by P. Bloechl, but also includes elements of a pseudocharge method proposed by M. Weinert for the full-potential linearized augmented plane wave method (FLAPW). Like the FLAPW-method, the PAW-method is an all-electron method. In the later case, the hamiltonian takes quite a simple form similar to the one obtained when using normconserving Kleinman-Bylander-type pseudopotentials or ultrasoft Vanderbilt pseudopotentials. The PAW-method allows for an efficient calculation of systems containing virtually any element of the periodic table, including those which require high numerical effort when treated using normconserving pseudopotentials (e.g. 2p-elements like oxygen or 3d-transitional metals like copper). In addition, ...

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We have developed a kinetic Monte Carlo (kMC) simulator that links atomic migration and binding energies determined primarily from first principles calculations to macroscopic phenomena and laboratory time scales. Input for the kMC simulation is obtained from a combination of ab initio planewave pseudopotential calculations, molecular dynamics simulations, and experimental data. The simulator is validated against an extensive series of experimental studies of the diffusion of B spikes in self-implanted Si. The implant energy, dose, and dose rate, as well as the detailed thermal history of the sample, are included. Good agreement is obtained with the experimental data for temperatures between 750 and 950 C and times from 15 to 255 s. At 1050o C we predict too little diffusion after 105 s compared to experiment: apparently, some mechanism which is not adequately represented by our model becomes important ...

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This book examines some of the basic principles behind chemical reactions kinetics. Topics considered include ab initio determination of potential energy for chemical reactions; semi-empirical potential energy surfaces; general theory of reactive scattering: different equation approach; and integral equation approach to reactive scattering.

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We present results from ab-initio electronic-structure calculations of mechanical properties of the rhombohedral phase of vanadium reported in recent experiments (R Ia), and other predicted high-pressure phases (R Ib and bcc), focusing on properties relevant to dynamic experiments. We find that of the three transitions the largest volume collapse (1.3%) is for the R Ia to R Ib transition. Calculations of the single crystal and polycrystal elastic constants reveal a remarkably small discontinuity across the phase transitions even at zero temperature where the transitions are first order.

International Nuclear Information System (INIS)

The electronic structures of the set of molecular clusters of dielectric oxide crystals AWO4 (A = Pb, Cd, Zn), the sizes of which increase sequentially are ab-initio calculated by the Restricted Hartree-Fock (RHF) method. The results of calculations of molecular orbitals and energy dependences of partial densities of electronic states of different clusters are compared each to other and to experimental data. It is found that calculated electronic structures of the tungstate groups and cations which are surrounded in cluster by certain number of the nearest neighbor atoms of the crystals quite well represent the experimentally obtained value of the forbidden gap of corresponding AWO4 crystal. (authors)

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This paper presents fundamental researches based on the electronic structure calculations and X absorption spectroscopy, allowing the knowledge on nuclear fuels at an atomic scale. They bring a better understanding of these material behavior to accurate the macroscopic simulation. The calculation methods, the experimental techniques of validation and the ab initio calculations results are detailed. (A.L.B.)

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The IR double-resonance techniques IR/R2PI (infrared/resonant 2-photon ionization), IR/PIRI (infrared-photo-induced Rydberg ionization) and IR-photodissociation spectroscopy are valuable tools to investigate structure, vibrations, and dynamical processes of neutral and ionic hydrogen-bonded clusters containing aromatic molecules. In this paper we report on the application of the IR double-resonance techniques to determine the NH and OH stretching vibrations of 4-aminophenol and 4-aminophenol(H{sub 2}O){sub 1}, both in the neutral (S{sub 0}) and ionic (D{sub 0}) ground state. All vibrational frequencies obtained for 4-aminophenol and the cluster are compared with the values obtained from ab initio and DFT calculations. In the S{sub 0} state, a trans-linear arrangement of 4-aminophenol(H{sub 2}O){sub 1} is obtained containing an O-H. O hydrogen bond. In the D{sub 0} state an overlay of two spectra can be observed resulting ...

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This conference was held December 4--8, 1994 in Asilomar, California. The purpose of this meeting was to provide a forum for exchange of state-of-the-art information concerning the prediction of protein structure. Attention if focused on the following: comparative modeling; sequence to fold assignment; and ab initio folding.

UK PubMed Central (United Kingdom)

Electronic and structural properties of antiphase boundaries in group III-V semiconductor compounds have been receiving increased attention due to the potential to integration of optically-active III-V...Full Text Available

International Nuclear Information System (INIS)

Ab initio total-energy calculations, based on the exact muffin-tin orbital method, are used to determine the elastic properties of Pd1-xAgx random alloys in the face-centered-cubic crystallographic phase. The compositional disorder is treated within the coherent-potential approximation. The single crystal and polycrystalline elastic constants and the Debye temperature are calculated for the whole range of concentration, 0?x?1. It is shown that the variation in the elastic parameters of Pd-Ag alloys with chemical composition strongly deviates from a simple linear or parabolic trend. The complex electronic origin of these anomalies is demonstrated.

CERN Document Server

This thesis is divided up into five chapters as outlined below. Chapter 1 gives the background to the techniques used in this thesis including X-ray structure determination and ab initio methods. An overview of some recent studies using ab initio methods to study transition metal complexes is also given. Chapter 2 investigates structural trans influence in a number of transition metal and p-block complexes. The database and ab initio studies showed that the classical trans influence model based on Pt(II) chemistry does not always hold. For some systems (eg. d sup 1 sup 0 s sup 0 for Sb sup V and Sn sup I sup V) the cis influence is of similar magnitude to the trans influence. For other systems (d sup 0), the trans influence is not as powerful as usually assumed. Chapter 3 is an investigation into the bridging chloride unit. A database study was performed on ...

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The structure of ammonium azide (NH{sub 4})N{sub 3} was (re-)determined ab initio from x-ray powder diffraction experiment using synchrotron radiation. We tried to detail and comment the different steps involved in the structure determination. The compound crystallize in the orthorhombic Pmna space group (no.53) with a = 8.937(1) A, b= 3.8070(5) A, c = 8.664(1) A, V = 294.79(7) A{sup 3}; Z= 4. It was possible to locate and refine the hydrogen coordinates, in two different approaches, and to establish the H-bonds. The final structural parameters are in good agreement with previous results based on three-dimensional neutron diffraction. (Author)

British Library Electronic Table of Contents (United Kingdom)

We carried out theoretical analyses based on ab initio calculations that incorporate free energy of the vapor phase in order to determine the initial growth process of cubic GaN on GaN (001)-(4x1). The results suggest that a N-adsorbed structure appears at the initial growth stage and then Ga adsorbs on the N-adsorbed GaN (001)-(4x1) surface. Considering this process, we performed Monte Carlo simulations. The results suggest that the maximum point of Ga coverage after supplying a Formula Not Shown monolayer of atoms shifted toward a Ga-rich condition from V/III=1.0.

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Ab initio planewave pseudopotential method is used to study carbon diffusion and pairing in crystalline silicon. The calculation is performed with a 40 Ry planewave cutoff and 2x2x2 special k-point sampling with a supercell of 64 atoms. It is found that substitutional carbon attracts interstitial Si forming a <001> C interstitial with a large binding energy of 1.45 eV. The interstitial carbon is mobile and can migrate with a migration energy of 0.5 eV. The interstitial carbon can bind further to another substitutional carbon forming a substitutional carbon-interstitutional carbon pair with a binding energy of 1.0 eV. This model is used to understand the effect of high C concentration on the transient enhanced diffusion in Si.

UK PubMed Central (United Kingdom)

Model phosphate-metal solvation complexes have been studied by ab-initio self-consistent-field techniques. The complexes studied include (RO)2PO2-(R = H or CH3) with Li+, Na+, K+, Be++, Mg++, Ca++,...Full Text Available

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We report on large-scale applications of the ab initio, no-core shell model with the primary goal of achieving an accurate description of nuclear structure from the fundamental inter-nucleon interactions. In particular, we show that realistic two-nucleon interactions are inadequate to describe the low-lying structure of {sup 10}B, and that realistic three-nucleon interactions are essential.

International Nuclear Information System (INIS)

Complete text of publication follows. We have published on the spectroscopic study on the formation of a 1:1 molecular complex of fluoranthene (F) with benzene (B) in cyclohexane and estimated the equilibrium constant K(F-B) (0.147 dm3 mol-1 at 298 K), enthalpy change DH(F-B) (-5.9 kJ mol-1) and entropy change DS(F-B) (-36 JK-1mol-1 at 298 K) for this complex formation (S. Enomoto et al., Bull. Chem. Soc. Jpn., 75 (2002) 689-693). In this study, the electronic absorption spectra have been observed for the fluoranthene derivatives in cyclohexane-benzene and/or cyclohexane-ethanol mixed solvents to investigate the weak intermolecular interactions between fluoranthene derivatives and benzene or ethanol. The electronic absorption spectra of 3-aminofluoranthene (AF) in the mixed solvent mentioned above showed isosbestic points with varying B and ethanol (E) concentrations. These observations indicate that AF forms a 1:1 molecular complex with B or ...

International Nuclear Information System (INIS)

The structural parameters of various Haegg phases (H or M_n_+_1AX_n phases) are studied experimentally by x-ray and electron spectroscopies, x-ray diffraction, and ab initio full potential as well as full mutiple scattering theoretical calculations. Experimentally it was found that the structure of all ternary compounds analyzed herein are relaxed. The values of the lattice parameters and relaxations obtained from ab initio calculations are in excellent agreement with those deduced from the analysis of the experimental data. The bonding scheme has been analyzed and the charge transfer between constituting atoms determined. It is demonstrated that the strength and electrical transport properties in these materials are principally governed by the metallic planes. For the solid solution (Ti_0_._5Nb_0_._5)_2AlC, the most salient result is that the basal planes are corrugated, which could explain the solid ...

CERN Document Server

Over the last decade {\\it ab initio} modeling of material properties has become widespread in diverse fields of research. It has proved to be a powerful tool for predicting various properties of matter under extreme conditions. We apply modern computational chemistry and materials science methods, including density functional theory (DFT), to solve lingering problems in the modeling of the dense atmospheres of cool white dwarfs ($T_{\\rm eff}\\rm <7000 \\, K$). Our work on the revision and improvements of the absorption mechanisms in the hydrogen and helium dominated atmospheres resulted in a new set of atmosphere models. By inclusion of the Ly-$\\rm \\alpha$ red wing opacity we successfully fitted the entire spectral energy distributions of known cool DA stars. In the subsequent work we fitted the majority of the coolest stars with hydrogen-rich models. This finding challenges our understanding of the spectral evolution of cool white ...

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We report a study of the nonmetal-metal transition of free-standing Pd{sub N} clusters (2{<=}N{<=}21) carried out through two different theoretical approaches that are extensively employed in electronic structure calculations: a semi-empirical tight-binding (TB) model and an ab initio DFT pseudopotential model. The calculated critical size for the metallic transition decreases rapidly with the temperature and an oscillatory dependence with the cluster size is obtained, particularly in the DFT approach. The TB model describes the metallic behavior for cluster sizes beyond N{approx}12 well. Our obtained critical size at room temperature is of the order of the experimental estimation.

UK PubMed Central (United Kingdom)

AbstractWe combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our...Full Text Available

British Library Electronic Table of Contents (United Kingdom)

By means of ab-initio electronic structure calculation and one-dimensional Boltzmann transport equation solution, we investigate the size dependent thermoelectric (TE) properties of n-type ZnO nanowires (NWs) and surface passivation effects. As demonstrated by our calculations, largest figure of merit ZT achievable in thin NWs is larger than that in wide NWs, whereas being restrained by higher demand of n-type doping. Moreover, bare NWs are superior in TE application comparing with the passivated. To compete with conventional TE materials, lattice thermal conductivity of ZnO NWs should be at least 2 orders of magnitude lower than bulk value.

International Nuclear Information System (INIS)

We present results from a kinetic Monte Carlo simulation of boron transient enhanced diffusion (TED) in silicon. Our approach avoids the use of phenomenological fits to experimental data by using a complete and self-consistent set of values for defect and dopant energetics derived mostly from ab initio calculations. The results predict that, during annealing of 40 keV B-implanted Si at 800 degree C, there exists a time window during which all the implanted boron atoms are substitutional. At earlier or later times, the interactions between free silicon self-interstitials and boron atoms drive the growth of boron clusters and result in an inactive boron fraction. The results show that the majority of boron TED takes place during the growth period of interstitial clusters and not during their dissolution. copyright 1998 American Institute of Physics.

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A first-principles quasiparticle approach to the electronic excitation energies in crystals and at surfaces is described. The quasiparticle energies are calculated within the GW approximation for comparison with photoemission and other spectroscopic experiments. Applications of the method to bulk semiconductors and the Si(111)2[times]l, Ge(111)2[times]l. and H/Si(III) surfaces are presented. In both cases, significant self-energy corrections arising from many-electron effects to the excitation energies are found. Using atomic positions from total energy minimization, the calculated excitation energies explain quantitatively the experimental spectra. This approach thus provides an ab initio means for analyzing and predicting results from spectroscopic probes.

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Electrostatic fields of the order of 1 V/Angst, as they occur at field emission tips, are comparable to those experienced by valence electrons in atoms and molecules. Such fields are strong enough to induce a significant redistribution of the valence charge in chemical bonds. In this work we investigate the effects on the electronic properties of a single adatom on a metal surface induced by the presence of an electrostatic field. In particular we present the results of a full ab initio DFT calculation, within the embedding method, of the CCV Auger spectra of Si and Mg atoms in and on a jellium-Ag host. Differently from impurities in bulk, Auger spectral profiles of adsorbates on metal surfaces can show notable modifications due to the applied electric field.

International Nuclear Information System (INIS)

We have performed ab initio calculations on a wide range of small molecules, demonstrating the accuracy and flexibility of an alternative method for calculating the electronic structure of molecules, solids, and surfaces. It is based on the local-density approximation (LDA) for exchange and correlation and the nonlinear augmented-plane-wave method. Very accurate atomic forces are obtained directly. This allows for implementation of Car-Parrinello-like techniques to determine simultaneously the self-consistent electron wave functions and the equilibrium atomic positions within an iterative scheme. We find excellent agreement with the best existing LDA-based calculations and remarkable agreement with experiment for the equilibrium geometries, vibrational frequencies, and dipole moments of a wide variety of molecules, including strongly bound homopolar and polar molecules, hydrogen-bound and electron-deficient molecules, and weakly bound alkali ...

International Nuclear Information System (INIS)

A systematic study for the materials design of III-V and II-VI compound-based ferromagnetic diluted magnetic semiconductors is given based on ab initio calculations within the local spin density approximation. The electronic structures of 3d-transition-metal-atom-doped GaN and Mn-doped InN, InP, InAs, InSb, GaN, GaP, GaAs, GaSb, AlN, AlP, AlAs and AlSb were calculated by the Korringa-Kohn-Rostoker method combined with the coherent potential approximation. It is found that the ferromagnetic ground states are readily achievable in V-, Cr- or Mn-doped GaN without any additional carrier doping treatments, and that InN is the most promising candidate for high-T_C ferromagnet. A simple explanation of the systematic behavior of the magnetic states in III-V and II-VI compound-based diluted magnetic semiconductors is also given. It is also shown that V or Cr-doped ZnS, ZnSe, and ZnTe are ferromagnetic without p- or n-type doping treatment. However, Mn-, ...

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(12/11)CASSCF and (12/11)CASPT2 ab initio electronic structure calculations with both the cc-pVDZ and cc-pVTZ basis sets find that there is a barrier to the very exothermic hydrogen shift that converts singlet methylnitrene, CH{sub 3}N, to methyleneimine, H{sub 2}C{double{underscore}bond}NH. These two energy minima are connected by a transition structure of C{sub s} symmetry, which is computed to lie 3.8 kcal/mol above the reactant at the (12/11)CASPT2/cc-pVTZ//(12/11)CASSCF/cc-pVTZ level of theory. The (12/11)CASSCF/cc-pVTZ value for the lowest frequency vibration in the transition structure is 854 cm{sup {minus}1}, and CASPT2 calculations concur that this a{double{underscore}prime} vibration does indeed have a positive force constant. Thus, there is no evidence that this geometry is actually a mountain top, rather than a transition structure, on the global potential energy surface or that a C{sub 1} pathway of lower energy connects the ...

Wastenet

...Correction Discussion Editorial Letter Opinion Review Short Note Technical Note Special Issue all A Systematic Development Method for Rational Drug Design Advances in Molecular Electronic Structure Calculations Algorithms and Molecular Sciences Antimicrobial Agents Application of Density Functional Theory Applications of Density Functional Theory Applications of Molecular Dynamics Atoms in Molecules ...

UK PubMed Central (United Kingdom)

Advances in modern neuroscience require the identification of principles that connect different levels of experimental analysis, from molecular mechanisms to explanations of cellular functions,...Full Text Available

UK PubMed Central (United Kingdom)

The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target...Full Text Available

International Nuclear Information System (INIS)

We studied the influence of alloying on the structural and electronic properties of the unrelaxed and relaxed Si_1_-_yC_y random alloys by means of ab initio theoretical calculations using two methods: (i) a supercell approach in connection with the plane-wave pseudopotential method; (ii) the full-potential augmented plane-wave plus local orbitals (APW+lo) method. The first method is used to obtain the relaxed atomic structure. The relaxed atomic positions obtained by pseudopotential calculations were used to calculate the band structure via the second method. The local density approximation was used for the exchange and correlation energy density functional. We investigated the lattice parameters and band gap energies. We found that a quite smaller gap appears in the neighborhood of y=0.03125 concentration of C atoms. The band gap shows a large anomalous bowing and is strongly composition dependent. The electron densities of states for the ...

British Library Electronic Table of Contents (United Kingdom)

Some kind of one-dimensional (1D) peanut-shaped fullerene polymers (PSFPs) exhibit metallic properties, but their occurrence conditions are not yet clarified. By using the VASP (Vienna ab-initio simulation package) with density functional theory (DFT) and projector augmented wave (PAW) method, we have performed first-principles electronic structure calculations of four basic 1D PSFPs, T1, T2, T6, and T7 (the name of T1-T6 is the same as that of Wang et al. [9]) and two associated 1D PSFPs, T1SW1 and T6SW that are created by generalized Stone-Wales transformation (GSW) from T1 and T6. We found that almost regular six-membered rings connected throughout the tube are necessary to get metallic properties for the 1D PSFPs, although there may be several other conditions to expect metallic proper...

International Nuclear Information System (INIS)

We have measured the lattice relaxation around As in Si at a homogeneous As concentration of 4x10"1"8 cm"-"3 by EXAFS spectroscopy. From the absorption spectra, distances up to the 4th shell could be extracted. A sizeable misfit due to an increased distance is only observed for the 1st shell. Complementing our experimental work we have performed ab initio calculations based on the density functional theory with the WIEN97 package which uses the linearised augmented plane wave method and with the FHI96md program which uses first-principles pseudo-potentials and a plane wave basis set to investigate the size dependence of the super-cells constructed around one substitutional As atom. The calculations yielded good agreement with our EXAFS experiment so that the determined relaxations can be used as a solid basis for further interpretations of derived parameters such as hyperfine interaction parameters in defect complexes.

International Nuclear Information System (INIS)

In the presence of hydroxyl anion, both formaldehyde and glyoxal are known to undergo rearrangements involving intermolecular and intramolecular hydride transfer (the Cannizzaro and Benzilic acid rearrangements respectively). The authors report ab initio SCF-MO calculations of the transition state geometries, the activation barriers, and the hydrogen isotope effects for these two reactions. The structure of the transition state for the rection involving formaldehyde is usually basis set dependent, becoming more linear and symmetrical as the basis set size increases. In contrast, the analogous transition state for the glyoxal reaction involves a highly non-linear hydride transfer. They find the isotope effects to be quite low for the Cannizzaro reaction, and significantly larger for the non-linear benzilic acid rection, in apparent contradiction to Westheimer's suggestion the isotope effects reach a maximum for linear hydrogen transfers. Since ...

Energy Technology Data Exchange (ETDEWEB)

The isotope shifts of the levels 5p/sup 2/ /sup 1/D/sub 2/, /sup 1/S/sub 0/ and 5sns /sup 1/S/sub 0/(n = 7,8) of strontium have been measured between the isotopes 84, 86, 87 and 88 in two-photon transitions from the ground state, using two lasers with different wavelengths. These levels occur below the beginning of the Rydberg series, and are known to exhibit very strong configuration mixing. Mass and field isotope shifts are calculated ab initio by means of the MCHF method for these levels and 5s4d /sup 1/D2, 5s6s /sup 1/S/sub 0/. The qualitative agreement between theory and experiment confirms the necessity of taking into account the mixing (up to 50%) with both the 5p/sup 2/ and 4d/sup 2/ perturbers in the wavefunction expansions.

CERN Document Server

We show that accretion disks, both in the subcritical and supercritical accretion rate regime, may exhibit significant amplitude luminosity oscillations. The luminosity time behavior has been obtained by performing a set of time-dependent 2D SPH simulations of accretion disks with different values of alpha and accretion rate. In this study, to avoid any influence of the initial disk configuration, we produced the disks injecting matter from an outer edge far from the central object. The period of oscillations is 2 - 50 s respectively for the two cases, and the variation amplitude of the disc luminosity is 10^38 - 10^39 erg/s. An explanation of this luminosity behavior is proposed in terms of limit cycle instability: the disk oscillates between a radiation pressure dominated configuration (with a high luminosity value) and a gas pressure dominated one (with a low luminosity value). The origin of this instability is the difference between the heat produced by viscosity and the energy ...

CERN Document Server

Without using any moduli, sheaves, stacks, nor any analytic, nor category-type arguments, we exhibit an analogue to Geometric Langlands Theory in an entirely model-independent, non-perturbative,purely smooth topological context in Artin Presentation Theory. A basic initial feature is that AP Theory, as a whole, is already, ab initio, a universal canonical 2D sigma-model, targeting smooth, compact, simply-connected 4-manifolds with a connected boundary, and its topological Planckian quantum starting point, as well as its cone-like, infinitely-generated at each stage, graded group of homology-preserving, but topology-changing transitions/interactions, exhibit the most general qualitative S-duality. We first point out the numerous mathematically rigorous, model-free, (i.e., intrinsic), topological AP analogues with the heuristic Kapustin-Witten version of Geometric Langlands theory, as well as the crucial differences between the two theories. The ...

International Nuclear Information System (INIS)

This paper is concerned with the determination of a unique scaling parameter in complex scaling analysis and with accurate calculation of dynamics resonances. In the preceding paper we have presented a theoretical analysis and provided a formalism for dynamical resonance calculations. In this paper we present accurate numerical results for two non-trivial dynamical processes, namely, models of diatomic molecular predissociation and of barrier potential scattering for resonances. The results presented in this paper confirm our theoretical analysis, remove a theoretical ambiguity on determination of the complex scaling parameter, and provide an improved understanding for dynamical resonance calculations in rigged Hilbert space.

CERN Document Server

We investigate the chemical and observational implications of repetitive transient dense core formation in molecular clouds. We allow a transient density fluctuation to form and disperse over a period of 1 Myr, tracing its chemical evolution. We then allow the same gas immediately to undergo further such formation and dispersion cycles. The chemistry of the dense gas in subsequent cycles is similar to that of the first, and a limit cycle is reached quickly (2 - 3 cycles). Enhancement of hydrocarbon abundances during a specific period of evolution is the strongest indicator of previous dynamical history. The molecular content of the diffuse background gas in the molecular cloud is expected to be strongly enhanced by the core formation and dispersion process. Such enhancement may remain for as long as 0.5 Myr. The frequency of repetitive core formation should strongly determine the level of background ...

British Library Electronic Table of Contents (United Kingdom)

Orientational constraints obtained from solid state NMR experiments on anisotropic samples are used here in molecular dynamics (MD) simulations for determining the structure and dynamics of several different membrane-bound molecules. The new MD technique is based on the inclusion of orientation dependent pseudo-forces in the COSMOS-NMR force field. These forces drive molecular rotations and re-orientations in the simulation, such that the motional time-averages of the tensorial NMR properties approach the experimentally measured parameters. The orientational-constraint-driven MD simulations are universally applicable to all NMR interaction tensors, such as chemical shifts, dipolar couplings and quadrupolar interactions. The strategy does not depend on the initial choice of coordinates, and...

UK PubMed Central (United Kingdom)

BackgroundGene promoters can be in various epigenetic states and undergo interactions with many molecules in a highly transient, probabilistic and combinatorial way, resulting in...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

Although studied for many years the nature of the light scalar mesons remains controversial. Here we shall present a method, applicable for s-wave states located close to a threshold, that allows one to quantify the molecular part of a given state. When applied to the f{sub 0}(980) a dominance of the molecular component is found. In the second part, we show that requirements of field-theoretic consistency and chiral symmetry, when applied to the scattering of light pseudo-scalars, naturally lead to the appearance of dynamical poles in the scalar sector. A program is proposed on how to further investigate experimentally the mixing between these dynamical states and possible genuine quark states. (orig.)

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This contribution is an informal essay based on a talk delivered at the Institute for Mathematics and its Applications (IMA) in Minneapolis, under the summer program in molecular biology, July 18-22, 1994. I exclude many technical details, which can be found elsewhere, and instead focus on the basic ideas of molecular dynamics simulations, with the goal of conveying to students and non-specialists the key concepts of the theory and practice of large-scale simulations. Following a description of the basic idea in molecular dynamics, I discuss some of the practical details involved in simulations of large biological molecules, the numerical timestep problem, and approaches to this problem based on implicit-integration techniques. I end with a perspective of open challenges in the field and directions for future research. 79 refs., 6 figs., 1 tab.

International Nuclear Information System (INIS)

A formalism for the dynamical treatment of the molecular orbitals of valence nucleons in nucleus-nucleus collisions is developed with the use of the coupled-reaction-channel (CRC) method. The Coriolis coupling effects as well as the finite mass effects of the nucleon are taken into account in this model, of rotating molecular orbitals, RMO. First, the validity of the concept is examined from the viewpoint of the multi-step processes in a standard CRC calculation for systems containing two identical [core] nuclei. The calculations show strong CRC effects particularly in the case where the mixing of different l-parity orbitals - called hybridization in atomic physics - occurs. Then, the RMO representation for active nucleons is applied to the same systems and compared to the CRC results. Its validity is investigated with respect to the radial motion (adiabaticity) and the rotation of the molecular axis ...

International Nuclear Information System (INIS)

The effects of hydrostatic pressure on the electronic band structure of the semiconductor mineral iron pyrite FeS_2 have been investigated theoretically by an ab initio full-potential linearized-augmented plane wave (FPLAPW) method within a local approximation (LDA/GGA) to the density functional theory. The calculations predict that at a pressure of 94.1 GPa the indirect band gap of pyrite FeS_2 vanishes and the material becomes a metal. This is due to the presence of the S-S and Fe-S bonds, which provide novel energy band distortions in the process of attaining the metallic state. Analysis indicates that, under increasing high pressure, the conduction bands (3p_z of sulfur and 3d_x_"2_-_y_"2+3d_x_y of iron) intrude downwards into the valence bands, which are predominantly 3d in nature. At normal pressure, the lattice constant, the bulk modulus, sulfur position parameter u, S-S bond length, and the indirect band gap of pyrite FeS_2 are ...

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From the crystal field analysis of optical absorption spectra on monoclinic S.G. P2{sub 1}/c MgNd(BO{sub 2}){sub 5}, where Nd{sup 3+} occupies a single crystallographic position with no symmetry elements, energy level schemes and an expression of the associated wavefunctions for the 4f{sup 3} configuration of Nd{sup 3+} have been derived, considering approximate C{sub 2v} and C{sub s} (C{sub 2}) symmetries. Despite of the low symmetry of Nd{sup 3+}, resulting rms deviations between calculated and experimental levels are very satisfactory. The composition of the crystal field wavefunctions from both sets of phenomenological free-ion and crystal field parameters has been checked through a calculation of the thermal evolution of the paramagnetic susceptibility {chi}, according to the Van Vleck formula. The same simulation was performed with crystal field parameters (CFPs) resulting from the ab initio simple overlap model (SOM), considering the ...

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The reactions of CF{sub 3}O radicals with (1) NO and (2) NO{sub 2} were studied using two different experimental techniques. A laser photolysis/LIF detection method was applied for measuring the rate constants as a function of temperature (T=222-302 K) and total pressure (p{sub tot}=7-107 mbar). Whereas the reaction with (1) NO was found to be independent of temperature and pressure with k{sub 1}=(4.5{+-}1.2) x 10{sup -11} cm{sup 3}s{sup -1}, the reaction with (2) NO{sub 2} was found to be dependent on both of these variables. The temperature dependence of k{sub 2} in the high pressure limit can be given by the expression k{sub 2{infinity}}{sup -}(T)=(8{+-}5) x 10{sup -13} exp ((863{+-}194) K/T) cm{sup 3}s{sup -1}. The product distributions of the two reactions were determined in separate experiments using steady-state photolysis combined with FTIR spectroscopy. For reaction (1) only CF{sub 2}O was found as a reaction product with a yield of 0.93{+-}0.10, independent of temperature. ...

International Nuclear Information System (INIS)

We use the Generalized Quasi-Chemical Approach (GQCA) combined with ab initio ultrasoft pseudopotential calculations within density functional theory in order to obtain the structural and electronic properties of Al_xGa_yIn_1_-_x_-_yX (X=As, P or N) quaternary alloys in the zincblende structure. Results for the bond lengths show that their variations with composition are approximately linear and that they do not deviate much from the values of the corresponding binary compounds. For the variation of the band gaps, we obtain a bowing parameter b=0.26 eV for the (Ga_0_._4_7In_0_._5_3As)_z(Al_0_._4_8In_0_._5_2As)_1_-_z quaternary alloy lattice matched to InP, in very good agreement with experimental data. In the case of AlGaInN, a bowing parameter of 0.22 eV is obtained for zincblende AlGaInN lattice matched to GaN. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Energy Technology Data Exchange (ETDEWEB)

The total and state-specific electron-ion recombination rate coefficients are obtained for FeI. The calculations are carried out using a new ab initio method that incorporates both the radiative and the dielectronic recombination processes in an unified and self-consistent manner. The computations employ the close coupling approximation and the R-matrix method from atomic collision theory. A 52 state close coupling eigenfunction expansion dominated by the states of the ground 3d{sup 6}4s and excited 3d{sup 7}, 3d{sup 6}4p, 3d{sup 5}4s{sup 2}, and 3d{sup 5}4s4p configurations of FeII are used in the present calculations. The important electron correlation and radiation damping effects are included via explicit coupling of autoionization and radiative channels. This is the first detailed atomic calculation for the recombination rates for FeI. The present rates are considerably higher than the radiative recombination rates being used currently in ...

International Nuclear Information System (INIS)

Ab initio total energy calculations within the framework of density functional theory have been performed for atomic hydrogen and oxygen chemisorption on the (0001) surface of double hexagonal packed (dhcp) americium using a full-potential all-electron linearized augmented plane wave plus local orbitals method. Chemisorption energies were optimized with respect to the distance of the adatom from the relaxed surface for three adsorption sites, namely top, bridge, and hollow hcp sites, the ad-layer structure corresponding to the coverage of a 0.25 monolayer in all cases. Chemisorption energies were computed at the scalar-relativistic level (no spin-orbit coupling NSOC) and at the fully relativistic level (with spin-orbit coupling SOC). The two-fold bridge adsorption site was found to be the most stable site for O at both the NSOC and SOC theoretical levels with chemisorption energies of 8.204 eV and 8.368 eV respectively, while the three-fold ...

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Orientational constraints obtained from solid state NMR experiments on anisotropic samples are used here in molecular dynamics (MD) simulations for determining the structure and dynamics of several different membrane-bound molecules. The new MD technique is based on the inclusion of orientation dependent pseudo-forces in the COSMOS-NMR force field. These forces drive molecular rotations and re-orientations in the simulation, such that the motional time-averages of the tensorial NMR properties approach the experimentally measured parameters. The orientational-constraint-driven MD simulations are universally applicable to all NMR interaction tensors, such as chemical shifts, dipolar couplings and quadrupolar interactions. The strategy does not depend on the initial choice of coordinates, and is in principle suitable for any flexible molecule. To test the method on three systems of increasing complexity, ...

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The buckling behaviors of double-walled carbon nanotubes (DWCNTs) under torsion are investigated by using molecular dynamics (MD) simulations. The effect of length on the torsional buckling behaviors of DWCNTs is examined for the first time. The simulation results show that the DWCNTs experience gradual or simultaneous buckling deformations depending on their lengths. In addition, the effect of the inner tube in a DWCNT on its torsional buckling behavior is also examined. The presence of the inner tube triggers van der Waals (vdW) interactions between it and the outer tube and thus leads to a stiffening effect of the DWCNT against torsional deformation. Whether the ends of the inner tube are free or fixed and whether it is subject to a torque or not, the critical torque and the critical torsional angle of the outer tube are only marginally affected.

British Library Electronic Table of Contents (United Kingdom)

Thin films of Ni and Ni alloy have been widely used in microelectromechanical systems (MEMS) and magnetic storage systems. As the dimensions of components in these systems decrease to the micro-scale, even the nano-scale, the interfacial phenomena significantly differ to the counterparts on the macro-scale. A better understanding of micro-/nano-tribology will benefit the fabrication of the small components. In this manuscript parallel molecular dynamics (MD) simulations have been conducted to investigate the nanoscratch behavior of nickel. The simulations are performed for two cases with different indenter shapes. Case I has a sharp indenter, while the indenter in Case II is blunt. It has been found that the indenter shape significantly influences the nanoscratch deformation. The sharp ind...

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Abstract The air-water interface presents several interesting features, namely a) a molecularly flat environment, b) a boundary region between two phases with different dielectric constants, c) permits or promotes dynamic interactions within the interface region, and d) a point of interaction between hydrophobic compounds and aqueous molecules. Accordingly, Langmuir monolayers at the air-water interface have several unique characteristics and properties, which require investigation. In this review-type personal account, typical examples of molecular recognition and molecular patterning at air-water interfaces are first introduced, followed by descriptions of specific and unusual properties of monolayers on water. In addition, two examples of our own results concerning Langmuir monolayers a...

CERN Document Server

We have used the SINFONI integral field spectrograph to map the near-infrared K-band emission lines of molecular and ionised hydrogen in the central regions of two cool core galaxy clusters, Abell 2597 and Sersic 159-03. Gas is detected out to 20 kpc from the nuclei of the brightest cluster galaxies and found to be distributed in clumps and filaments around it. The ionised and molecular gas phases trace each other closely in extent and dynamical state. Both gas phases show signs of interaction with the active nucleus. Within the nuclear regions the kinetic luminosity of this gas is found to be somewhat smaller than the current radio luminosity. Outside the nuclear region the gas has a low velocity dispersion and shows smooth velocity gradients. There is no strong correlation between the intensity of the molecular and ionised gas emission and either the radio or X-ray emission. The ...

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Classical molecular dynamics simulations are carried out to investigate the salvation shell exchange kinetics of potassium ion in bulk water, chloroform, and carbon tetrachloride. The reactive flux method is used to compute the dissociation rates. The influence of the solvent on the reaction rates and kinetic properties of this exchange process will be discussed. Comparison will be also be made to the prediction of the Grote-Hynes theory.

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A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to assess the validity and reproducibility of different sampling approaches. These simulations include Car-Parrinello molecular dynamics simulations using the program CPMD with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born-Oppenheimer molecular dynamics using the programs CPMD and CP2K in the microcanonical ensemble, and Metropolis Monte Carlo using CP2K in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. It is found that the structural and thermodynamic properties of these simulations are in excellent agreement with each other as long as adiabatic sampling is maintained in the ...

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The authors consider the dynamics of interacting elastic disks in the plane. This is an experimentally realizable two-dimensional model of dry granular flow where the stresses can be visualized using the photoelastic effect. As the elastic disks move in a vacuum, they interact through collisions with each other and with the surrounding geometry. Because of the finite propagation speed of deformations inside each grain it can be difficult to capture computationally even simple experiments involving just a few interacting grains. The goal of this project is to improve our ability to simulate dense granular flow in complex geometry. They begin this process by reviewing some past work, how they can improve upon previous work. the focus of this project is on capturing the elastic dynamics of each grain in an approximate, computationally tractable, model that can be coupled to a molecular dynamics scheme.

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The development of nano/molecular devices will require atomic-sized electrical contacts or nano metric conductors for wiring. As metal nano wires exhibit quantized conductance at room temperature, quantum transport effects will play an important role in the practical implementation of nano devices. As copper is currently used as interconnecting metal in standard microelectronics, the characterization of Cu nano wire properties deserves special attention. In this work, we show a detailed study of structural and electronic properties of atomic-sized Cu wires. In particular, we have established a complete correlation between the conductance and the structure by associating real-time atomic resolution transmission electron microscopy imaging with molecular dynamic simulations, conductance measurements and conductance calculations. Our study has revealed the structural relaxation of Cu wires forming a pentagonal atomic ...

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The herpes simplex virus type 1 thymidine kinase (HSV1-TK) reporter system is being used to directly and indirectly monitor therapeutic gene expression, immune cell trafficking and protein-protein interactions in various living animals. However, the issues of HSV1-TK enzyme stability in living cells and whether this reporter system is optimal for dynamic studies of gene expression events in genetic imaging have not be addressed. The purpose of the present study was to evaluate the application of this reporter system in dynamic studies of transcriptional gene regulation. To achieve this purpose, we established two tetracycline-inducible murine sarcoma cell lines, tetracycline-turn-off HSV1-tk-expressing cell line (NG4TL4/tet-off-HSV1-tk) and tetracycline-turn-off Luc-expressing cell line (NG4TL4/tet-off-Luc), to create an artificially regulated gene expression model in vitro. The dynamic transcriptional events mediating a ...

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The interaction between molecules and solid surfaces plays important roles in various applications, including catalysis, sensors, nanoelectronics, and solar cells. Surprisingly, a full understanding of molecule-surface interaction at the quantum mechanical level has not been achieved even for very simple molecules, such as water. In this mini-review, we report recent progresses and current status of studies on interaction between representative molecules and surfaces. Taking water/metal, DNA bases/carbon nanotube, and organic dye molecule/oxide as examples, we focus on the understanding on the microstructure, electronic property, and electron-ion dynamics involved in these systems obtained from first-principles quantum mechanical calculations. We find that a quantum mechanical description ...

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Large-scale three dimensional molecular dynamics simulations of hopper flow are presented. The flow rate of the system is controlled by the width of the aperture at the bottom. As the steady-state flow rate is reduced, the force distribution P(f) changes only slightly, while there is a large change in the impulse distribution P(i). In both cases, the distributions show an increase in small forces or impulses as the systems approach jamming, the opposite of that seen in previous Lennard-Jones simulations. This occurs dynamically as well for a hopper that transitions from a flowing to a jammed state over time. The final jammed P(f) is quite distinct from a poured packing P(f) in the same geometry. The change in P(i) is a much stronger indicator of the approach to jamming. The formation of a peak or plateau in P(f) at the average force is not a general feature of the approach to jamming.

International Nuclear Information System (INIS)

Angelin Pedra is a specie found in the north of Mato Grosso State in Brazil, where an expressive volume of waste of this wood is produced. An alternative to recycle this waste is to produce wood plastic composites. However, structural and chemical investigations are fundamental to generate information for this use. In the present work, low field NMR was used to determine the spin-lattice and spin-spin relaxation times with objective to investigate the molecular dynamic behavior of the alburnu and cerne regions of Angelin Pedra aiming at a potential use of this waste wood in polymeric composites. The results of the proton spin-lattice relaxation time (T1H) and the proton spin-spin relaxation time (T2H) showed at least three different mobility domains for both regions. Among the values, one was very flexible and other was rigid. Knowing that wood is a polymer composite basically constituted by cellulose, hemicellulose and lignin can attribute the ...

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We have performed a detailed analysis of water clustering and percolation in hydrated Nafion configurations generated by classical molecular dynamics simulations. Our results show that at low hydration levels H2O molecules are isolated and a continuous hydrogen-bonded network forms as the hydration level is increased. Our quantitative analysis has established a hydration level (?) between 5 and 6 H2O/SO3- as the percolation threshold of Nafion. We have also examined the effect of such a network on proton transport by studying the structural diffusion of protons using the quantum hopping molecular dynamics method. The mean residence time of the proton on a water molecule decreases by two orders of magnitude when the ? value is increased from 5 to 15. The proton diffusion coefficient in Nafion at a ? value of 15 is about 1.1x10-5 cm2/s in agreement with experiment. The results provide quantitative ...

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We numerically constructed elementary phase-correct global quantum gates by using molecular electronic and vibrational states to encode two qubits and implement the Deutsch-Jozsa algorithm. The calculations were based on optimal control theory (OCT). The molecular species we chose were Na{sub 2} and Li{sub 2}. The electronic X{sup 1}{sigma}{sub g}{sup +} and A{sup 1}{sigma}{sub u}{sup +} states were taken as two orthonormalized energy levels of the electronic qubit. The vibrational qubits were those involved in these electronic states. The time duration of the optimized pulses with high fidelity was typically 500-900 fs, which reflects the wavepacket dynamics in electronically ground and excited states. When implementing the Deutsch-Jozsa algorithm by combining these elementary gates, we obtained a maximum probability 83.12% for Li{sub 2} molecule, which indicates that the electronic-vibrational qubits are worse than the ...

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The computer aided coal structure construction system is proposed, and a computational construction example is presented. The coal structure construction engine of this system fabricates molecular structure by connecting fragments sequentially inputted through a user interface. The best structure candidate is determined using construction knowledge and partial energy evaluation every addition of one fragment, and this process is subsequently repeated. The structure evaluation engine analyzes the 3-D conformation candidate by molecular dynamics, and evaluates the conformation by determining the energy value of an optimum structure. As an example, this system was applied to construction of coal molecular structure based on the actual data of partial structure composed of 26 structures from 2l kinds of aromatic cluster structures, 27 bonds from 2 kinds of bridged bonds, and 16 groups from 2 kinds of ...

International Nuclear Information System (INIS)

We have performed molecular dynamics simulations of radiation damage in fused silica. In this study, we discuss the role of successive cascade overlap on the saturation and self-healing of oxygen vacancy defects in the amorphous fused silica network. Furthermore, we present findings on the topological changes in fused silica due to repeated energetic recoil atoms. These topological network modifications consistent with experimental Raman spectroscopic observation on neutron and ion irradiated fused silica are indicators of permanent densification that has also been observed experimentally.

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The primary objective is to perform a fundamental study of filtration of nanoparticles, and to obtain filtration knowledge necessary to design particle collection devices/systems for nanoparticle processing and for preventing nanoparticle emissions into the environment. The research covered a wide area relevant to nanoparticle filtration, under these main topics: (1) nanoparticle filtration and molecular dynamics simulation, (2) nanoparticle virtual impactor, (3) particle transport under low pressure, and (4) development of a high-throughput nanoparticle generator. A number of novel tools and numerical models have been developed under the DOE support.

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This paper is devoted to investigate the influences of thermal dispersion and magnetic field on a hot semi-infinite vertical porous plate embedded in a saturated Darcy-Forchheimer-Brinkman porous medium. The coefficient of thermal diffusivity has been assumed to be the sum of the molecular diffusivity and the dynamic diffusivity due to mechanical dispersion. The effects of transverse magnetic field parameter (Hartmann number Ha), Reynolds number Re (different velocities), Prandtl number Pr (different types of fluids) and dispersion parameter on the wall shear stress and the heat transfer rate are discussed.

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The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory-and of its extension to other Lie and quantum groups-by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to ...

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The wavefunction of a particle extends into the classically forbidden barrier region of the potential energy surface. The consequence of this partial delocalisation is the phenomenon of quantum tunnelling, an effect which enables a particle to penetrate a potential barrier of magnitude greater than the energy of the particle. The tunnelling probability is an exponential function of the particle mass. The effect is therefore an important contribution to the behaviour of light atoms, in particular the proton. The hydrogen bond has long been appreciated to be an essential component of many biological and chemical systems, and the proton transfer reaction in the hydrogen bond is fundamental to many of these processes. The proton behaviour in the hydrogen bonds of benzoic acid, acetylacetone and calix-4-arene has been studied. A variety of techniques, both experimental and computational, were adopted for the study of the three hydrogen bonded systems. The complementary spectroscopic ...

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Molecular simulation aims at simulating particles in interaction, describing a physico-chemical system. When considering Markov Chain Monte Carlo sampling in this context, we often meet the same problem of statistical efficiency as with Molecular Dynamics for the simulation of complex molecules (polymers for example). The search for a correct sampling of the space of possible configurations with respect to the Boltzmann-Gibbs distribution is directly related to the statistical efficiency of such algorithms (i.e. the ability of rapidly providing uncorrelated states covering all the configuration space). We investigated how to improve this efficiency with the help of Artificial Evolution (AE). AE algorithms form a class of stochastic optimization algorithms inspired by Darwinian evolution. Efficiency measures that can be turned into efficiency criteria have been first searched before identifying parameters that could be ...

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When liquids are confined in nano-scopic dimensions, their properties differ from the corresponding bulk liquid, due to their reduced dimensionality and surface effects. Phase transition temperatures and pressures are often shifted from the bulk values and new phases can appear due to the strong interactions of the molecules with the confining walls. We have studied the structural and dynamical properties of aromatic liquids such as benzene, toluene, and ortho-terphenyl confined in nano-porous materials, MCM-41 and SBA-15, synthesized and characterized in our laboratory. A non-trivial dependence of the glass transition temperature, T{sub g}, on the pore size and surface treatment of nano-porous materials is confirmed and interpreted as resulting from a competition between the fluid-wall and fluid-fluid intermolecular interactions. An increase of T{sub g} is observed for small pore sizes and attractive surface while T{sub g} decreases for non attractive surface, ...

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Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized states, unliganded GroEL, ATP?S-bound, ADP-AlFx/GroES-bound, and ADP/GroES bound, using translation-libration-screw (TLS) analysis. Remarkably, the TLS results show that the inherent motions of unliganded GroEL, a polypeptide-accepting state, are biased along the transition pathway that leads to the folding-active state. In the ADP-AlFx/GroES-bound folding-active state the dynamic modes of the apical domains become reoriented and coupled to the motions of bound GroES. The ADP/GroES complex exhibits these same motions, but they are increased in magnitude, potentially reflecting the decreased stability of the complex after nucleotide hydrolysis. Our results ...

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The diffusion of methane confined in nano-porous carbon aerogel with the average pore size 48 {angstrom} and porosity 60% was investigated as a function of pressure at T = 298 K using quasi-elastic neutron scattering (QENS). The diffusivity of methane shows a clear effect of confinement: it is about two orders of magnitude lower than in bulk at the same thermodynamic conditions and is close to the diffusivity of liquid methane at 100 K (i.e. {approx} 90 K below the liquid-gas critical temperature T{sub C} {approx} 191 K). The diffusion coefficient (D) of methane initially increases with pressure by a factor of {approx}2.5 from 3.47 {+-} 0.41 x 10{sup -10} m{sup 2} s{sup -1} at 0.482 MPa to D = 8.55 {+-} 0.33 x 10{sup -10} m{sup 2} s{sup -1} at 2.75 MPa and starts to decrease at higher pressures. An explanation of the observed non-monotonic behavior of the diffusivity in the confined fluid is based on the results of small-angle neutron scattering experiments of the phase behavior of ...

British Library Electronic Table of Contents (United Kingdom)

Abstract Grazing incidence X-ray diffraction (GI-XRD) is used to characterize the crystallographic dynamics of low molecular weight (LMW) and high molecular weight (HMW) poly(3-hexylselenophene) (P3HS) films and blend films of P3HS with [6-6-]-phenyl-C61-butyric acid methyl ester (PCBM) as a function of -step-by-step- thermal annealing, from room temperature to 250-C. The temperature-dependent GIXRD data show how the melting point of P3HS crystallites is decreased by the presence of PCBM. P3HS crystallite domain sizes dramatically increase upon annealing to the P3HS melting temperature. The formation of well-oriented HMW P3HS crystallites with the (100) plane parallel to the substrate (edge-on orientation), when cooled from melt, are observed. We compare the behaviour of P3HS pure and blen...

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The utilization of thermal fluctuations or Johnson/Nyquist noise as a spectroscopic method to determine transport properties in conductors or semiconductors is developed. The autocorrelation function is obtained from power spectral density measurements thus enabling electronic transport property calculation through the Green-Kubo formalism. This experimental approach is distinct from traditional numerical methods such as molecular dynamics simulations, which have been used to extract the autocorrelation function and directly related physics only. This work reports multi-transport property measurements consisting of the electronic relaxation time, resistivity, mobility, diffusion coefficient, electronic contribution to thermal conductivity and Lorenz number from experimental data. Double va...

British Library Electronic Table of Contents (United Kingdom)

SummaryBackground Intracellular transport via processive kinesin, dynein, and myosin molecular motors plays an important role in maintaining cell structure and function. In many cases, cargoes move distances longer than expected for single motors; there is significant evidence that this increased travel is in part due to multiple motors working together to move the cargoes. Although we understand single motors experimentally and theoretically, our understanding of multiple motors working together is less developed. Results We theoretically investigate how multiple kinesin motors function. Our model includes stochastic fluctuations of each motor as it proceeds through its enzymatic cycle. Motors dynamically influence each other and function in the presence of thermal noise and viscosity. We...

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Raman and infrared spectroscopy of para-H{sub 2} to pressures in excess of 200GPa and to 8K using new ultrapure synthetic diamond anvils reveals numerous new vibrational excitations in the three high-pressure phases. Highly resolved Raman-active librons indicate differences in orientational ordering between phasesII and III, including evidence for changes within phaseII. The librons in phaseIII are strongly pressure dependent and reflect a substantial increase in ordering with pressure. Multiple vibrons in all three phases (I, II, and III) are observed. The results place new bounds on predicted crystal structures and dynamics of the dense molecular solid. {copyright} {ital 1997} {ital The American Physical Society}

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Molecular dynamics simulations have been carried out of the radial distribution function of the hard sphere fluid for a range of densities in the equilibrium fluid and just into the metastable region. The first derivative of the hard-sphere radial distribution function at contact was computed and its density dependence fitted to a simple analytic form. Comparisons were made with semi-empirical formulae from the literature, and of these the formula proposed by Tao et al (1992 Phys. Rev. A 46 8007) was found to be in best agreement with the simulation data, although it slightly underestimates the derivative at the higher packing fractions in excess of about 0.45. Close to contact, within a few per cent of the particle diameter, the radial distribution function can be represented well by a second order polynomial. An exponential function, which has some useful analytic features, can also be applied in this region.

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Although computer simulation has played a central role in the study of nucleation and growth since the earliest molecular dynamics simulations almost 50 years ago, confusion surrounding the effect of finite size on such simulations have limited their applicability. Modeling solidification in molten tantalum on the BlueGene/L computer, we report here on the first atomistic simulation of solidification that verifies independence from finite size effects during the entire nucleation and growth process, up to the onset of coarsening. We show that finite size scaling theory explains the observed maximal grain sizes for systems up to about 8,000,000 atoms. For larger simulations, a cross-over from finite size scaling to more physical size-independent behavior is observed.

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We review our recent work on an atomistic approach to the development of predictive process simulation tools. First principles methods, molecular dynamics simulations, and experimental results are used to construct a database of defect and dopant energetics in Si. This is used as input for kinetic Monte Carlo simulations. C and B trapping of the Si self- interstitial is shown to help explain the enormous disparity in its measured diffusivity. Excellent agreement is found between experiments and simulations of transient enhanced diffusion following 20-80 keV B implants into Si, and with those of 50 keV Si implants into complex B-doped structures. Our simulations predict novel behavior of the time evolution of the electrically active B fraction during annealing.

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Here we present evidence that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. An NMR-derived human insulin monomer structure in H{sub 2}O/CD{sub 3}CN, 65/35 vol%, pH 3.6 is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Acta Crystallogr. 2003 Sec. D59, 474) and with NMR structures in water and organic cosolvent. Detailed analysis using PFGSE NMR, temperature-dependent NMR, dilution experiments and CSI proves that the structure is monomeric in the concentration and temperature ranges 0.1-3 mM and 10-30 deg. C, respectively. The presence of long-range interstrand NOEs, as found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Starting from structures calculated by the program CYANA, two different molecular ...

Science.gov (United States)

Genetics, Genomics, and Molecular Biology USGS scientists develop and integrate new genetic and molecular techniques into systematic analyses to describe individuals and populations of fish .....

CERN Document Server

The composition of the lower mantle can be investigated by examining densities and seismic velocities of compositional models as functions of depth. In order to do this, it is necessary to know the volumes and thermoelastic properties of the compositional constituents under lower mantle conditions. We determined the thermal equation of state (EoS) of MgSiO3 perovskite using the non-empirical VIB interatomic potential with molecular dynamics simulations at pressures and temperatures of the lower mantle. We fit our P-V-T results to a thermal EoS of the form P(V,T) = P0(V,T0) + Delta Pth(T), where T0 = 300 K and P0 is the isothermal Universal EoS. The thermal pressure Delta Pth can be represented by a linear relationship Delta Pth = a + b T. We find V0 = 165.40 A^3, KT0 = 273 GPa, K'T0 = 3.86, a = -1.99 GPa, and b = 0.00664 GPa/K for pressures of 0-140 GPa and temperatures of 300-3000 K. By fixing V0 to the experimentally determined value of ...

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Analysis of ENSO Dynamics and ThermoDynamics in the Western Pacific Warm Pool - An Application of Multi-Sensor Satellite Observations. ...

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Energy Technology Data Exchange (ETDEWEB)

In the present work temperature dependences of heat capacity of carbosilane dendrimers with butyl terminal groups of the third and the fourth generations as well as of the fifth and the sixth generations have been determined first in the range from 6 to 340K and between 6 and 600K, respectively, by precision adiabatic vacuum and dynamic calorimetry. In the above temperature ranges the physical transformations have been detected and their thermodynamic characteristics have been estimated and analyzed. The experimental data were used to calculate standard thermodynamic functions, namely the heat capacity C{sub p}{sup o}(T), enthalpy H{sup o}(T)-H{sup o}(0), entropy S{sup o}(T)-S{sup o}(0) and Gibbs function G{sup o}(T)-H{sup o}(T), for the range from T->0 to (340-600)K. Linear dependences of changing the corresponding thermodynamic functions of the dendrimers on their molecular weight and the number of butyl groups on an outer sphere have ...

International Nuclear Information System (INIS)

Benchmark calculations of differential neutron yields were made for intranuclear cascade evaporation (INCE) codes HETC/KFA1 and HIC, and a quantum molecular dynamics (QMD) code. The INCE model showed fairly well productibility of the data. The QMD generally gave better results than the INCE model. At lower energies, the QMD gave overprediction to the measured data, but the relative variation of the data was very well reproduced by the method. Neutron production cross sections were systematically estimated at 337 MeV/u for combinations of several projectiles and targets. Using the obtained cross sections, analytical expressions for cross sections of equilibrium and nonequilibrium neutron productions previously proposed at lower energy range through the analysis of experimental data, were extended to the higher energy. The extended expressions well reproduced the systematic behaviors of the cross sections for the variation of both the projectile ...

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Attacks by herbivorous insects reduce biomass production in willow plantations. The long-term goal of our research is to develop sustainable plant protection against these insect pests. Two lines of research are pursued. The first concentrates on identifying factors involved in the regulation of leaf-eating beetles. These insects vary in density among plantations, sometimes reaching outbreak levels resulting in complete defoliation. Mortality factors of eggs and larvae in plantations with low and high beetle densities have been investigated. The importance of plant resistance has also been investigated. The second line of research considers the mechanisms behind an earlier demonstrated resistance in certain willow clones against a gall midge. By using molecular techniques we have searched for markers of resistance. Promising results have been found concerning so called PR proteins; in particular chitinase seems to be present in high activities in plants expressing ...

British Library Electronic Table of Contents (United Kingdom)

A tertiary structure of recombinant A22^G-B31^K-B32^R-human insulin monomer (insulin GKR) has been characterized by ^1H, ^1^3C NMR at natural isotopic abundance using NOESY, TOCSY, ^1H/^1^3C-GHSQC, and ^1H/^1^3C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculation...

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This thesis consists of five chapters, each of which is a self-contained unit. The first chapter overviews methods for electronic-structure calculations. Chapter 2 introduces a new method to generate a rapidly converging configuration expansion. The approach iteratively combines (1) a least-squares fitting of a configuration expansion to a many-body wave function with (2) a transfer-matrix method for projecting out the ground state. Results are shown to be equivalent to multiconfiguration Hartree-Fock. Results from test calculations are given for a simple finite difference model of the helium atom. In Chapter 3 the use of the finite-element method in electronic structure calculations is discussed. Chapters 4 and 5 discuss developments in Monte Carlo methods based on Hubbard-Stratonovich transformations. Chapter 4 introduces a canonical ensemble formulation of the method, which is more appropriate than the usual grand canonical formulation for electronic structure. Chapter 5 considers ...

Science.gov (United States)

Understanding the influence of interfacial structures on the nanoarchitecture mechanical properties is of particular importance for its mechanical applications. Due to a small size of constituting nanostructural units and a consequently high volume ratio of such interfacial regions, this question becomes crucial for the overall mechanical performance. Boron nitride bamboo-like nanotubes, called hereafter boron nitride nanobamboos (BNNBs), are composed of short BN nanotubular segments with specific interfaces at the bamboo-shaped joints. In this work, the mechanical properties of such structures are investigated by using direct in situ transmission electron microscopy tensile tests and molecular dynamics simulations. The mechanical properties and deformation behaviors are correlated with the interfacial structure under atomic resolution, and a geometry strengthening effect is clearly demonstrated. Due to the interlocked joint interfacial ...

Science.gov (United States)

Symplastic transport occurs between neighbouring plant cells through functionally and structurally dynamic channels called plasmodesmata (PD). Relatively little is known about the composition of PD or the mechanisms that facilitate molecular transport into neighbouring cells. While transmission electron microscopy (TEM) provides 2-dimensional information about the structural components of PD, 3-dimensional information is difficult to extract from ultrathin sections. This study has exploited high-resolution scanning electron microscopy (HRSEM) to reveal the 3-dimensional morphology of PD in the cell walls of algae, ferns and higher plants. Varied patterns of PD were observed in the walls, ranging from uniformly distributed individual PD to discrete clusters. Occasionally the thick walls of the giant alga Chara were fractured, revealing the surface morphology of PD within. External structures such as spokes, spirals and mesh were observed ...

Energy Technology Data Exchange (ETDEWEB)

The Pacific Northwest National Laboratory (PNNL) operates a number of research and development (R and D) facilities for the Department of Energy on the Hanford Site. According to DOE Order 5400.1, a Facility Effluent Monitoring Plan is required for each site, facility, or process that uses, generates, releases, or manages significant pollutants or hazardous materials. Three of the R and D facilities: the 325, 331, and 3720 Buildings, are considered major emission points for radionuclide air sampling and thus individual Facility Effluent Monitoring Plans (FEMPs) have been developed for them. Because no definition of ''significant'' is provided in DOE Order 5400.1 or the accompanying regulatory guide DOE/EH-0173T, this FEMP was developed to describe monitoring requirements in the DOE-owned, PNNL-operated facilities that do not have individual FEMPs. The remainder of the DOE-owned, PNNL-operated facilities are referred to as Balance-of-Plant (BOP) ...

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Iron undergoes a polymorphic phase transformation from alpha phase (bcc) to the epsilon phase (hcp) when compressed to stresses exceeding 13 CPa. Bccause the epsilon phase is denser than the alpha phase, a single shock wave is unstable and breaks up into an elastic wave, a plastic wave, and a phase transition wave. Examination of this structured wave coupled with various phase transformation models has been used to indirectly examine the transition kinetics. Recently, multimillion atom simulations (molecular dynamics) have been used to examine the shock-induced transition in single crystal iron illustrating an orientation dependence of the transition stress, mechanisms, and kinetics. The objective of the current work was to perform plate impact experiments to examine the shock-response of polycrystalline and single crystal iron with nanosecond resolution for impact stresses spanning the {alpha} - {epsilon} transition. The current data reveal an ...

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Solid-state nuclear magnetic resonance (NMR) has been used to explore the nanometer-scale structure of Nafion, the widely used fuel cell membrane, and its composites. We have shown that solid-state NMR can characterize chemical structure and composition, domain size and morphology, internuclear distances, molecular dynamics, etc. The newly-developed water channel model of Nafion has been confirmed, and important characteristic length-scales established. Nafion-based organic and inorganic composites with special properties have also been characterized and their structures elucidated. The morphology of Nafion varies with hydration level, and is reflected in the changes in surface-to-volume (S/V) ratio of the polymer obtained by small-angle X-ray scattering (SAXS). The S/V ratios of different Nafion models have been evaluated numerically. It has been found that only the water channel model gives the measured S/V ratios in the normal hydration ...

International Nuclear Information System (INIS)

Although B-spline techniques have been used to solve two-point boundary value problems with Dirac Hamiltonians for more than 20 years, the treatment of boundary conditions is still a matter of controversy. Spurious, non-physical, solutions are endemic when boundary conditions are not handled correctly. These pathological problems are absent when traditional finite difference methods are used as in computer packages such as GRASP. Accurate approximation using both finite differences and B-splines depends on controlling local approximation errors, and this common property suggests no a priori reason to suppose that B-spline algorithms should be more prone to generate spurious solutions. The relativistic Bloch operators of [24], when added to the Dirac differential operator, permit the construction of a self-adjoint differential operator for the two-point boundary value problem on a finite interval. Approximate solution of this problem exploiting the properties of B-splines in variational ...

Energy Technology Data Exchange (ETDEWEB)

Measurements of the relaxation of the D{sub 2}O stretch mode in vitreous As{sub 2}S{sub 3} are presented. Because the bending mode of the molecule offers an intra-molecular decay channel for the stretch mode, the decay scheme of the D{sub 2}O molecule is more complex than that of diatomic molecules. The asymmetric stretch mode of D{sub 2}O has a frequency of 2680 cm{sup -1}. To study the relaxation of this mode we applied a pump-probe technique, using intense psec; pulses of the Stanford Free Electron Laser. Due to the small cross-section of the vibrational mode, successful efforts were made to improve the signal to noise ratio by using a laser stabilization system and a tightly focused beam to increase the intensity, by averaging the signal with a kHz repetition rate and by using samples with an optimized D{sub 2}O concentration. A rapid relaxation rate on the order of 5 x 10{sup 9} sec{sup -1} at low temperature is found that increases with temperature. Recalling ...

UK PubMed Central (United Kingdom)

Accumulation of molecular damage and increased molecular heterogeneity are hallmarks of cellular aging. Mild stress-induced hormesis can be an effective way for reducing the accumulation of molecular...Full Text Available

International Nuclear Information System (INIS)

Medical imaging using single gamma-ray-emitting radionuclides typically makes use of parallel hole collimators or pinholes in order to achieve good spatial resolution. However, a tradeoff in sensitivity is inherent in the use of a collimator, and modern preclinical single photon emission computed tomography (SPECT) systems detect a very small fraction of emitted gamma rays, often less than 0.1%. A system for small animal SPECT imaging which uses no collimators could potentially achieve very high sensitivity-several tens of percent-with reasonably sized detectors. This would allow two significant improvements in preclinical studies: images could be obtained more rapidly, allowing higher throughput for screening applications, or for dynamic processes to be observed with very good time resolution; and images could be obtained with less radioactive tracer, making possible the in vivo imaging of low-capacity receptor systems, aiding research into new tracer compounds, ...

UK PubMed Central (United Kingdom)

Woolfolk, C. A. (University of Washington, Seattle). Reduction of inorganic compounds with molecular hydrogen by Micrococcus lactilyticus. II. Stoichiometry with inorganic...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

With the improvements accomplished during the past 15 years in detection techniques and instrumentation and with the opening of space exploration, molecular spectroscopy has become a very efficient way to probe planetary atmospheres.

Science.gov (United States)

... 041889 Molecular Cloning and Characterization of Three Novel Lysozyme-Like Genes, Predominantly Expressed in the Male Reproducti...

UK PubMed Central (United Kingdom)

BackgroundMany molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC)...Full Text Available

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Short communication.

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Shewanella oneidensis MR-1 is a model environmental organism that possesses diverse respiratory capacities, including the ability to reduce soluble Cr(VI) to sparingly soluble, less toxic Cr(III). Effective bioremediation of Cr-contaminated sites requires knowledge of the molecular mechanisms and regulation of heavy metal resistance and biotransformation by dissimilatory metal-reducing bacteria. Towards this goal, our ERSP-funded work is focused on the identification and functional analysis of genes/proteins comprising the response pathways for chromate detoxification and/or reduction. Previous transcriptomic profiling and whole-cell proteomic analyses implicated the involvement of a functionally undefined DNA-binding response regulator (SO2426) and a putative azoreductase (SO3585) in the chromate stress response of MR-1. Here we describe a detailed functional analysis of SO2426 and SO3585 in order to begin to understand the role of these proteins in the cellular ...

Science.gov (United States)

This study addresses the modeling of transdermal diffusion of drugs, to better understand the permeation of molecules through the skin, and especially the stratum corneum, which forms the main permeation barrier of the skin. In transdermal delivery of systemic drugs, the drugs diffuse from a patch placed on the skin through the epidermis to the underlying blood vessels. The epidermis is the outermost layer of the skin and can be further divided into the stratum corneum (SC) and the viable epidermis layers. The SC consists of keratinous cells (corneocytes) embedded in the lipid multi-bilayers of the intercellular space. It is widely accepted that the barrier properties of the skin mostly arises from the ordered structure of the lipid bilayers. The diffusion path, at least for lipophilic molecules, seems to be mainly through the lipid bilayers. Despite the advantages of transdermal drug delivery compared to other drug delivery routes such as oral dosing and injections, the low ...

International Nuclear Information System (INIS)

This is the 1st revision of the INIS/ETDE Joint Thesaurus. It contains 20 953 valid descriptors and 8 600 forbidden terms. It was last updated in December 2003. The Joint Thesaurus contains the controlled terminology for indexing all information within the subject scope of both INIS (International Nuclear Information System) and ETDE (Energy Technology Data Exchange) information systems. The terminology is intended for use in subject description for input or retrieval of information in those systems. The thesaurus is a terminological control device used in translating from the natural language of documents, indexers or users into a more constrained system language It is also a controlled and dynamic vocabulary of semantically and generically related terms which covers a specific domain of knowledge. The domain of knowledge covered by this Thesaurus includes physics (in particular, plasma physics, atomic and molecular physics, and especially ...

Energy Technology Data Exchange (ETDEWEB)

Mechanisms and associated energetics for adatom diffusion on the (100) and (110) surfaces of Ni, Cu, Rh, Pd, and Ag are investigated. Self-diffusion was studied on (100) and (I 10) surfaces of Ni, Cu, Pd and Ag using corrected effective medium method (CEM) and approximation to CEM used for molecular dynamics and Monte Carlo studies (MD/MC-CEM). Self-diffusion on Pd(100), Ag(100), Ni(110), Cu(110), Pd(110), and Ag(110) is accomplished by classical diffusion: the adatom hops from its equilibrium adsorption site over an intervening bridge site to an adjacent equilibrium site. Self-diffusion on Ni(100) and Cu(100) proceeds by atomic-exchange diffusion: the adatom on the surface displaces an atom in the first surface layer. Aside from explicit inclusion of the kinetic-exchange-correlation energy, it is critical to include enough movable atoms in the calculation to insure correct energetics. Distortions induced by these diffusion mechanisms, ...

UK PubMed Central (United Kingdom)

Molecular Misreading (MM) is the inaccurate conversion of genomic information into aberrant proteins. For example, when RNA polymerase II transcribes a GAGAG motif it synthesizes at low frequency RNA...Full Text Available

British Library Electronic Table of Contents (United Kingdom)

Solid molecular orthohydrogen exhibits orientational order at low temperatures. The orthohydrogen molecules, which are quadrupoles, order in the Pa3 structure. We have simulated this ordering, and explored the behaviour under dilution by spherical parahydrogen molecules.

UK PubMed Central (United Kingdom)

In this study we compared the molecular signalling elicited by rexinoids, selective retinoid X receptor (RXR)-activators, in several organs (i.e. liver, kidney,...Full Text Available

UK PubMed Central (United Kingdom)

This article describes the molecular cloning and expression of a hemolysin gene from a serotype 1 strain of Actinobacillus pleuropneumoniae. The hemolysin was a thermolabile protein with an apparent...Full Text Available

UK PubMed Central (United Kingdom)

A detailed molecular characterization of nuclear mRNA export will require an in vitro system, allowing a biochemical reconstitution of transport. To this end, an mRNA export assay has...Full Text Available

Science.gov (United States)

MWo = average molecular weight of fuel est. 105 g/mole for gasoline est. 165 g/mole for Jet fuel est. 230 g/mole for diesel fuel MWX = molecular weight of selected chemical...

UK PubMed Central (United Kingdom)

The molecular diversity of the gene encoding the outer membrane protein A (OmpA) of Haemophilus parasuis has been unclear. In this study, the structural characteristics, sequence types,...Full Text Available

UK PubMed Central (United Kingdom)

Alpha-hemoglobin-stabilizing protein (AHSP) is an erythroid-specific protein that acts as a molecular chaperone for the free α chains of hemoglobin. Evidence strongly suggests...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

Despite their simplicity, diatomic molecules of first row elements can exhibit very complex phase diagrams. Determination of the phase diagrams can be further complicated by the existence of hysteretic molecular phases that can be observed over large regions of coexistence. Here we present evidence for a previously unreported molecular phase of nitrogen existing at room temperature at least over the range of 33-74 GPa. Our measurements show that sample history may have a significant impact on the thermodynamic states accessed by the molecular nitrogen solid and, by extension, also on the established phase diagram.

International Nuclear Information System (INIS)

... e Biologia Molecular (SBBq), Sao Paulo, SP (Brazil) 217 p. APPLIED LIFE

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Scheme of theoretical method of molecular configuration definition for small organic molecules in solution has been presented. The method bases on measurements of nuclear Overhauser effects for proton-proton interactions and molecular mechanics calculations. 3 refs, 1 fig.

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A study of the electron beam dynamics in the linac is conducted for the FERMI free electron laser (FEL) founded for construction at the Sincrotrone Trieste

UK PubMed Central (United Kingdom)

In this paper, we suggest that perception could be modeled by assuming that sensory input is generated by a hierarchy of attractors in a dynamic system. We describe a mathematical model which exploits...Full Text Available

UK PubMed Central (United Kingdom)

Fungal and oomycete populations and their dynamics were investigated following the introduction of the biocontrol agent Pythium oligandrum into the rhizosphere of tomato plants grown...Full Text Available

UK PubMed Central (United Kingdom)

Dynamic clamp is a powerful method that allows the introduction of artificial electrical components into target cells to simulate ionic conductances and synaptic inputs. This method is based...Full Text Available

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... of the cycle shows that the separation area ea. ... with suitable flow solvers based on the Reynolds ... AGARD 75th Fluid Dynamics Panel Meeting and ...

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The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, or (4) ...

Science.gov (United States)

S.M. Goltz; NASA Goddard Space Flight Center, Forest Ecosystem Dynamics Project ...

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... Netherlands Kormendy, J. Dominion Astrophysical Observatory, Victoria, British

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Science.gov (United States)

Three aspects of the physical geographic environment of the Amazon Basin are considered: (1)

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CERN Document Server

In the present paper we prove moderate deviations for a Curie-Weiss model with external magnetic field generated by a dynamical system, as introduced by Dombry and Guillotin-Plantard. The results extend those already obtained in the case of a constant external field by Eichelsbacher and L\\"owe. The Curie-Weiss model with dynamic external field is related to the so called dynamic Z-random walks. We also prove a moderate deviation result for the dynamic Z-random walk, completing the list of limit theorems for this object.

Science.gov (United States)

A dialyzable factor(s) in human serum is known to stimulate gonococcal oxygen consumption. Its effect on other human pathogens was investigated. A 10% serum solution increased peak O2 consumption for Escherichia coli and Staphylococcus aureus to 157% (P less than 0.05) and 199% (P less than 0.02), respectively, of their O2 consumption when suspended in Hanks balanced salt solution, compared with a 356% increase for Neisseria gonorrhoeae with serum. Dialyzed serum lacked stimulatory capacity. Bacteria, serum, and neutrophils are often incubated to evaluate neutrophil bactericidal activity. Samples of 10(8) N. gonorrhoeae, S. aureus, and E. coli turned resazurin colorless (anaerobic conditions, Eh less than -42 mV) after 7.4, 13.3, and 15.1 min, respectively. Because neutrophil formation of reactive oxygen intermediates requires ambient O2, the effect of live bacteria and serum on this process was explored. After 5 min of incubation of 10(8) N. gonorrhoeae or S. aureus in 10% normal or ...

British Library Electronic Table of Contents (United Kingdom)

We describe a class of organic molecular magnets based on zwitterionic molecules (betaine derivatives) possessing donor, p bridge, and acceptor groups. Using extensive electronic structure calculations we show the electronic ground-state in these systems is magnetic. In addition, we show that the large energy differences computed for the various magnetic states indicate a high Neel temperature. The quantum mechanical nature of the magnetic properties originates from the conjugated p bridge (only p electrons) in cooperation with the molecular donor-acceptor character. The exchange interactions between electron spin are strong, local, and independent on the length of the p bridge.

British Library Electronic Table of Contents (United Kingdom)

The thermodynamic characteristics of adsorption of iodobenzene, 2-iodothiophene, and 1- and 2-iodoadamantanes on the surface of graphitized thermal carbon black were determined experimentally. The influence of the special features of the molecular structure of the adsorbates on the thermodynamic characteristics of adsorption was studied. The atom-atom approximation of the semiempirical molecular-statistical theory of adsorption was used to calculate the thermodynamic characteristics of adsorption of the adsorbates using the newly determined potential function parameters of pair intermolecular interaction (?(r)) of I with C atoms of the basal graphite face. For the example of isostructural monohalogenated benzenes, thiophenes, and adamantanes, a comparative analysis of the contributions of ...

Energy Technology Data Exchange (ETDEWEB)

Ultraviolet photoelectron spectra were measured for vanadyl phthalocyanine (VOPc) ultrathin films prepared on graphite to study effects of the molecular orientation and the electric dipole layer on the organic electronic states. VOPc has a permanent electric dipole perpendicular to the molecular plane, hence a well-defined electric dipole layer could be intentionally prepared by using the oriented monolayer. The observed binding-energy difference of the highest occupied molecular orbital (HOMO) bands between the oriented monolayer and the double layer was found to agree with the vacuum level shift, leading to a conclusion that the molecular energy level with respect to the substrate Fermi level is changed when the molecule is in the electric dipole layer.

Science.gov (United States)

Models are proposed which explain the mechanism of action on a molecular level for the initiation of cancer by electrons or alpha particles. (ACR)

International Nuclear Information System (INIS)

... 16, 2001 0006-2979 BIORAK v. 40(2) APPLIED LIFE SCIENCES azido

UK PubMed Central (United Kingdom)

For a process intimately connected to an immense range of physiological processes, the molecular understanding of macroautophagy remains far from complete. Recent large-scale studies, including...Full Text Available

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German (15 Jun 1974). Switzerland Kocian, P. Ecole Polytechnique Federale,

British Library Electronic Table of Contents (United Kingdom)

The use of Funtumia latex and nitrobenzene as molecular weight depressants for natural rubber was studied. Portions of a given sample of natural rubber latex were treated with these materials, and this provided a means of ascertaining the amount of Funtumia latex in a blend with natural rubber that could produce a lowering of the molecular weight equivalent to that from known concentrations of nitrobenzene in natural rubber latex. The molecular weight of the products decreased to an equilibrium value after 10 h of reaction with nitrobenzene. The calculations revealed that a 27.9% substitution of natural rubber latex (300 mL) with Funtumia rubber latex achieved the same result as nitrobenzene in the same polymer at concentrations of 0.5-2.0 wt % of the dry rubber content of the latex after ...

British Library Electronic Table of Contents (United Kingdom)

A new method of the synthesis of high molecular polybutylene terephthalate (PBT) is developed with the use of Irganox 1010, tris(nonylphenyl) phosphite and hypophosphite as stabilizers and boron nitride or boron oxide as a catalyst is proposed.

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... Here we will summarize the synthesis, structure activity relationships , and molecular sites of action of mGluR5 PAMs. We will also review preclinical studies ...

UK PubMed Central (United Kingdom)

Gangliosides are amphiphilic molecules found in the outer layer of plasma membranes of all vertebrate...Full Text Available

International Nuclear Information System (INIS)

... argon carbon dioxide cations electric fields gases helium ion mobility molecular

International Nuclear Information System (INIS)

We investigate the magnetic braking of the core of an axisymmetric cloud whose rotation axis is parallel to the mean direction of the magnetic field. (author).

Energy Technology Data Exchange (ETDEWEB)

To establish a relationship between the molecular structure of polycarboxylates and their growth-retarding influence on barium sulfate, seeded-suspension-growth experiments were performed at various inhibitor concentrations and pH values. Two types of polycarboxylates with a molecular structure based on their polyacrylic or maleic acid were studied. The molecular structure of these compounds were varied by particle substitution with monomers containing hydroxyl, amide, and sulfonic acid, as well as hydrophobic groups. Hydrophobic groups are detrimental to good inhibitor performance, whereas the introduction of OH, NH {sub 2}, or SO {sub 3} H groups presents opportunities to enhance the inhibitor effectiveness. The sequence in performance of the compounds on barium sulfate was compared with the sequence formerly obtained for calcium sulfate dihydrate.

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The nitric oxide molecule is being studied in order to understand the energetics and chemistry of initiation and detonation in liquid NO at the molecular level. An overview is presented of the work being done. (DLC)

UK PubMed Central (United Kingdom)

The biosynthesis of insect juvenile hormone (JH) and its neuroendocrine control are attractive targets for chemical control of insect pests and vectors of disease. To facilitate the molecular...Full Text Available

UK PubMed Central (United Kingdom)

Aggregatibacter (Actinobacillus) actinomycetemcomitans is a facultative anaerobic gram-negative bacterium associated with severe forms of periodontitis. A leukotoxin, which belongs...Full Text Available

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... shareware for population genetic analysis. Molecular Biology and Biotecnology Centre, Univ. of Alberta, Canada. enlarge figure Fig. ... ...

International Nuclear Information System (INIS)

This paper describes a long term course of research into the fundamentals of two phase flow regime dynamics that had lead to a differential description of regime properties. The development has included experiment, microscale simulation, and mathematical averaging to produce a dynamic equation for interfacial area.

UK PubMed Central (United Kingdom)

Reliable characterization of locomotor dynamics of human walking is vital to understanding the neuromuscular control of human locomotion and disease diagnosis. However, the inherent oscillation and...Full Text Available

UK PubMed Central (United Kingdom)

Specific criteria have been developed based on computerized dynamic posturography (CDP) to assist clinicians in identifying patients with psychogenic balance problems (Cyr and Cevette, Full Text Available

Energy Technology Data Exchange (ETDEWEB)

The aim of this project was to develop an understanding of the dynamical processes that evolve within an electric utility firm, and without it. This volume covers organizational dynamics and control, and planning under uncertainty. (DLC)

UK PubMed Central (United Kingdom)

Understanding the dynamics of porcine reproductive and respiratory syndrome virus (PRRSV) vertical transmission is important to enhance the accuracy of monitoring protocols for endemically infected...Full Text Available

UK PubMed Central (United Kingdom)

In order to maintain stable functionality in the face of continually changing input, neurones in the CNS must dynamically modulate their electrical characteristics. It has been hypothesized that in...Full Text Available

Science.gov (United States)

... 4.4+9 4.30 ds~ ;'* Page 24. Table 3 Ultimate Compressive Strength Data Static Dynamic Round Strength Range Strength Range No. Avg Rise 0No. ...

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SummaryWe develop a new class of models, dynamic conditionally linear mixed models, for longitudinal data by decomposing the within-subject covariance matrix using a special Cholesky...Full Text Available

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This book contains over 20 selections. Some of the titles are: Continuum damage mechanics studies on the dynamic fracture of concrete; Dynamic compressive strength of cementitious materials; Rate-sensitivity of mode I and mode II fracture concrete; and An impact damage model of concrete.

UK PubMed Central (United Kingdom)

The realization theory linear dynamical systems, previously developed over a field, are extended to a large class of commutative rings. The principal result is that the existence criterion for a finite...Full Text Available

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... Tunable semiconductor lasers are essential components for links employing optical frequency modulation (OFM) for enhanced dynamic range or ...

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Wikileaks was inevitable. The Dynamics of. Information. Take advantage of the eddy currents. You can't step in the same river ...

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... Dynamics Panel Executive AGARD 7 rue ... 4 AXIAL FLOW IN CORNERS AT SUPERSONIC ... AND HYPERSONIC FLOWS INCLUDING SEPARATION ...

British Library Electronic Table of Contents (United Kingdom)

This article presents a decentralized control scheme for the complex problem of simultaneous position and internal force control in cooperative multiple manipulator systems. The proposed controller is composed of a sliding mode control term and a force robustifying term to simultaneously control the payloads position/orientation as well as the internal forces induced in the system. This is accomplished independently of the manipulators dynamics. Unlike most controllers that do not require prior knowledge of the manipulators dynamics, the suggested controller does not use fuzzy logic inferencing and is computationally inexpensive. Using a Lyapunov stability approach, the controller is proven to be robust in the face of varying systems dynamics. The payloads position/orientation and the inte...

Energy Technology Data Exchange (ETDEWEB)

The microstructures of magnesium AZ31 are examined following hot compression testing and annealing. The grain size, fraction dynamically recrystallized and, in a couple of cases, the crystallographic texture are reported. It was found that the progress of dynamic recrystallization is strongly sensitive to processing conditions but that the dynamically recrystallized grain size was less sensitive to stress than in other metals. It was also found that, for structures containing between 80 and 95% dynamic recrystallization, abnormal grain growth occurs during annealing. The crystallographic texture produced is also sensitive to the deformation conditions. (orig.)

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Udgivelsesdato: 2008-Sep