Haut PDF Spinodal decomposition in nuclear molecular dynamics

Spinodal decomposition in nuclear molecular dynamics

Spinodal decomposition in nuclear molecular dynamics

molecular dynamics approaches based on gaussian single particle wave packets.. We observMhat zero-sound properties are significantly affected when the gaussian.[r]

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Nuclear quantum effects in molecular dynamics simulations

Nuclear quantum effects in molecular dynamics simulations

3 CEA, DAM, DIF, F-91297 Arpajon, France hichem.dammak@centralesupelec.fr Abstract. To take into account nuclear quantum effects on the dynamics of atoms, the path integral molecular dynamics (PIMD) method used since 1980s is based on the formalism developed by R. P. Feynman. However, the huge computation time required for the PIMD reduces its range of applicability. Another drawback is the requirement of additional techniques to access time correlation functions (ring polymer MD or centroid MD). We developed an alternative technique based on a quantum thermal bath (QTB) which reduces the computation time by a factor of ~20. The QTB approach consists in a classical Langevin dynamics in which the white noise random force is replaced by a Gaussian random force having the power spectral density given by the quantum fluctuation-dissipation theorem. The method has yielded satisfactory results for weakly anharmonic systems: the quantum harmonic oscillator, the heat capacity of a MgO crystal, and isotope effects in 7 LiH and 7 LiD. Unfortunately, the QTB is
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Molecular dynamics simulation of ballistic effects in simplified nuclear waste glasses

Molecular dynamics simulation of ballistic effects in simplified nuclear waste glasses

2.3 Choice of the initial glass density for glass preparation A recent study by Kilymis et al. [10] revealed the importance of the choice of the initial density on the final glass density. Consequently, depending on the glass density, swelling or contraction can be observed after series of displacement cascades. It was observed that when the pristine glass is prepared with an initial density corresponding to the minimum of the potential energy (PE), the radiation effects are in best agreement with experimental results. A similar study by Jolley et al.[36] using current potentials, revealed that the simulated glasses with experimental density actually may not correspond to the glass with minimum PE. Hence, in order to make sure the simulated pristine glasses correspond to a minimum of the PE, a specific algorithm was applied. In this algorithm, a glass composition (4000 atoms) was prepared with different densities (+/-15% the experimental one) using the preparation scheme shown in Fig. 1 but without the relaxation in the NPT ensemble (i.e. the volume was kept constant during the whole glass preparation). Afterwards, the potential energy and pressure of the equilibrated glass were plotted versus density and the curves were fitted to determine two equilibrium densities corresponding to the minimum PE and zero pressure, respectively (see
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Theoretical gas to liquid shift of 15 N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations

Theoretical gas to liquid shift of 15 N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations

simulations were performed first on a model containing 8 molecules in a cubic box of 9.0 Å of length for a density value of 65 1.1 g.cm -3 at 298 K. A dynamical time step of 0.5 fs was employed for all runs, to obtain trajectories of 10 ps, thanks to a first-order Verlet extrapolation scheme 34 . Initial geometries and velocities were randomly chosen. A kinetic energy cut-off of 400 eV was found to be sufficient to achieve a total energy

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Time-resolved Coulomb explosion imaging: a method to measure structure and dynamics of molecular nuclear wave packets

Time-resolved Coulomb explosion imaging: a method to measure structure and dynamics of molecular nuclear wave packets

To exert control of the outcome of the nonlinear processes driven by the pump pulse it will be advantageous to use laser beams with a constant spatial intensity profile. Presently, Gaussian shaped beams are employed with the result that, within the focal volume, a variety of different states are ex- cited depending on the maximum intensity reached at a par- ticular position in the focus. Since the signals recorded in our experiment represent an average over the entire focal vol- ume, they consist of contributions from all states excited. Using a laser pulse with an essentially flat spatial profile should ensure a more selective state excitation. This will make the interpretation of the signals easier and increase the population transfer to desired states. A constant transverse intensity profile is achieved, for instance, by selecting the central part of a Gaussian beam with an undersized pinhole and imaging it. In the longitudinal direction the constant in- tensity is obtained by restricting the laser-molecule interac- tion to a dimension much smaller than the Rayleigh length.
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Nuclear Dynamics in Polyatomic Molecules and High-Order Harmonic Generation

Nuclear Dynamics in Polyatomic Molecules and High-Order Harmonic Generation

Because at short times the displacement of c decreases as m 1 , the two effects partially compensate, and signifi- cant modulation of the HHG spectra may occur. Equation ( 1 ) is already an approximation. It assumes that the ionization and recombination amplitudes do not depend on the molecular geometry, no depletion of the ground-state occurs, and that the Born-Oppenheimer po- tential energy surfaces of both species are not affected by the laser field. Although approximate, Eq. ( 1 ) is a useful starting point for studies of polyatomic molecules, where the exact treatment is at present prohibitively expensive.
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Molecular dynamics simulation of energetic uranium recoil damage in zircon

Molecular dynamics simulation of energetic uranium recoil damage in zircon

1. Introduction The immobilization of high-level nuclear waste and excess weapons plutonium in a suitable ceramic host material is an urgent concern from the standpoint of environmental protection, national security, and non-proliferation. Due to the anticipated expanded use of nuclear energy to meet growing global energy demand, there is a pressing need to design nuclear waste form materials based on a fundamental understanding of radiation effects in ceramics. Atomistic computer simulation is needed to develop such an understanding; because the small time (ps) and distance (nm) scales of primary radiation damage production in materials preclude direct experimental observation. At the same time, energetic radiation damage processes cannot be simulated by accurate ab initio calculations due to computational limitations. Thus, classical molecular dynamics (MD) simulation using reliable empirical potentials is ideally suited to the task at hand.
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Structure of Strontium Aluminosilicate Glasses from Molecular Dynamics Simulations, Neutron Diffraction and Nuclear Magnetic Resonance Studies

Structure of Strontium Aluminosilicate Glasses from Molecular Dynamics Simulations, Neutron Diffraction and Nuclear Magnetic Resonance Studies

11 Figure 3 shows the 29 Si MAS NMR spectra, the variations of the mean isotopic chemical shift 678 (i.e., center of gravity) and widths of the spectra; dashed lines represent linear regression of 678 values on specific ranges of composition (see below). For both glass series, increase of silica content yields a decrease of the isotropic chemical shift and increase of the spectrum’s width. In the R = 1 glass series, according to previous studies of aluminosilicate glasses, 9,53–55 the variation of 678 can be interpreted in terms of the Si/Al mixing. It has been generally observed that one substitution of one bonded silicon for an aluminum leads to shift between +3 and +5 ppm, in qualitative agreement with the observed slope of 2.1 ± 0.3 ppm/Al for the second part (for ;< ⁄ = > 1.5 , i.e, SA50.25, SA57.21, SA63.18 and SA75.12) whereas the first part (for ;< ⁄ = < 1.5, i.e, SA26.37, SA33.33 and SA42.29)shows a slope of 12 ± 3 ppm/Al. This value approaches the R=3 glass series ones, with a higher slope for the increase of 678 , 18 ± 3 ppm/Al, which is clearly indicative of the contribution of two mechanisms : Al/Si mixing and decrease of the amount of non-bridging oxygens O [1] . Each aluminum is coming with 1.5 Sr 2+ : the difference between the slopes, about 6 ppm/Al, can be ascribed to the effect of one added NBO in the case R=3. The residual of about 12 ppm/Al suggests that other mechanisms exist; MD can help understanding them.
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Molecular simulation of non-equilibrium methane Hydrate Decomposition.

Molecular simulation of non-equilibrium methane Hydrate Decomposition.

Abstract We recently performed constant energy molecular dynamics simulations of the endothermic decomposition of methane hydrate in contact with water to phenomenologically study the role of mass and heat transfer in the decomposition rate [ Alavi, Ripmeester, J. Chem. Phys. 132 (2010) 144703]. We observed that, with the progress of the decomposition front temperature gradients are established between the remaining solid hydrate and the solution phases. In this work, we provide further quantitative macroscopic and molecule level analysis of the methane hydrate decomposition process with an emphasis on elucidating microscopic details and how they affect the predicted rate of methane hydrate decomposition in natural methane hydrate reservoirs. A quantitative criterion is used to characterize the decomposition of the hydrate phase at different times. Hydrate dissociation occurs in stepwise fashion with rows of sI cages parallel to the interface decomposing simultaneously. The correlations between decomposition times of subsequent layers of the hydrate phase are discussed.
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Lattice dynamics in spin-crossover nanoparticles through nuclear inelastic scattering

Lattice dynamics in spin-crossover nanoparticles through nuclear inelastic scattering

configuration can exhibit a reversible switching between the molecular low-spin (LS) and high-spin (HS) states upon the application of an external stimulus such as temperature, pressure, intense magnetic field, or light irradiation. This phenomenon is accompanied by a spectacular modification of the magnetic, optical, electrical, and mechanical properties of the material. Due to the strong electron-lattice coupling, the molecule occupies a smaller volume in the LS state, which implies a higher density and stiffness when compared to the HS form. In bulk SCO solids, this misfit between the HS and LS molecular volumes leads to strong elastic interactions, which play a major role in the cooperativity of spin transition [ 2 ] and its spatiotemporal dynamics [ 3 , 4 ]. In addition, new attractive applications of SCO materials such as microactuators [ 5 , 6 ], magnetostrictive heterostructures [ 7 ], or bistable composites [ 8 ] are based on the important spontaneous strain accompanying the SCO. Hence the knowledge of the elastic constants of these materials and their spin-state dependence is of significant importance. Unfortunately, the lattice dynamics and, in particular, the acoustic phonon modes of SCO materials remain largely unknown and their elastic constants have been determined only in a few occasions (and usually in only one spin state), using AFM [ 9 ], x-ray diffraction [ 10 , 11 ], and Brillouin spectroscopy [ 12 ]. In this context, nuclear inelastic scattering (NIS) is a very suitable technique [ 13 ], which allows to extract many lattice dynamical parameters and this even in nano-objects, which are of current interest in the SCO field.
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Adaptive-boost molecular dynamics simulation of carbon diffusion in iron

Adaptive-boost molecular dynamics simulation of carbon diffusion in iron

Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA (Received 4 April 2011; revised manuscript received 1 December 2011; published 21 February 2012) We have developed an accelerated molecular dynamics (MD) method to model atomic-scale rare events. In this method, a smooth histogram of collective variables is first estimated by canonical ensemble molecular dynamics calculations, and then a temperature-dependent boost potential is iteratively constructed to accelerate the MD simulation. This method not only allows us to observe the rare events but also to evaluate the profile of free energy and trial frequency along the reaction coordinate. We employed this method to study carbon diffusion in bcc iron and evaluated carbon’s temperature-dependent diffusivity. The obtained diffusivities agree well with the experimental measurements. Even at low temperature for which, to the best of our knowledge, no experimental data are available, the diffusivity can be evaluated accurately. Additionally, we study carbon diffusion inside the edge dislocation core in bcc iron, and demonstrate the applicability of the method to rare events on a rugged free-energy surface.
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Non-equilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

Non-equilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

共Received 26 October 2009; accepted 16 March 2010; published online 13 April 2010兲 Nonequilibrium, constant energy, constant volume 共NVE兲 molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed. © 2010 American Institute
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Surface-directed spinodal decomposition in hafnium silicate thin films

Surface-directed spinodal decomposition in hafnium silicate thin films

DOI: 10.1103/PhysRevB.80.041403 PACS number共s兲: 68.37.Og, 64.75.St, 05.70.Fh Spinodal decomposition 共SD兲 is a diffusional phase sepa- ration whereby a local composition fluctuation reduces the overall free energy of the system. 1 In the bulk of a binary mixture experiencing SD, a description of the composition in the solution will be a superposition of sine waves of fixed wavelength, but random in orientation, phase, and amplitude in the initial stage where the linear theory is applicable. 2 The average size of the single-phase domains then grows with time corresponding to a coarsening of the structure. 3 Re- cently, it has been recognized that for thin-film geometry, SD may interact with wetting phenomena resulting in a very different structure at the surfaces compared to the bulk behavior. 4 – 7 This phenomenon has been called surface- directed spinodal decomposition 共SDSD兲. SDSD simulations show that a composition wave perpendicular to the surface forms at the surface due to the preferential attraction of the surface to one of the two components. 6 This wave then propagates into the bulk of the film and decays because of thermal noise. Most experimental studies in SDSD have been carried out in polymer mixtures where a small self-diffusion coefficient slows the SD dynamics and the associated phase diagrams can be tailored. 4 , 5 While it is predicted that SD could occur generally in any two-component system whose phase diagram shows a miscibility gap, such as ZrO 2 -SiO 2 , HfO 2 -SiO 2 , La 2 O 3 -SiO 2 , Y 2 O 3 -SiO 2 , 8 and Al 2 O 3 -SiO 2 , ex- perimental observations of SDSD in thin solid films have never been reported.
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Ultrafast electro-nuclear dynamics of H2 double ionization

Ultrafast electro-nuclear dynamics of H2 double ionization

proach which takes into account the dissociative dynam- ics of the molecule. For large field values, and because of the recollision, the two electrons are thus forced to lo- calize on the same nucleus. Every 115 as, this ionic state is transiently populated by recollision, and in this con- figuration the two electrons can easily escape by tunnel ionization. We therefore observe a very fast succession of Recollision-induced Field-assisted Double Ionization (RFDI, see the four double ionization arrows in Fig. 3(c)). As mentioned previously, the last efficient pathway to double ionization takes place after the end of the pulse, and therefore results from an autoionization process. This interpretation is confirmed by the snapshot of the electronic wave packet shown in Fig. 3(d). For t > 3.0 fs, the two electrons escape in opposite directions since the ionization is now mainly driven by the electron repulsion. This ionization pathway, as well as the RFDI pathway of Fig. 3(c), are suppressed when we introduce absorbing boundaries for the rescattering flux. The origin of both ionization channels is therefore to be found in the elec- tron recollision. We therefore name the post-pulse ion- ization process “Recollision-induced Auto-Double Ioniza- tion”, or RADI. Additional calculations performed with fixed nuclei show that RADI also takes place when the vibrational dynamics is frozen. This process is there- fore not induced by a vibrational coupling [17], but is certainly due to transiently populated dressed molecular states lying above the field-free double ionization thresh- old. When the field is suddenly switched off, these highly excited states decay rapidly by double ionization. This interpretation is confirmed by the fact that RADI disap- pears for pulse durations longer than 4 optical cycles.
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Molecular dynamics, Monte Carlo simulations, and langevin dynamics: a computational review

Molecular dynamics, Monte Carlo simulations, and langevin dynamics: a computational review

he next section is concerned with the reinement of experimentally determined macrostructures. 3.2. How to Minimize the Energy of the Conformation or How to Reine Experimentally Determined Structures. he position of the constituent atoms of a macromolecular structure is usually determined either through X-ray crystallography for the larger structure or through nuclear magnetic resonance (NMR) for the smaller molecules. If only the amino acid sequence is available, the three-dimensional structure may be inferred either from methods based on homology, such as threading, or from ab initio methods, which predict the structure from the sequence alone [ 44 ]. Among the larger structures associated with inluenza are the hemag- glutinin and the neuraminidase. Because a protein has to be crystallised to apply X-ray crystallography, the position of its constituent atoms may be distorted from their natural positions by the crystallisation process. Consequently, bond lengths and bond angles may be distorted and steric clashes in between atoms may occur. herefore, it is recommended to minimise the potential energy of the macromolecular structure to remediate this deiciency and to create a more realistic structure [ 45 ].
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Improved Adaptive Resolution Molecular Dynamics Simulation

Improved Adaptive Resolution Molecular Dynamics Simulation

In the current paper, it is proposed a method for obtaining the interaction forces by applying the Hamiltonian derivation, where potentials can be scaled. The advantage of this method is that, derivation is based on the sound Hamiltonian model and energies can be reported correctly. The improved algorithm was implemented in GROMACS, a molecular dynamics software, that runs in parallel using the Message Passing Interface (MPI). Simulations have been done on butane. The MARTINI coarse-grained force field which was implemented by the Molecular Dynamics Group from the University of Groningen was also applied.
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Study of nuclear receptor dynamics by BRET

Study of nuclear receptor dynamics by BRET

Breast cancer and the estrogen receptor‐alpha      ERα expression or overexpression is observed in a majority (two thirds) of breast  tumors.  Mammary  gland  tumors  that  express  the  estrogen  receptor  are  defined  as  luminal because normal epithelial cells expressing ERα are found in the lumen of ducts  and lobules in the mammary gland [315]. These luminal breast tumors are subdivided in  two  types,  A  and  B  by  gene  signatures  identified  from  unsupervised  hierarchical  clustering of tumors based on their gene expression levels (microarray analyses). Luminal  A tumors are generally HER2‐negative, p53 wt and poorly proliferative, while luminal B  tumors  have  increased  expression  of  cell  cycle  related  genes  and  can  overexpress  the  membrane  RTK  HER2  [316].  Moreover,  ERα  expression  is  positively  correlated  with  progesterone receptor (PR) expression since PR is a primary target gene of ERα [317, 318].  Note  however  that  other  ER  target  genes  may  be  more  tightly  correlated  with  ER  expression, at least at the mRNA level.  Other sybtypes of breast cancers are classified as  HER2+, a luminal‐like subtype that overexpress HER2 but not ERα expression, and triple  negative,  which  are  composed  of  cells  that  resemble  the  basal  layer  of  the  duct  and  lobules in that they do not express ERα, PR or HER2 [319, 320]. This latter tumor type is  the  most  aggressive,  being  often  associated  with  genomic  instability,  and  does  not  benefit from targeted therapies yet.  
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General molecular biology and architecture of nuclear receptors.: Transcriptional regulation by nuclear receptors

General molecular biology and architecture of nuclear receptors.: Transcriptional regulation by nuclear receptors

b.3. The mediator complex: Like the SWI/SNF complex, the Mediator complex has been originally identified in yeast and subsequently characterized in other eukaryotic cells. A number of studies described its role as a catalyzer of the transcription preinitiation complex (PIC) assembly at activated promoters. Through direct interaction with RNA polymerase II, general transcription factors (TFIID, TFIIH) and elongation factors, Mediator plays a key role in RNA polymerase II-controlled transcription [201] . Investigations about the role of Mediator in NR research gained momentum when it was realized that Mediator-like complexes bind directly to NRs [202-206] . Mediator is organized in four structural modules and includes more than 20 subunits, of which the Med1 subunit contains LXXLL motifs [207] . The liver-specific Med1 KO induces hepatic steatosis in a PPAR(-dependent manner [208] , in agreement with its adipogenic [209] and PPAR( coactivator roles [210] . Skeletal muscle- specific KO of Med1 enhances insulin sensitivity and improves glucose tolerance and confers resistance to high-fat diet-induced obesity [211] . Thus given its broad and key roles in transcriptional regulation through a direct interaction with RNA polymerase II, Mediator is viewed as being the last complex recruited cyclically to NR-regulated promoters [184] .
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Quantum nuclear many-body dynamics and related aspects

Quantum nuclear many-body dynamics and related aspects

static long-range correlations associated with collective modes, as for example deformation and pairing, with very moderate effort. However, the breaking of symmetries (translational, rotational, parity, particle number, to name the most current ones) forbids a trivial connection of the nuclear SR-EDF formalism to the original existence theorems (Engel, 2007; Giraud, 2008; Messud et al., 2009). Indeed, the density that minimizes the exact HK energy functional must reflect the symmetries of the exact ground state of the system. In fact, the appearance of symmetry-breaking solutions in nuclear EDF calculations underlines two important elements (i) it is crucial and numerically not too difficult to grasp the most important static correlations using rather simple approximate functionals and a single-determinantal reference state (ii) kinematic correlations associated with the corresponding symmetry modes (Goldstone modes) as well as the correlations due to the fluctuation of their order parameters are extremely difficult to incorporate into a single-determinantal approach. In other words, correlations associated with highly non-local processes such as large-amplitude collective motions can hardly be described within a SR approach based on a standard, nearly-local EDF. Last, it is important to keep in mind that broken symmetries like pairing or deformation are directly observed experimentally for instance in odd-even mass effects or through the observation of rotational bands.
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Mössbauer characterisations and magnetic properties of iron cobaltites CoxFe3−xO4 (1 ≤ x ≤ 2.46) before and after spinodal decomposition

Mössbauer characterisations and magnetic properties of iron cobaltites CoxFe3−xO4 (1 ≤ x ≤ 2.46) before and after spinodal decomposition

H eff ¼ H hf ÿ H ext and A 2,5 /A 1,6 ¼ 0, the latter condition meaning that the middle lines in the external-field spectrum of that compound are absent. The observed and calculated applied-field spectra are repro- duced in Fig. 3 . It is noticed that for the oxides with cobalt contents x ¼1.00, 1.22, and 1.73 the two sextet sub-spectra arising from iron on A- and B-sites, respectively, are clearly shifted apart due to the external field. This effect is well known to occur in ferrimagnetic substances, whereby the individual spins of the sublattice with the larger net magnetic moment order parallel to the external field, and those of the sublattice with the smaller net magnetic moment antiparallel, so that for the former sublattice sites the external field subtracts from the hyperfine field, and for the latter ones the external field adds to the hyperfine field. For the present cobaltites, the alignment is not complete as evidenced by the presence of the middle absorption lines (lines 2 and 5) in the respective MS. This deviation from total alignment is gen- erally due to the magnetic anisotropy, which forces the magnetic moment of a randomly oriented (with respect to the external
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