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Sample records for crystal nonequilibrium molecular

  1. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    1990-11-01

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

  2. Nonequilibrium-molecular-dynamics measurement of the Leslie coefficients of a Gay-Berne nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Qian, Tiezheng

    2007-03-01

    We carried out nonequilibrium molecular dynamics (MD) simulations to measure the six Leslie coefficients of a nematic liquid crystal composed of molecules interacting via the Gay-Berne potential. In the presence of a simple shear flow, an external field is applied to control the molecular orientation, and a uniform director is stabilized in the central region of the channel in which the liquid crystal is confined and sheared. With the director tuned by varying the applied field, a number of orientational states are stabilized in the presence of a shear flow, and various viscous stress components are measured in these states of different directors. The six Leslie coefficients αi are determined by interpreting the MD measurement data for viscous stress according to the constitutive relations in the Ericksen-Leslie-Parodi (ELP) theory. The Parodi relation α2+α3=α6-α5 is well satisfied. Given the values of the Leslie coefficients, liquid crystal orientations are evaluated for different field directions and shear rates. Comparison with those directly measured in MD simualtions demonstrates a quantitative agreement, showing that in the Gay-Berne nematic liquid crystal, the viscous stress and the coupling between orientation and flow are well described by the ELP theory.

  3. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    Hoover, W.G. |

    1992-08-01

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

  4. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  5. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

    Bubbles pushed through a quasi-two-dimensional channel self-organize into a variety of periodic lattices. The structures of these lattices correspond to local minima of the interfacial energy. The "flowing crystals" are long-lived metastable states, a small subset of possible local minima of confined quasi-two-dimensional foams [P. Garstecki and G. M. Whitesides, Phys. Rev. E 73, 031603 (2006)10.1103/PhysRevE.73.031603]. Experimental results suggest that the choice of the structures that we observe is dictated by the dynamic stability of the cyclic processes of their formation. Thus, the dynamic system that we report provides a unique example of nonequilibrium self-organization that results in structures that correspond to local minima of the relevant energy functional. PMID:16907453

  6. Specific mass increment and nonequilibrium crystal growth

    NASA Astrophysics Data System (ADS)

    Martyushev, Leonid M.; Terentiev, Pavel S.

    2013-09-01

    Unsteady nonequilibrium crystallization of ammonium chloride from an aqueous solution resulting in the formation of irregular, so-called seaweed, structures is experimentally investigated. It is shown that specific increment of mass for the coexisting structures (or parts thereof) is the same and changes with time (t) according to the power law a/t-b, where the factor a=1.87±0.09 and the factor b is determined by the system relaxation time. The normalization of the power law to the total time of structure growth allows obtaining a universal law that describes the specific mass increment with time for both seaweed and dendrite structures (including the non-coexisting ones).

  7. Cell list algorithms for nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew; Fox, Ian; Saracino, Alexandra

    2016-06-01

    We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.

  8. Density Functional Theory for Steady-State Nonequilibrium Molecular Junctions

    NASA Astrophysics Data System (ADS)

    Liu, Shuanglong; Nurbawono, Argo; Zhang, Chun

    2015-10-01

    We present a density functional theory (DFT) for steady-state nonequilibrium quantum systems such as molecular junctions under a finite bias. Based on the steady-state nonequilibrium statistics that maps nonequilibrium to an effective equilibrium, we show that ground-state DFT (GS-DFT) is not applicable in this case and two densities, the total electron density and the density of current-carrying electrons, are needed to uniquely determine the properties of the corresponding nonequilibrium system. A self-consistent mean-field approach based on two densities is then derived. The theory is implemented into SIESTA computational package and applied to study nonequilibrium electronic/transport properties of a realistic carbon-nanotube (CNT)/Benzene junction. Results obtained from our steady-state DFT (SS-DFT) are compared with those of conventional GS-DFT based transport calculations. We show that SS-DFT yields energetically more stable nonequilibrium steady state, predicts significantly lower electric current, and is able to produce correct electronic structures in local equilibrium under a limiting case.

  9. Welding Molecular Crystals.

    PubMed

    Adolf, Cyril R R; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2015-12-16

    Both for fundamental and applied sciences, the design of complex molecular systems in the crystalline phase with strict control of order and periodicity at both microscopic and macroscopic levels is of prime importance for development of new solid-state materials and devices. The design and fabrication of complex crystalline systems as networks of crystals displaying task-specific properties is a step toward smart materials. Here we report on isostructural and almost isometric molecular crystals of different colors, their use for fabrication of core-shell crystals, and their welding by 3D epitaxial growth into networks of crystals as single-crystalline entities. Welding of crystals by self-assembly processes into macroscopic networks of crystals is a powerful strategy for the design of hierarchically organized periodic complex architectures composed of different subdomains displaying targeted characteristics. Crystal welding may be regarded as a first step toward the design of new hierarchically organized complex crystalline systems. PMID:26581391

  10. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W. G.; Hoover, C. G.

    1993-08-01

    Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

  11. Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective.

    PubMed

    Gao, Yi; Galperin, Michael

    2016-05-01

    We consider optical spectroscopy of molecular junctions from the quantum transport perspective when radiation field is quantized and optical response of the system is simulated as photon flux. Using exact expressions for photon and electronic fluxes derived within the nonequilibrium Green function (NEGF) methodology and utilizing fourth order diagrammatic perturbation theory (PT) in molecular coupling to radiation field, we perform simulations employing realistic parameters. Results of the simulations are compared to the bare PT which is usually employed in studies on nonlinear optical spectroscopy to classify optical processes. We show that the bare PT violates conservation laws, while flux conserving NEGF formulation mixes optical processes. PMID:27155631

  12. Optical spectroscopy of molecular junctions: Nonequilibrium Green's functions perspective

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Galperin, Michael

    2016-05-01

    We consider optical spectroscopy of molecular junctions from the quantum transport perspective when radiation field is quantized and optical response of the system is simulated as photon flux. Using exact expressions for photon and electronic fluxes derived within the nonequilibrium Green function (NEGF) methodology and utilizing fourth order diagrammatic perturbation theory (PT) in molecular coupling to radiation field, we perform simulations employing realistic parameters. Results of the simulations are compared to the bare PT which is usually employed in studies on nonlinear optical spectroscopy to classify optical processes. We show that the bare PT violates conservation laws, while flux conserving NEGF formulation mixes optical processes.

  13. Simulations of a molecular plasma in collisional-radiative nonequilibrium

    NASA Technical Reports Server (NTRS)

    Cambier, Jean-Luc; Moreau, Stephane

    1993-01-01

    A code for the simulation of nonequilibrium plasmas is being developed, with the capability to couple the plasma fluid-dynamics for a single fluid with a collisional-radiative model, where electronic states are treated as separate species. The model allows for non-Boltzmann distribution of the electronic states. Deviations from the Boltzmann distributions are expected to occur in the rapidly ionizing regime behind a strong shock or in the recombining regime during a fast expansion. This additional step in modeling complexity is expected to yield more accurate predictions of the nonequilibrium state and the radiation spectrum and intensity. An attempt at extending the code to molecular plasma flows is presented. The numerical techniques used, the thermochemical model, and the results of some numerical tests are described.

  14. Non-equilibrium phase transitions in a liquid crystal

    NASA Astrophysics Data System (ADS)

    Dan, K.; Roy, M.; Datta, A.

    2015-09-01

    The present manuscript describes kinetic behaviour of the glass transition and non-equilibrium features of the "Nematic-Isotropic" (N-I) phase transition of a well known liquid crystalline material N-(4-methoxybenzylidene)-4-butylaniline from the effects of heating rate and initial temperature on the transitions, through differential scanning calorimetry (DSC), Fourier transform infrared and fluorescence spectroscopy. Around the vicinity of the glass transition temperature (Tg), while only a change in the baseline of the ΔCp vs T curve is observed for heating rate (β) > 5 K min-1, consistent with a glass transition, a clear peak for β ≤ 5 K min-1 and the rapid reduction in the ΔCp value from the former to the latter rate correspond to an order-disorder transition and a transition from ergodic to non-ergodic behaviour. The ln β vs 1000/T curve for the glass transition shows convex Arrhenius behaviour that can be explained very well by a purely entropic activation barrier [Dan et al., Eur. Phys. Lett. 108, 36007 (2014)]. Fourier transform infrared spectroscopy indicates sudden freezing of the out-of-plane distortion vibrations of the benzene rings around the glass transition temperature and a considerable red shift indicating enhanced coplanarity of the benzene rings and, consequently, enhancement in the molecular ordering compared to room temperature. We further provide a direct experimental evidence of the non-equilibrium nature of the N-I transition through the dependence of this transition temperature (TNI) and associated enthalpy change (ΔH) on the initial temperature (at fixed β-values) for the DSC scans. A plausible qualitative explanation based on Mesquita's extension of Landau-deGennes theory [O. N. de Mesquita, Braz. J. Phys. 28, 257 (1998)] has been put forward. The change in the molecular ordering from nematic to isotropic phase has been investigated through fluorescence anisotropy measurements where the order parameter, quantified by the

  15. Thermal Conductivity of GaN Nanotubes Simulated by Nonequilibrium Molecular Dynamics

    SciTech Connect

    Wang, Zhiguo; Gao, Fei; Crocombette, J.-P.; Zu, Xiaotao; Yang, Li; Weber, William J.

    2007-04-15

    Thermal conductivity of GaN nanotubes along the tube axis is investigated over the temperature range of 600K-2300K using homogeneous nonequilibrium molecular dynamics. In general, the thermal conductivity of nanotubes is smaller than that for the bulk GaN single crystal. The thermal conductivity is also found to decrease with temperature and increase with increasing wall thickness of the nanotubes. The change of phonon spectrum and surface inelastic scattering may account for the reduction of thermal conductivity in the nanotubes, while thermal softening and high frequency phonon interactions at high temperatures may provide an explanation for its decrease with increasing temperature.

  16. Fluxes of nonequilibrium photo-excited phonons along surfaces of crystals without an inversion center

    SciTech Connect

    Blokh, M.D.

    1988-01-01

    The flux of nonequilibrium phonons excited by light in the near-surface domain of a crystal or a thin plate is investigated. An exact expression is obtained for the phonon energy flux for a crystal with a polar direction and its polarization dependence is analyzed. The magnitude of the energy flux can reach the incident light intensity. The temperature difference produced by the flux of nonequilibrium photo-excited phonons is found.

  17. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

    The Direct Simulation Monte Carlo (DSMC) method typically used to model thermochemical nonequilibrium rarefied gases requires accurate total collision cross sections, reaction probabilities, and molecular internal energy exchange models. However, the baseline total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, reaction probabilities are defined such that experimentally determined equilibrium reaction rates are replicated, and internal energy relaxation models are phenomenological in nature. Therefore, these models have questionable validity in modeling strongly nonequilibrium gases with temperatures greater than those possible in experimental test facilities. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method can be used to accurately compute total collision cross sections, reaction probabilities, and internal energy exchange models based on first principles for hypervelocity collision conditions. In this thesis, MD/QCT-based models were used to improve simulations of two unique nonequilibrium rarefied gas systems: the Ionian atmosphere and hypersonic shocks in Earth's atmosphere. The Jovian plasma torus flows over Io at ≈ 57 km/s, inducing high-speed collisions between atmospheric SO2 and the hypervelocity plasma's O atoms and ions. The DSMC method is well-suited to model the rarefied atmosphere, so MD/QCT studies are therefore conducted to improve DSMC collision models of the critical SO2-O collision pair. The MD/QCT trajectory simulations employed a new potential energy surface that was developed using a ReaxFF fit to a set of ab initio calculations. Compared to the MD/QCT results, the baseline DSMC models are found to significantly under-predict total cross sections, use reaction probabilities that are unrealistically high, and give unphysical internal energies above the dissociation energy for non-reacting inelastic collisions and under-predicts post

  18. Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations.

    PubMed

    Okumura, Hisashi; Itoh, Satoru G

    2014-07-30

    We describe the disruption of amyloid fibrils of Alzheimer's amyloid-β peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium all-atom molecular dynamics simulations with sinusoidal pressure and visualized the process with movies. When the pressure is negative, a bubble is formed, usually at hydrophobic residues in the transmembrane region. Most β-strands maintain their secondary structures in the bubble. When the pressure becomes positive, the bubble collapses, and water molecules crash against the hydrophilic residues in the nontransmembrane region to disrupt the amyloid. Shorter amyloids require longer sonication times for disruption because they do not have enough hydrophobic residues to serve as a nucleus to form a bubble. These results agree with experiments in which monodispersed amyloid fibrils were obtained by ultrasonication. PMID:24987794

  19. Plasticity induced by shock waves in nonequilibrium molecular-dynamics simulation

    SciTech Connect

    Holian, B.L.

    1998-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations of shock waves in single crystals have shown that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. Later calculations quantified the apparent threshold strength, namely the yield strength of the perfect crystal. Subsequently, pulsed x-ray experiments on shocked single crystals showed relative shifts in diffraction peaks, confirming the authors NEMD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, the authors have been able to simulate shock waves in 10-million atom crystals with cross sectional dimensions of 100 x 100 fcc unit cells (compared to earlier 6 x 6 systems). They have seen that the increased cross-section allows the system to slip along all of the available {l_brace}111{r_brace} slip planes, in different places along the now non-planar shock front. These simulations conclusively eliminate the worry that the kind of slippage they have observed is somehow an artifact of transverse periodic boundary conditions. Moreover, they have introduced a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, and show that for weaker shock waves (below the perfect crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

  20. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene

    PubMed Central

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-01-01

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties. PMID:27609305

  1. The non-equilibrium phase diagrams of flow-induced crystallization and melting of polyethylene.

    PubMed

    Wang, Zhen; Ju, Jianzhu; Yang, Junsheng; Ma, Zhe; Liu, Dong; Cui, Kunpeng; Yang, Haoran; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-01-01

    Combining extensional rheology with in-situ synchrotron ultrafast x-ray scattering, we studied flow-induced phase behaviors of polyethylene (PE) in a wide temperature range up to 240 °C. Non-equilibrium phase diagrams of crystallization and melting under flow conditions are constructed in stress-temperature space, composing of melt, non-crystalline δ, hexagonal and orthorhombic phases. The non-crystalline δ phase is demonstrated to be either a metastable transient pre-order for crystallization or a thermodynamically stable phase. Based on the non-equilibrium phase diagrams, nearly all observations in flow-induced crystallization (FIC) of PE can be well understood. The interplay of thermodynamic stabilities and kinetic competitions of the four phases creates rich kinetic pathways for FIC and diverse final structures. The non-equilibrium flow phase diagrams provide a detailed roadmap for precisely processing of PE with designed structures and properties. PMID:27609305

  2. Shockwave-induced plasticity via large-scale nonequilibrium molecular dynamics

    SciTech Connect

    Holian, B.L.

    1998-07-01

    Nonequilibrium molecular-dynamics (MD) simulations of shock waves in single crystals have shown that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. Later calculations quantified the apparent threshold strength, namely the yield strength of the perfect crystal. Subsequently, pulsed x-ray experiments on shocked single crystals showed relative shifts in diffraction peaks, confirming our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have been able to simulate shock waves in 10-million atom crystals with cross-sectional dimensions of 100{times}100 fcc unit cells (compared to earlier 6{times}6 systems). We have seen that the increased cross-section allows the system to slip along all of the available {l_brace}111{r_brace} slip planes, in different places along the now non-planar shock front. These simulations conclusively eliminate the worry that the kind of slippage we have observed is somehow an artifact of transverse periodic boundary conditions. Thus, future simulations are much more likely to show that weak-shock plasticity is nucleated by pre-existing extended defects embedded in the sample. {copyright} {ital 1998 American Institute of Physics.}

  3. Disorder-driven nonequilibrium melting studied by electron diffraction, brillouis scattering, and molecular dynamics

    SciTech Connect

    Okamoto, P. R.; Lam, N. Q.; Grimsditch, M.

    1999-12-21

    In the present paper, a brief overview of the electron diffraction, Brillouin scattering and molecular dynamics studies of radiation-induced amorphization of ordered intermetallic compounds is presented. In these studies, measured changes in the velocity of surface acoustic phonons, lattice constant, and the Bragg-Williams long-range order parameter induced by irradiation were compared with the results of computer simulations of defect-induced amorphization. The results indicate that progressive chemical disordering of the superlattice structure during irradiation is accompanied by an expansion of the lattice and a large change in sound velocity corresponding to a {approximately} 50% decrease in the average shear modulus. The onset of amorphization occurs when the average shear modulus of the crystalline compound becomes equal to that of the amorphous phase. This elastic softening criterion for the onset of amorphization and the dependence of the average shear modulus on the long-range-order parameter are in excellent agreement with molecular dynamics simulations. Both the experimental observations and computer simulations confirm the predictions of the generalized Lindemann melting criterion which stipulates that thermodynamic melting of a defective crystal occurs when the sum of the dynamic and static mean-square atomic displacements reaches a critical value identical to that for melting of the defect-free crystal. In this broader view of melting, the crystal-to-glass transformation is a disorder-driven nonequilibrium melting process occurring at temperatures below the Kauzmann isentropic glass-transition temperature.

  4. Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Ripmeester, J. A.

    2010-04-01

    Nonequilibrium, constant energy, constant volume (NVE) 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.

  5. Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

    SciTech Connect

    Bresme, F.; Armstrong, J.

    2014-01-07

    We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.

  6. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states

    NASA Astrophysics Data System (ADS)

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2016-04-01

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  7. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states.

    PubMed

    Bjorgaard, J A; Velizhanin, K A; Tretiak, S

    2016-04-21

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited statemolecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited statemolecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission. PMID:27389206

  8. The molecular photo-cell: quantum transport and energy conversion at strong non-equilibrium.

    PubMed

    Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan

    2015-01-01

    The molecular photo-cell is a single molecular donor-acceptor complex attached to electrodes and subject to external illumination. Besides the obvious relevance to molecular photo-voltaics, the molecular photo-cell is of interest being a paradigmatic example for a system that inherently operates in out-of-equilibrium conditions and typically far from the linear response regime. Moreover, this system includes electrons, phonons and photons, and environments which induce coherent and incoherent processes, making it a challenging system to address theoretically. Here, using an open quantum systems approach, we analyze the non-equilibrium transport properties and energy conversion performance of a molecular photo-cell, including both coherent and incoherent processes and treating electrons, photons, and phonons on an equal footing. We find that both the non-equilibrium conditions and decoherence play a crucial role in determining the performance of the photovoltaic conversion and the optimal energy configuration of the molecular system. PMID:25660494

  9. The Molecular Photo-Cell: Quantum Transport and Energy Conversion at Strong Non-Equilibrium

    PubMed Central

    Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan

    2015-01-01

    The molecular photo-cell is a single molecular donor-acceptor complex attached to electrodes and subject to external illumination. Besides the obvious relevance to molecular photo-voltaics, the molecular photo-cell is of interest being a paradigmatic example for a system that inherently operates in out-of-equilibrium conditions and typically far from the linear response regime. Moreover, this system includes electrons, phonons and photons, and environments which induce coherent and incoherent processes, making it a challenging system to address theoretically. Here, using an open quantum systems approach, we analyze the non-equilibrium transport properties and energy conversion performance of a molecular photo-cell, including both coherent and incoherent processes and treating electrons, photons, and phonons on an equal footing. We find that both the non-equilibrium conditions and decoherence play a crucial role in determining the performance of the photovoltaic conversion and the optimal energy configuration of the molecular system. PMID:25660494

  10. Shockwave-Induced Plasticity Via Large-Scale Nonequilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Holian, Brad Lee

    1997-07-01

    In nonequilibrium molecular-dynamics (MD) simulations of shock waves in single crystals, carried out in 1979 at Los Alamos,(B.L. Holian and G.K. Straub, Phys. Rev. Lett. 43), 1598 (1979). we discovered that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. We realized, of course, that real materials could yield at much lower thresholds, and speculated then that pre-existing defects could nucleate plastic flow at lower shock strengths than those characteristic of pure single crystals. (Historical note: at about the same time as our earliest dynamical shockwave simulations, Mogilevsky, working independently in the Soviet Union, carried out relaxation MD calculations under uniaxial strain, and observed spontaneous production of dislocations.(M.A. Mogilevsky, in Shock Waves and High Strain Rate Phenomena in Metals) (Plenum, New York, 1981), p.531.) Further Los Alamos calculations, carried out nearly a decade later in five-times larger systems (up to 10,000 atoms), confirmed this observation and quantified the threshold strength, namely the yield strength of the perfect crystal.(B.L. Holian, Phys. Rev. A 37), 2562 (1988); for a review, see B.L. Holian, Shock Waves 5, 149 (1995). Subsequently, Zaretskii and co-workers,(E.B. Zaretskii, G.I. Kanel, P.A. Mogilevskii, and V.E. Fortov, Sov. Phys. Dokl. 36), 76 (1991). using x-ray diffraction of shocked single crystals, confirmed our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have recently studied systems with over six-times larger cross-sectional area and four-times longer distance of run to the steady state (approximately 270,000 atoms). We have seen that the increased cross-section allows the system to slip along both available forward slip systems, in

  11. High-Pressure Unconditionally Stable Nonequilibrium Molecular Plasmas

    NASA Astrophysics Data System (ADS)

    Palm, Peter; Ploenjes, Elke; Adamovich, Igor; Rich, J. William

    2000-10-01

    A novel method of sustaining unconditionally stable, large-volume, high-pressure nonequilibrium plasmas is suggested. The plasma is initiated by resonance absorption of CO laser radiation by carbon monoxide gas mixed with nitrogen and oxygen or nitric oxide in an absorption cell followed by overpopulation of high vibrational levels of CO in vibration-vibration (V-V) energy exchange collisions, [ CO(v) + CO(w) leftharpoons CO(v-1) + CO(w+1) ] and subsequent ionization by an associative ionization mechanism, [ CO(v) + CO(w) arrow (CO)_2^+ + e^-, Ev + Ew >= E_ion. ] Free electrons produced by associative ionization are heated by a sub-breakdown RF field applied to the optically pumped plasma. The heated electrons lose their energy primarily in collisions with the molecules, thereby vibrationally exciting all molecules. This is followed by overpopulation of high vibrational levels of the molecules by the V-V exchange process and further associative ionization. Unconditional stability is enabled by a negative feedback between gas heating and ionization due to an increase of vibration-translation relaxation rates with temperature leading to rapid depopulation of high vibrational levels needed for associative ionization.

  12. Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water

    NASA Astrophysics Data System (ADS)

    Bresme, Fernando

    2001-10-01

    Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water (CFM) [Lemberg and Stillinger, J. Chem. Phys. 62, 1677 (1975)] are presented. We consider a model based on a functional form introduced in theoretical studies of associating systems employing integral equations [F. Bresme, J. Chem. Phys. 108, 4505 (1998)]. Results on thermodynamic, dynamic, dielectric, and coexistence properties are presented. The central force model shows satisfactory agreement with the experimental results in all these cases. In addition, nonequilibrium molecular-dynamics simulations show that the CFM predicts a decrease of the thermal conductivity with temperature, as observed in the experiment, but this dependence is reproduced qualitatively at temperatures characteristic of supercooled states. These results emphasize the need for further studies of the heat conduction and properties of water in these conditions. Overall the present potential should provide a basis for further theoretical and simulation studies of complex systems where water is present.

  13. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    SciTech Connect

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

    1980-09-29

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

  14. Exciton coupling in molecular crystals

    NASA Technical Reports Server (NTRS)

    Ake, R. L.

    1976-01-01

    The implications of perfect exciton coupling and molecular vibrations were investigated, as well as the effect they have on the lifetime of singlet and triplet excitons coupled in a limiting geometry. Crystalline bibenzyl, Cl4Hl4, provided a situation in which these mechanisms involving exciton coupling can be studied in the limit of perfect coupling between units due to the crystal's geometry. This geometry leads to a coupling between the two halves of the molecule resulting in a splitting of the molecular excited states. The study reported involves an experimental spectroscopic approach and begins with the purification of the bibenzyl. The principal experimental apparatus was an emission spectrometer. A closed cycle cryogenic system was used to vary the temperature of the sample between 20 K and 300 K. The desired results are the temperature-dependent emission spectra of the bibenzyl; in addition, the lifetimes and quantum yields measured at each temperature reveal the effect of competing radiationless processes.

  15. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

  16. Reduced thermal conductivity of a nanoparticle decorated nanowire: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Masnoon, Ahmed Shafkat; Bipasha, Ferdaushi Alam; Morshed, A. K. M. M.

    2016-07-01

    The effect of nanoparticles decoration on the thermal conductivity of a nanowire is studied using Non Equilibrium Molecular Dynamics (NEMD) simulation. The simulation was conducted using simplified molecular model with Lennard-Jones potential. Argon-like solid was used as the material for both the nanowire and nanoparticles. Nanoparticles were placed on the surface of the nanowire and also embedded inside the structure. Non-equilibrium molecular dynamics simulation was conducted by imposing temperature gradient along the length of the nanowire and thermal conductivity of the nanowire was calculated. Nanowire without any nanoparticles was used as the baseline data. Due to presence of nanoparticles thermal conductivity of the nanowire was observed to decrease and up to 40% reduction in thermal conductivity was observed. With the increase in number of the nanoparticles, thermal conductivity was observed to decrease; however size of nanoparticles has little effect.

  17. Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading

    NASA Astrophysics Data System (ADS)

    Aghaei, Amin; Dayal, Kaushik

    2011-06-01

    We report on non-equilibrium molecular dynamics calculations of chiral single-wall carbon nanotubes using the framework of Objective Structures. This enables us to adapt molecular dynamics to the symmetry of chiral nanotubes and efficiently simulate these systems with small unit cells. We outline the method and the adaptation of a conventional thermostat and barostat to this setting. We then apply the method in order to examine the behavior of nanotubes with various chiralities subject to a constant extensional strain rate. We examine the effects of temperature, strain rate, and pre-compression/pre-tension. We find a range of failure mechanisms, including the formation of Stone-Wales defects, the opening of voids, and the motion of atoms out of the cross-section.

  18. Dynamic molecular crystals with switchable physical properties.

    PubMed

    Sato, Osamu

    2016-06-21

    The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials. PMID:27325090

  19. Synthesis of calcium oxalate crystals in culture medium irradiated with non-equilibrium atmospheric-pressure plasma

    NASA Astrophysics Data System (ADS)

    Kurake, Naoyuki; Tanaka, Hiromasa; Ishikawa, Kenji; Nakamura, Kae; Kajiyama, Hiroaki; Kikkawa, Fumitaka; Mizuno, Masaaki; Yamanishi, Yoko; Hori, Masaru

    2016-09-01

    Octahedral particulates several tens of microns in size were synthesized in a culture medium irradiated through contact with a plume of non-equilibrium atmospheric-pressure plasma (NEAPP). The particulates were identified in the crystalline phase as calcium oxalate dihydrate (COD). The original medium contained constituents such as NaCl, d-glucose, CaCl2, and NaHCO3 but not oxalate or oxalic acid. The oxalate was clearly synthesized and crystallized in the medium as thermodynamically unstable COD crystals after the NEAPP irradiation.

  20. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics—Monte Carlo simulations

    SciTech Connect

    Chen, Yunjie; Roux, Benoît

    2015-01-14

    A family of hybrid simulation methods that combines the advantages of Monte Carlo (MC) with the strengths of classical molecular dynamics (MD) consists in carrying out short non-equilibrium MD (neMD) trajectories to generate new configurations that are subsequently accepted or rejected via an MC process. In the simplest case where a deterministic dynamic propagator is used to generate the neMD trajectories, the familiar Metropolis acceptance criterion based on the change in the total energy ΔE, min[1,  exp( − βΔE)], guarantees that the hybrid algorithm will yield the equilibrium Boltzmann distribution. However, the functional form of the acceptance probability is more complex when the non-equilibrium switching process is generated via a non-deterministic stochastic dissipative propagator coupled to a heat bath. Here, we clarify the conditions under which the Metropolis criterion remains valid to rigorously yield a proper equilibrium Boltzmann distribution within hybrid neMD-MC algorithm.

  1. Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Clarke, Elaine T.

    2013-09-01

    Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

  2. Manipulating crystallization with molecular additives.

    PubMed

    Shtukenberg, Alexander G; Lee, Stephanie S; Kahr, Bart; Ward, Michael D

    2014-01-01

    Given the importance of organic crystals in a wide range of industrial applications, the chemistry, biology, materials science, and chemical engineering communities have focused considerable attention on developing methods to control crystal structure, size, shape, and orientation. Tailored additives have been used to control crystallization to great effect, presumably by selectively binding to particular crystallographic surfaces and sites. However, substantial knowledge gaps still exist in the fundamental mechanisms that govern the formation and growth of organic crystals in both the absence and presence of additives. In this review, we highlight research discoveries that reveal the role of additives, either introduced by design or present adventitiously, on various stages of formation and growth of organic crystals, including nucleation, dislocation spiral growth mechanisms, growth inhibition, and nonclassical crystal morphologies. The insights from these investigations and others of their kind are likely to guide the development of innovative methods to manipulate crystallization for a wide range of materials and applications. PMID:24579880

  3. Finite elements and the discrete variable representation in nonequilibrium Green's function calculations. Atomic and molecular models

    NASA Astrophysics Data System (ADS)

    Balzer, Karsten; Bauch, Sebastian; Bonitz, Michael

    2010-04-01

    In this contribution, we discuss the finite-element discrete variable representation (FE-DVR) of the nonequilibrium Green's function and its implications on the description of strongly inhomogeneous quantum systems. In detail, we show that the complementary features of FEs and the DVR allow for a notably more efficient solution of the two-time Schwinger/Keldysh/Kadanoff-Baym equations compared to a general basis approach. Particularly, the use of the FE-DVR leads to an essential speedup in computing the self-energies. As atomic and molecular examples we consider the He atom and the linear version of H+3 in one spatial dimension. For these closed-shell models we, in Hartree-Fock and second Born approximation, compute the ground-state properties and compare with the exact findings obtained from the solution of the few-particle time-dependent Schrödinger equation.

  4. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    PubMed

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation. PMID:27121070

  5. Nonequilibrium molecular dynamics simulations with a backward-forward trajectories sampling for multidimensional infrared spectroscopy of molecular vibrational modes

    NASA Astrophysics Data System (ADS)

    Hasegawa, Taisuke; Tanimura, Yoshitaka

    2008-02-01

    A full molecular dynamics (MD) simulation approach to calculate multidimensional third-order infrared (IR) signals of molecular vibrational modes is proposed. Third-order IR spectroscopy involves three-time intervals between three excitation and one probe pulses. The nonequilibrium MD (NEMD) simulation allows us to calculate molecular dipoles from nonequilibrium MD trajectories for different pulse configurations and sequences. While the conventional NEMD approach utilizes MD trajectories started from the initial equilibrium state, our approach does from the intermediate state of the third-order optical process, which leads to the doorway-window decomposition of nonlinear response functions. The decomposition is made before the second pump excitation for a two-dimensional case of IR photon echo measurement, while it is made after the second pump excitation for a three-dimensional case of three-pulse IR photon echo measurement. We show that the three-dimensional IR signals are efficiently calculated by using the MD trajectories backward and forward in time for the doorway and window functions, respectively. We examined the capability of the present approach by evaluating the signals of two- and three-dimensional IR vibrational spectroscopies for liquid hydrogen fluoride. The calculated signals might be explained by anharmonic Brownian model with the linear-linear and square-linear system-bath couplings which was used to discuss the inhomogeneous broadening and dephasing mechanism of vibrational motions. The predicted intermolecular librational spectra clearly reveal the unusually narrow inhomogeneous linewidth due to the one-dimensional character of HF molecule and the strong hydrogen bond network.

  6. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    PubMed

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-01

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches. PMID:26539729

  7. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    NASA Astrophysics Data System (ADS)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  8. A localized momentum constraint for non-equilibrium molecular dynamics simulations.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2015-02-21

    A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case. PMID:25702005

  9. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressurea)

    NASA Astrophysics Data System (ADS)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2012-07-01

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  10. F 3 - molecular ions in fluoride crystals

    NASA Astrophysics Data System (ADS)

    Radzhabov, E. A.

    2016-02-01

    The UV absorption spectra of F 3 - molecular ions in LaF3, SrF2, CaF2, and BaF2 crystals doped with rare-earth elements are studied. Comparison of radiation-colored and additively colored crystals reveals the absorption bands of F 3 - hole centers in the region near 6 eV. Nonempirical calculations of optical transitions agree well with experimental results.

  11. Collective sliding states for colloidal molecular crystals

    SciTech Connect

    Reichhardt, Charles; Reichhardt, Cynthia

    2008-01-01

    We study the driving of colloidal molecular crystals over periodic substrates such as those created with optical traps. The n-merization that occurs in the colloidal molecular crystal states produces a remarkably rich variety of distinct dynamical behaviors, including polarization effects within the pinned phase and the formation of both ordered and disordered sliding phases. Using computer simulations, we map the dynamic phase diagrams as a function of substrate strength for dimers and trimers on a triangular substrate, and correlate features on the phase diagram with transport signatures.

  12. Photoinduced molecular reorientation of absorbing liquid crystals

    NASA Astrophysics Data System (ADS)

    Marrucci, L.; Paparo, D.

    1997-08-01

    The phenomenon of photoinduced molecular reorientation of absorbing nematic liquid crystals is analyzed in a macroscopic general framework and with a specific molecular model. The photoinduced torque responsible for the reorientation is shown to describe a transfer of angular momentum from the molecule center-of-mass degrees of freedom to the rotational ones, mediated by molecular friction. As a consequence, a photoinduced stress tensor is predicted to develop together with the torque in the illuminated fluid. A molecular expression of the photoinduced torque is derived with a rigorous procedure, valid both for a pure material and for a dye-liquid-crystal mixture. This torque expression corrects those reported in previous works on the same subject. The photoinduced torque is evaluated analytically in a simple approximate limit.

  13. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  14. Effects of vacancy defects on thermal conductivity in crystalline silicon: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lee, Yongjin; Lee, Sangheon; Hwang, Gyeong S.

    2011-03-01

    We examine the effects of vacancy defects on thermal conductivity in bulk crystalline silicon (c-Si) using nonequilibrium molecular dynamics simulations. While most vacancies are thought to remain in the form of clusters in bulk c-Si, recent theoretical studies have predicted that small vacancy clusters energetically prefer to be fourfold coordinated by nullifying dangling bonds. Hence, in this work, we consider three different-sized fourfold vacancy clusters, tetra- (V4), hexa- (V6), and dodeca-vacancy (V12), with particular interest in studying how phonon transport is affected by vacancy concentration and cluster size in association with fourfold coordination-induced lattice distortions. Our simulations show that thermal conductivity (κ) rapidly drops with vacancy concentration (nv) with an inverse power-law relation (κ∝nv-α, with α ≈ 0.7-1.1 depending on cluster size); the presence of 1.5% vacancies leads to a 95% reduction in κ as compared to the defect free c-Si. When nv is low (<1%), the reduction of κ with nv appears to be a function of cluster size, and the size effect becomes unimportant as nv increases above 1%. We discuss the correlation between phone scattering and cluster size, based on the relative rates of phonon-vacancy scattering associated with defect-induced strain fields. We also estimate the dependence of phonon mean free path on vacancy concentration and cluster size.

  15. Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew

    2014-11-01

    This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box deforms with the flow, and it is possible for image particles to become arbitrarily close, causing a breakdown in the simulation. The KR boundary conditions avoid this problem for planar elongational flow and general planar mixed flow [T. A. Hunt, S. Bernardi, and B. D. Todd, J. Chem. Phys. 133, 154116 (2010)] through careful choice of the initial simulation box and by periodically remapping the simulation box in a way that conserves image locations. In this work, the ideas are extended to a large class of three-dimensional flows by using multiple remappings for the simulation box. The simulation box geometry is no longer time-periodic (which was shown to be impossible for uniaxial and biaxial stretching flows in the original work by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)]. The presented algorithm applies to all flows with nondefective flow matrices, and in particular, to uniaxial and biaxial flows.

  16. Nonlinear rheological behavior associated with structural transitions in block copolymer solutions via nonequilibrium molecular dynamics.

    PubMed

    Rychkov, Igor; Yoshikawa, Kenichi

    2004-02-15

    The nonequilibrium molecular dynamics computer simulation method was used to study microsegregated block copolymer systems in a selective solvent under a shear flow field. Two polymer concentrations were considered, 0.3 and 0.4, corresponding to the body centered cubic spherical and hexagonal cylindrical zero-shear phases, respectively. As the shear rate increased, both systems exhibited two-stage shear thinning, a peak in the scalar pressure, and normal stress differences. Microscopic connections were investigated by calculating the gyration and bond orientation tensors and the interaction energies per particle. At high shear rates, polymer chains elongate and orient along the direction of shear, and this is accompanied by the breaking-up of domains. The structure-rheology relation was discussed with regard to the morphological changes reported in our last study for the same systems. In particular, the structurally relevant critical values of the shear rate were found to delimit different behaviors of the shear rate-dependencies obtained in this work. PMID:15268506

  17. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

    NASA Astrophysics Data System (ADS)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2013-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  18. Nonequilibrium versus equilibrium molecular dynamics studies of solvation dynamics after photoexcitation of OClO

    NASA Astrophysics Data System (ADS)

    Gunnerson, Kim N.; Brooksby, Craig; Prezhdo, Oleg V.; Reid, Philip J.

    2007-10-01

    The results of our earlier work [C. Brooksby, O. V. Prezhdo, and P. J. Reid, J. Chem. Phys. 119, 9111 (2003)] rationalizing the surprisingly weak solvent dependence of the dynamics following photoexcitation of chlorine dioxide in water, chloroform, and cyclohexane are thoroughly tested. Comparisons are made between equilibrium and nonequilibrium solvent response, equilibrium response in the ground and excited electronic states, as well as the cumulant and direct evaluation of the optical response function. In general, the linear response and cumulant approximations are found to hold, although minor deviations are found with all solvents. The ground state, linear response, and cumulant data show best agreement with experiment, most likely due to the better tested ground-state force field and the robust behavior of the linear response and cumulant approximations. The main conclusion of our earlier work explaining the weak solvent dependence by the domination of the van der Waals interaction component remains intact within the more advanced treatments. However, the molecular origin of this surprising experimental observation is different in water and chloroform compared to cyclohexane.

  19. Non-equilibrium molecular dynamics simulation of the unstirred layer in the osmotically driven flow

    NASA Astrophysics Data System (ADS)

    Konno, Keito; Itano, Tomoaki; Seki, Masako

    2015-11-01

    We studied the solvent flows driven by the osmotic pressure difference across the semi-permeable membrane. The flow penetrating from the low concentration side transports away solutes adjacent of the membrane, so that the concentration is reduced significantly only at the vicinity of the membrane. It is expected that the relatively low solute concentration develops into a thin boundary layer in the vicinity of the membrane in the case of absence of external stirring process, which is termed as un-stirred layer (USL). To investigate concentration distribution in USL, we carried out non-equilibrium molecular dynamics simulations. The flows driven by th osmotic pressure are idealized as 2 dimensional hard disk model, which is composed of solvent and solute molecules. The membrane is modeled as a medium composed of stationary parallel rods distributed by a spatial interval, which is less than the diameter of the solute molecules. The following results were obtained from the numerical simulation. First, the thickness of USL, which was estimated from the obtained concentration distribution, is on the order of a length determined by mean free path. Second, USL was semicircle the center of which is on the end of pore of membrane.

  20. Protein crystallization facilitated by molecularly imprinted polymers

    PubMed Central

    Saridakis, Emmanuel; Khurshid, Sahir; Govada, Lata; Phan, Quan; Hawkins, Daniel; Crichlow, Gregg V.; Lolis, Elias; Reddy, Subrayal M.; Chayen, Naomi E.

    2011-01-01

    We present a previously undescribed initiative and its application, namely the design of molecularly imprinted polymers (MIPs) for producing protein crystals that are essential for determining high-resolution 3D structures of proteins. MIPs, also referred to as “smart materials,” are made to contain cavities capable of rebinding protein; thus the fingerprint of the protein created on the polymer allows it to serve as an ideal template for crystal formation. We have shown that six different MIPs induced crystallization of nine proteins, yielding crystals in conditions that do not give crystals otherwise. The incorporation of MIPs in screening experiments gave rise to crystalline hits in 8–10% of the trials for three target proteins. These hits would have been missed using other known nucleants. MIPs also facilitated the formation of large single crystals at metastable conditions for seven proteins. Moreover, the presence of MIPs has led to faster formation of crystals in all cases where crystals would appear eventually and to major improvement in diffraction in some cases. The MIPs were effective for their cognate proteins and also for other proteins, with size compatibility being a likely criterion for efficacy. Atomic force microscopy (AFM) measurements demonstrated specific affinity between the MIP cavities and a protein-functionalized AFM tip, corroborating our hypothesis that due to the recognition of proteins by the cavities, MIPs can act as nucleation-inducing substrates (nucleants) by harnessing the proteins themselves as templates. PMID:21690356

  1. Nonequilibrium Molecular Dynamics Simulations of Organic Friction Modifiers Adsorbed on Iron Oxide Surfaces.

    PubMed

    Ewen, James P; Gattinoni, Chiara; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

    2016-05-10

    For the successful development and application of lubricants, a full understanding of the nanoscale behavior of complex tribological systems is required, but this is difficult to obtain experimentally. In this study, we use nonequilibrium molecular dynamics (NEMD) simulations to examine the atomistic structure and friction properties of commercially relevant organic friction modifier (OFM) monolayers adsorbed on iron oxide surfaces and lubricated by a thin, separating layer of hexadecane. Specifically, acid, amide, and glyceride OFMs, with saturated and Z-unsaturated hydrocarbon tail groups, are simulated at various surface coverages and sliding velocities. At low and medium coverage, the OFMs form liquidlike and amorphous monolayers, respectively, which are significantly interdigitated with the hexadecane lubricant, resulting in relatively high friction coefficients. At high coverage, solidlike monolayers are formed for all of the OFMs, which, during sliding, results in slip planes between well-defined OFM and hexadecane layers, yielding a marked reduction in the friction coefficient. When present at equal surface coverage, OFMs with saturated and Z-unsaturated tail groups are found to yield similar structure and friction behavior. OFMs with glyceride head groups yield significantly lower friction coefficients than amide and particularly carboxylic acid head groups. For all of the OFMs and coverages simulated, the friction coefficient is found to increase linearly with the logarithm of sliding velocity; however, the gradient of this increase depends on the coverage. The structure and friction details obtained from these simulations agree well with experimental results and also shed light on the relative tribological performance of these OFMs through nanoscale structural variations. This has important implications in terms of the applicability of NEMD to aid the development of new formulations to control friction. PMID:27064962

  2. Shear viscosity of a supercooled polymer melt via nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Varnik, F.; Binder, K.

    2002-10-01

    Using nonequilibrium molecular dynamics simulations, we compute the shear viscosity, ηs, of a glass forming polymer melt at temperatures ranging from the normal liquid state down to the supercooled state. For this purpose, the polymer melt is confined between two solid walls and a constant force pointing in direction parallel to the walls is applied on each monomer thus giving rise to a Poiseuille flow. It is shown that ηs(T) does not exhibit an Arrhenius-type behavior but can be described both by a power law (mode coupling theory) and by a Vogel-Fulcher-Tammann law. A similar behavior is observed in recent experiments above the glass transition temperature. The diffusion coefficient is computed using the mean square displacements in direction perpendicular to the flow. Combined with the knowledge of ηs(T), it is then shown that the Stokes-Einstein relation is valid at high temperatures, whereas deviations are observed in the supercooled regime in agreement with experiments. Moreover, the local viscosity, η(z), is also computed and its reliability is discussed. Using the sharp rise of η(z) close to the wall, we estimate zwall, the effective position of the wall. It is found that zwall moves towards the film center at lower T thus leading to a decrease of the (hydrodynamic) width of the system. Furthermore, we observe that the curves for η(z)/ηs at various temperatures superimpose if the data are depicted versus z-zwall(T). This suggests that the spatial and temperature dependence of the local viscosity separate if the effective position of the wall is chosen as a new reference plane.

  3. Star formation and molecular hydrogen in dwarf galaxies: a non-equilibrium view

    NASA Astrophysics Data System (ADS)

    Hu, Chia-Yu; Naab, Thorsten; Walch, Stefanie; Glover, Simon C. O.; Clark, Paul C.

    2016-06-01

    We study the connection of star formation to atomic (H I) and molecular hydrogen (H2) in isolated, low-metallicity dwarf galaxies with high-resolution (mgas = 4 M⊙, Nngb = 100) smoothed particle hydrodynamics simulations. The model includes self-gravity, non-equilibrium cooling, shielding from a uniform and constant interstellar radiation field, the chemistry of H2 formation, H2-independent star formation, supernova feedback and metal enrichment. We find that the H2 mass fraction is sensitive to the adopted dust-to-gas ratio and the strength of the interstellar radiation field, while the star formation rate is not. Star formation is regulated by stellar feedback, keeping the gas out of thermal equilibrium for densities n < 1 cm-3. Because of the long chemical time-scales, the H2 mass remains out of chemical equilibrium throughout the simulation. Star formation is well correlated with cold (T ≤ 100 K) gas, but this dense and cold gas - the reservoir for star formation - is dominated by H I, not H2. In addition, a significant fraction of H2 resides in a diffuse, warm phase, which is not star-forming. The interstellar medium is dominated by warm gas (100 K < T ≤ 3 × 104 K) both in mass and in volume. The scaleheight of the gaseous disc increases with radius while the cold gas is always confined to a thin layer in the mid-plane. The cold gas fraction is regulated by feedback at small radii and by the assumed radiation field at large radii. The decreasing cold gas fractions result in a rapid increase in depletion time (up to 100 Gyr) for total gas surface densities Σ _{H I+H_2} ≲ 10 M⊙ pc-2, in agreement with observations of dwarf galaxies in the Kennicutt-Schmidt plane.

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

    PubMed

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

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540

  5. Crystallization of nickel nanoclusters by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Gaminchev, K.

    2012-12-01

    We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.

  6. Autocatalytic Decomposition Mechanisms in Energetic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Kuklja, Maija; Rashkeev, Sergey

    2009-06-01

    Atomic scale mechanisms of the initiation of chemical processes in energetic molecular crystals, which lead to the decomposition and ultimately to an explosive chain reaction, are still far from being understood. In this work, we investigate the onset of the initiation processes in two high explosive crystals - diamino-dinitroethylene (DADNE) and triamino- trinitrobenzene (TATB). We found that an autocatalytic decomposition mechanism is likely to take place in DADNE crystal that consists of corrugated, dashboard-shaped molecular layers. The presence of a dissociated NO2 group in the interstitial space between two layers induces a significant shear-strain between these layers, which, in turn, facilitates the further dissociation of NO2 groups from surrounding molecules through lowering the C-NO2 decomposition barrier. Unlike this, in TATB (that consists of flat, graphite-like molecular layers), an interstitial NO2 group positioned between two layers tends to produce a tensile stress (rather than a shear-strain), which leads to local molecular disorder in these layers without any significant modification of the C-NO2 decomposition barrier. The observed differences between the two materials are discussed in terms of their structural, electronic, and chemical properties.

  7. Molecular Models of Liquid Crystal Elastomers

    NASA Astrophysics Data System (ADS)

    Rajshekhar

    Liquid crystal elastomers combine the elastic properties of conventional rubbers with the optical properties of liquid crystals. This dual nature gives rise to unusual physical properties, including the stress induced transition from a polydomain state, consisting of multiple nematic regions with independent orientations, to a monodomain state consisting of a single nematic region with a uniform director. We propose several molecular-scale coarse-grained models of liquid crystal elastomers with varying degrees of resolution. The models employ the Gay-Berne soft potential, and exhibit the chain connectivity of a diamond network. Simulation results show that these models are able to capture the polydomain state exhibited by liquid crystal elastomers in the absence of any external stress. When subjected to uniaxial stress, our models exhibit a polydomain to monodomain transition. We explain that the polydomain state occurs through the aggregation of liquid crystal molecules assisted by crosslinking sites, and conclude that the transition mechanism to the monodomain state is based on the reorientation of nematic domains along the direction of applied stress. Our modeling efforts are primarily focused on three models. The first two models consider the effects of rigid and flexible crosslinkers in liquid crystal elastomers with a diamond topology for chain connectivity. The third model deviates from the diamond network topology and adopts a random network topology.

  8. The temperature dependence of the heat conductivity of a liquid crystal studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2010-01-01

    The temperature dependence of the heat conductivity has been obtained for a liquid crystal model based on the Gay-Berne fluid, from the isotropic phase at high temperatures through the nematic phase to the smectic A phase at low temperatures. The ratio of the parallel and the perpendicular components of the heat conductivity is about 2.5:1 in the nematic phase, which is similar to that of real systems. Both Green-Kubo methods and nonequilibrium molecular dynamics methods have been applied and the results agree within in a relative error of a couple of percent, but the latter method is much more efficient.

  9. Nonequilibrium phenomena in N{sub 2}-cluster-surface collisions: A molecular-dynamics study of fragmentation, lateral jetting, and nonequilibrium energy distributions

    SciTech Connect

    Zimmermann, Steffen; Urbassek, Herbert M.

    2006-12-15

    Using molecular-dynamics simulation, we study the impact of (N{sub 2}){sub 2869} clusters on a flat rigid wall. We study the cluster fragmentation process, the formation of lateral jets, the energy redistribution among the resulting fragments, and the ratio of internal and translational energy of the emerging free molecules as a function of cluster impact energy in the range of 0.076-1520 meV/molecule. We find the fragmentation threshold energy to be in agreement with that found previously for (N{sub 2}){sub 13} clusters; the (scaled) number of fragments, however, increases more slowly with impact energy. Also the energy redistribution of the cluster impact energy among the internal and translational energy of the fragments is similar to that found for the small cluster. This means in particular that free molecules show a strong nonequilibrium energy partitioning in which the internal degrees of freedom are considerably less excited than the translational degrees of freedom. We also find that at impact energies above the fragmentation threshold the angular distribution of fragments is peaked parallel to the surface--i.e., the formation of lateral surface jets.

  10. Thermal conductivity behavior of superatom molecular crystals

    NASA Astrophysics Data System (ADS)

    Ong, Wee-Liat; O'Brien, Evan; Dougherty, Patrick; Epstein, Jillian; Higgs, C. Fred; McGaughey, Alan; Roy, Xavier; Malen, Jonathan

    The room temperature thermal conductivity of several superatom molecular crystals (SMCs) are measured and found to be below 0.3 W/mK. The trend of room temperature thermal conductivity of the different crystals agree well with their sound speeds obtained independently using nano-indentation. These crystals, however, can exhibit non-crystalline thermal conductivity behavior depending on their constituent elements. A superatom is a cluster of atoms that acts as a stable entity [e.g., fullerenes (C60)]. By careful mixing and assembling these nano-sized superatoms, the resulting superatom-assembled materials hold promises for improving various technological devices. Organic-inorganic superatoms can assemble into unary SMCs or co-crystallized with C60 superatoms into binary SMCs. Thermal transport is of considerable interest with possible new physics in these hierarchically atomic precise crystals in the low temperature regime. The thermal conductivity of the SMCs are measured using the frequency domain thermoreflectance setup. Unary SMCs exhibit an almost invariant thermal conductivity down to a temperature of 150 K. Binary SMCs, however, can either show a crystalline-like increase or an amorphous-like decrease with decreasing temperature.

  11. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  12. Shear thinning behavior of linear polymer melts under shear flow via nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Xu, Xiaolei; Chen, Jizhong; An, Lijia

    2014-05-01

    The properties of both untangled and entangled linear polymer melts under shear flow are studied by nonequilibrium molecular dynamics simulations. The results reveal that the dependence of shear viscosity η on shear rate dot{γ }, expressed by η ˜ dot{γ }^{-n}, exhibits three distinct regimes. The first is the well-known Newtonian regime, namely, η independent of shear rate at small shear rates dot{γ }<τ 0^{-1} (where τ0 is the longest polymer relaxation time at equilibrium). In the non-Newtonian regime (dot{γ }>τ 0^{-1}), the shear dependence of viscosity exhibits a crossover at a critical shear rate dot{γ }c dividing this regime into two different regimes, shear thinning regime I (ST-I) and II (ST-II), respectively. In the ST-I regime (τ ^{-1}_0dot{γ }c) a universal power law η ˜ dot{γ }^{-0.37} is found for considered chain lengths. Furthermore, the longer the polymer chain is, the smaller the shear viscosity for a given shear rate in the ST-II regime. The simulation also shows that a characteristic chain length, below which dot{γ }c will be equal to τ 0^{-1}, lies in the interval 30 < N < 50. For all considered chain lengths in the ST-II regime, we also find that the first and second normal stress differences N1 and N2 follow power laws of N1 ˜ dot{γ }^{2/3} and N2 ˜ dot{γ }^{0.82}, respectively; the orientation resistance parameter mG follows the relation mG ˜ dot{γ }^{0.75} and the tumbling frequency ftb follows f_{tb} ˜ dot{γ }^{0.75}. These results imply that the effects of entanglement on the shear dependences of these properties may be negligible in the ST-II regime. These findings may shed some light on the nature of shear thinning in flexible linear polymer melts.

  13. Pressure-induced transformations in molecular crystals

    SciTech Connect

    Taylor, R.D.; Hearne, G.R. |; Pasternak, M.P.

    1995-09-01

    A review is given on the unique features of the Moessbauer spectroscopy (MS) which by virtue of the quadrupole interaction and the lattice dynamics allows one to characterize some structural properties in the pressure-induced amorphous state of molecular crystals. Experiments were performed in GeI{sub 4}, SnI{sub 4} and SnBr{sub 4} by means of {sup 119}Sn and {sup 129}I MS with pressures to 35 GPa at cryogenic temperatures using diamond anvil cells.

  14. Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. [Viscosity and thermal conductivity of continuous, or polydisperse mixtures

    SciTech Connect

    Murad, S.

    1990-09-01

    This progress report covers research carried out during the period September 15, 1987--September 15, 1990. The main emphasis of the work was on dense fluid mixtures, although in some cases work had to be done on pure fluids before we could study mixtures in a meaningful way. A summary of our results is given. (1) An algorithm was developed and used to calculate the viscosity and thermal conductivity of continuous, or polydisperse mixtures with various distributions (e.g. linear, several gaussian distributions including unsymmetric, etc.) using nonequilibrium molecular dynamics (NEMD). (2) A method was developed to calculate the thermal conductivity of nonspherical (rigid) molecules using NEMD. (3) The NEMD method for thermal conductivity of nonspherical molecules was used to have a careful look at the contributions due to internal rotational degrees of freedom in linear compounds such as chlorine, nitrogen, etc. (4) It has long been speculated that polar fluids exhibit heat induced birefringence, i.e., the molecules will tend to align themselves along the direction of an external heat field. Using nonequilibrium molecular dynamics we were able to conclusively confirm this. (5) We completed a preliminary study of the viscosity of homonuclear diatomics and their mixtures (e.g. N{sub 2}, Cl{sub 2}, etc.). (6) We completed a study of the various flexibility (vibrational) effects, such as bond bending, bond stretching etc., on linear and nonlinear model triatomics. To examine these effects in our preliminary study, we looked at the pressure second virial coefficients.

  15. Ionic conductivity in Gd-doped CeO2: Ab initio color-diffusion nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nilsson, Johan O.; Vekilova, Olga Yu.; Hellman, Olle; Klarbring, Johan; Simak, Sergei I.; Skorodumova, Natalia V.

    2016-01-01

    A first-principles nonequilibrium molecular dynamics (NEMD) study employing the color-diffusion algorithm has been conducted to obtain the bulk ionic conductivity and the diffusion constant of gadolinium-doped cerium oxide (GDC) in the 850-1150 K temperature range. Being a slow process, ionic diffusion in solids usually requires simulation times that are prohibitively long for ab initio equilibrium molecular dynamics. The use of the color-diffusion algorithm allowed us to substantially speed up the oxygen-ion diffusion. The key parameters of the method, such as field direction and strength as well as color-charge distribution, have been investigated and their optimized values for the considered system have been determined. The calculated ionic conductivity and diffusion constants are in good agreement with available experimental data.

  16. Nonlinear vibrational excitations in molecular crystals molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Pumilia, P.; Abbate, S.; Baldini, G.; Ferro, D. R.; Tubino, R.

    1992-03-01

    The coupling constant for vibrational solitons χ has been examined in a molecular mechanics model for acetanilide (ACN) molecular crystal. According to A.C. Scott, solitons can form and propagate in solid acetanilide over a threshold energy value. This can be regarded as a structural model for the spines of hydrogen bond chains stabilizing the α helical structure of proteins. A one dimensional hydrogen bond chain of ACN has been built, for which we have found that, even though experimental parameters are correctly predicted, the excessive rigidity of the isolated chain prevents the formation of a localized distortion around the excitation. Yet, C=O coupling value with softer lattice modes could be rather high, allowing self-trapping to take place.

  17. Curl flux, coherence, and population landscape of molecular systems: Nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics

    SciTech Connect

    Zhang, Z. D.; Wang, J.

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  18. Molecular kinetic theory of strongly nonequilibrium processes of mass, momentum, and energy transfer: Local equilibrium criteria

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2015-09-01

    Consequences of the complete system of transfer equations of the properties (momentum, energy, and mass) of particles and their pairs are considered under local equilibrium conditions with regard to the Bogoliubov hierarchy of relaxation times between the first and second distribution functions (DFs) and distinctions in the characteristic relaxation times of particle momentum, energy, and mass. It is found that even under the local equilibrium condition in the Bogoliubov hierarchy of relaxation times between the first and second DFs, pair correlations are maintained between all dynamic variables (velocity, temperature, and density) whose values are proportional to the gradients of transferable properties. A criterion is introduced requiring there be no local equilibrium condition upon reaching the critical value at which the description of the transfer process becomes incorrect in classical nonequilibrium thermodynamics. External forces are considered in the equations for strongly nonequilibrium processes. Along with allowing for intermolecular potentials, it becomes possible to discuss the concept of passive forces (introduced in thermodynamics by Gibbs) from the standpoint of the kinetic theory. It is shown that use of this concept does not reflect modern representations of real processes.

  19. Non-equilibrium dynamics of 2D liquid crystals driven by transmembrane gas flow.

    PubMed

    Seki, Kazuyoshi; Ueda, Ken; Okumura, Yu-ichi; Tabe, Yuka

    2011-07-20

    Free-standing films composed of several layers of chiral smectic liquid crystals (SmC*) exhibited unidirectional director precession under various vapor transfers across the films. When the transferred vapors were general organic solvents, the precession speed linearly depended on the momentum of the transmembrane vapors, where the proportional constant was independent of the kind of vapor. In contrast, the same SmC* films under water transfer exhibited precession in the opposite direction. As a possible reason for the rotational inversion, we suggest the competition of two origins for the torques, one of which is microscopic and the other macroscopic. Next, we tried to move an external object by making use of the liquid crystal (LC) motion. When a solid or a liquid particle was set on a film under vapor transfer, the particle was rotated in the same direction as the LC molecules. Using home-made laser tweezers, we measured the force transmitted from the film to the particle, which we found to be several pN. PMID:21709328

  20. Non-equilibrium dynamics of 2D liquid crystals driven by transmembrane gas flow

    NASA Astrophysics Data System (ADS)

    Seki, Kazuyoshi; Ueda, Ken; Okumura, Yu-ichi; Tabe, Yuka

    2011-07-01

    Free-standing films composed of several layers of chiral smectic liquid crystals (SmC*) exhibited unidirectional director precession under various vapor transfers across the films. When the transferred vapors were general organic solvents, the precession speed linearly depended on the momentum of the transmembrane vapors, where the proportional constant was independent of the kind of vapor. In contrast, the same SmC* films under water transfer exhibited precession in the opposite direction. As a possible reason for the rotational inversion, we suggest the competition of two origins for the torques, one of which is microscopic and the other macroscopic. Next, we tried to move an external object by making use of the liquid crystal (LC) motion. When a solid or a liquid particle was set on a film under vapor transfer, the particle was rotated in the same direction as the LC molecules. Using home-made laser tweezers, we measured the force transmitted from the film to the particle, which we found to be several pN.

  1. New zinc-glycine-iodide complexes as a product of equilibrium and non-equilibrium crystallization in the Gly - ZnI2 - H2O system

    NASA Astrophysics Data System (ADS)

    Tepavitcharova, S.; Havlíček, D.; Matulková, I.; Rabadjieva, D.; Gergulova, R.; Plocek, J.; Němec, I.; Císařová, I.

    2016-09-01

    Equilibrium crystallization of two anhydrous complex compounds, [Zn(gly)2I2] and [Zn(gly)I2], and non-equilibrium crystallization of the [Zn3(H2O)4(μ-gly)2I6] complex have been observed in the Gly - ZnI2 - H2O system at 25°C. Different mixed zinc-glycine-iodide-aqua complexes exist in the studied solutions and those with the highest activity are responsible for the crystallization process. The stable [ZnI2O2(2Gly)]0 complexes are responsible for the large equilibrium crystallization field of the compound [Zn(gly)2I2] (monoclinic system, C2/c space group), in whose crystal structure they are incorporated as discrete distorted electroneutral tetrahedra. In zinc-iodide solutions with a low water activity it is more probable that the glycine zwitterions act as bidentate ligands and form polynuclear complexes. We assume the [ZnI2O2(2/2Gly)]0 infinite chains build the compound [Zn(gly)I2], for which we have found a narrow equilibrium crystallization field. We have failed to describe the crystal structure of this compound because of its limited stability in the air. Non-equilibrium crystallization of [Zn3(H2O)4(μ-gly)2I6] (triclinic system, P-1 space group) was demonstrated, with crystal structure built by trinuclear complexes [ZnI3O(1/2Gly)] [ZnO4(4H2O)O2(2/2Gly)(trans)][ZnI3O(1/2Gly)]. The FTIR and Raman spectra and also the thermal behaviour of the three compounds were discussed.

  2. Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Solomentsev, Gleb Y.; English, Niall J.; Mooney, Damian A.

    2010-12-01

    Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å-1. A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-à-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

  3. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics.

    PubMed

    English, Niall J; Garate, José-A

    2016-08-28

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region. PMID:27586951

  4. Molecular wires from discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Park, Ji Hyun; Labardi, Massimiliano; Scalia, Giusy

    2014-02-01

    Discotic liquid crystal (LC) can arrange in columnar structures along which electrical conduction occurs via π-π interaction between adjacent molecular cores. The efficiency of the conductivity is strongly dependent on the overlap of the orbitals of neighbor molecules and, in general, on the structural arrangements. The understanding of the factors that influence the organization is crucial for the optimization of the final conductive properties of the self-assembled columns. In this paper we present a study on the self-organization into molecular wires of a discotic LC using a solution based method. In particular, we focus on the effect of solvents used for preparing the LC solution. The resulting morphologies were investigated by atomic force microscopy (AFM) and optical microscopy, showing that diverse structures result from different solvents. With suitable conditions, we were able to induce very long fibers, with several tents of micrometer in length that, in turn, self-organize assuming a common orientation on a macroscopic scale.

  5. Equilibrium and Nonequilibrium Statistical Mechanics of Membranes, Liquid Crystal Films, and Other Layered Structures.

    NASA Astrophysics Data System (ADS)

    Chen, Chi-Ming

    In this thesis, we develop and analyze a continuum Landau theory for chiral and achiral lipid bilayers. This theory contains couplings between tangent-plane orientational order and curvature that lead to "rippled" phases with one-dimensional height modulations and to phases with two -dimensional height modulations. We calculate the mean -field phase diagrams by using both analytical and numerical methods. We generalize our theory to study the equilibrium phase diagrams of liquid crystal films. Both bulk smectics and freely suspended films are considered. For flexoelectric systems, continuous structural phase transitions are predicted among square-lattice, hexagonal, and distorted square-lattice phases as a function of the applied electric field. It is also shown that only uniform flat phases are predicted for thin films. One-dimensional ripple phases and two -dimensional square lattice phases can occur with increasing film thickness. Secondly we study the growth and instability of Myelin figures. For quasi-equilibrium growth, we predict a growth rate proportional to t^{-1/2 }, where t is the growth time. The proportional constant is inversely proportional to the viscosity of the fluid. Myelin figures are unstable under dehydration. The initial instability of myelin figures develops periodic arrays of bumps at the surface with a wave length of about 1 mum. This morphological change is induced by increasing the ratio of surface area to volume of myelin figures due to dehydration. We interpret this initial instability from energetical considerations and calculate the preferred wave length. Finally, we study theoretically the swelling kinetics of layered structures, particularly triblock copolymer mesogels. The gels are swollen by a solvent good for the bridging block but poor for the nonbridging block. At late stages the penetration front moves as in ordinary diffusion. However, the bending elasticity of the non -bridging layers leads to an initial t^{1/6 } relaxation

  6. THE ABUNDANCE OF MOLECULAR HYDROGEN AND ITS CORRELATION WITH MIDPLANE PRESSURE IN GALAXIES: NON-EQUILIBRIUM, TURBULENT, CHEMICAL MODELS

    SciTech Connect

    Mac Low, Mordecai-Mark; Glover, Simon C. O. E-mail: glover@uni-heidelberg.de

    2012-02-20

    Observations of spiral galaxies show a strong linear correlation between the ratio of molecular to atomic hydrogen surface density R{sub mol} and midplane pressure. To explain this, we simulate three-dimensional, magnetized turbulence, including simplified treatments of non-equilibrium chemistry and the propagation of dissociating radiation, to follow the formation of H{sub 2} from cold atomic gas. The formation timescale for H{sub 2} is sufficiently long that equilibrium is not reached within the 20-30 Myr lifetimes of molecular clouds. The equilibrium balance between radiative dissociation and H{sub 2} formation on dust grains fails to predict the time-dependent molecular fractions we find. A simple, time-dependent model of H{sub 2} formation can reproduce the gross behavior, although turbulent density perturbations increase molecular fractions by a factor of few above it. In contradiction to equilibrium models, radiative dissociation of molecules plays little role in our model for diffuse radiation fields with strengths less than 10 times that of the solar neighborhood, because of the effective self-shielding of H{sub 2}. The observed correlation of R{sub mol} with pressure corresponds to a correlation with local gas density if the effective temperature in the cold neutral medium of galactic disks is roughly constant. We indeed find such a correlation of R{sub mol} with density. If we examine the value of R{sub mol} in our local models after a free-fall time at their average density, as expected for models of molecular cloud formation by large-scale gravitational instability, our models reproduce the observed correlation over more than an order-of-magnitude range in density.

  7. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    PubMed

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  8. In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1

    PubMed Central

    Frentrup, Hendrik; Hart, Kyle E.; Colina, Coray M.; Müller, Erich A.

    2015-01-01

    We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers. PMID:25764366

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

    NASA Astrophysics Data System (ADS)

    Okumura, Hisashi

    2015-12-01

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

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

    SciTech Connect

    Okumura, Hisashi

    2015-12-31

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

  11. NONEQUILIBRIUM FLUCTUATIONS IN SHOCK COMPRESSION OF POLYCRYSTALLINE ALPHA-IRON

    SciTech Connect

    Y. HORIE; K. YANO

    2001-06-01

    We report a numerical study of heterogeneous and nonequilibrium fluctuations in shock compression of {alpha}-iron at the grain level. A quasi-molecular code called DM2 is used to model the interactions of a plane shock wave with grain boundaries and crystal anisotropy over the pressure range of 5-45 GPa. Highly transient eddies that were reported earlier are again observed. We show new features through an elementary statistical analysis. They are (1) a characteristic decay constant for the non-equilibrium fluctuation on the order of 20ns, (2) a resonance phenomenon at an intermediate shock pressure, and (3) a more uniform shock structure for very high pressures.

  12. Control of liquid crystal molecular orientation using ultrasound vibration

    NASA Astrophysics Data System (ADS)

    Taniguchi, Satoki; Koyama, Daisuke; Shimizu, Yuki; Emoto, Akira; Nakamura, Kentaro; Matsukawa, Mami

    2016-03-01

    We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5-25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distribution of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.

  13. An efficient nonequilibrium Green's function formalism combined with density functional theory approach for calculating electron transport properties of molecular devices with quasi-one-dimensional electrodes.

    PubMed

    Qian, Zekan; Li, Rui; Hou, Shimin; Xue, Zengquan; Sanvito, Stefano

    2007-11-21

    An efficient self-consistent approach combining the nonequilibrium Green's function formalism with density functional theory is developed to calculate electron transport properties of molecular devices with quasi-one-dimensional (1D) electrodes. Two problems associated with the low dimensionality of the 1D electrodes, i.e., the nonequilibrium state and the uncertain boundary conditions for the electrostatic potential, are circumvented by introducing the reflectionless boundary conditions at the electrode-contact interfaces and the zero electric field boundary conditions at the electrode-molecule interfaces. Three prototypical systems, respectively, an ideal ballistic conductor, a high resistance tunnel junction, and a molecular device, are investigated to illustrate the accuracy and efficiency of our approach. PMID:18035901

  14. Screened dipolar interactions in some molecular crystals

    NASA Astrophysics Data System (ADS)

    Munn, R. W.; Hurst, M.

    1990-10-01

    Screened dipole energies and dipole electric fields are calculated for the crystals of HCN, meta- and para-nitroaniline, the nonlinear optical compounds POM, MAP and DAN, meta-dinitrobenzene, and acetanilide. Only para-nitroaniline is centrosymmetric, but all the crystals have significant negative dipole energies (of the order of -20 kJ mol -1) except for POM and metadinitrobenzene, where they are positive but small in magnitude. Local dipole fields are of the order of 10 GV m -1. The results assume that surface charge annuls any macroscopic dipole field. It is speculated that the observed preponderance of centrosymmetric crystals of polar molecules may reflect a favourable dipole energy in the initial crystal nucleus rather than the macroscopic crystal.

  15. Thermal conductivity of carbon nanotube—polyamide-6,6 nanocomposites: Reverse non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Alaghemandi, Mohammad; Müller-Plathe, Florian; Böhm, Michael C.

    2011-11-01

    The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from naïve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.

  16. Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

    NASA Astrophysics Data System (ADS)

    Ghatage, Dhairyashil; Tomar, Gaurav; Shukla, Ratnesh K.

    2015-03-01

    Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.

  17. Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

    SciTech Connect

    Ghatage, Dhairyashil; Tomar, Gaurav Shukla, Ratnesh K.

    2015-03-28

    Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.

  18. Shear thinning and shear dilatancy of liquid n-hexadecane via equilibrium and nonequilibrium molecular dynamics simulations: Temperature, pressure, and density effects

    NASA Astrophysics Data System (ADS)

    Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu

    2008-07-01

    Equilibrium and nonequilibrium molecular dynamics (MD) simulations have been performed in both isochoric-isothermal (NVT) and isobaric-isothermal (NPT) ensemble systems. Under steady state shearing conditions, thermodynamic states and rheological properties of liquid n-hexadecane molecules have been studied. Between equilibrium and nonequilibrium states, it is important to understand how shear rates (γ˙) affect the thermodynamic state variables of temperature, pressure, and density. At lower shear rates of γ˙<1×1011s-1, the relationships between the thermodynamic variables at nonequilibrium states closely approximate those at equilibrium states, namely, the liquid is very near its Newtonian fluid regime. Conversely, at extreme shear rates of γ˙>1×1011s-1, specific behavior of shear dilatancy is observed in the variations of nonequilibrium thermodynamic states. Significantly, by analyzing the effects of changes in temperature, pressure, and density on shear flow system, we report a variety of rheological properties including the shear thinning relationship between viscosity and shear rate, zero-shear-rate viscosity, rotational relaxation time, and critical shear rate. In addition, the flow activation energy and the pressure-viscosity coefficient determined through Arrhenius and Barus equations acceptably agree with the related experimental and MD simulation results.

  19. Non-equilibrium molecular dynamics simulation of nanojet injection with adaptive-spatial decomposition parallel algorithm.

    PubMed

    Shin, Hyun-Ho; Yoon, Woong-Sup

    2008-07-01

    An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size. PMID:19051924

  20. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale.

    PubMed

    Juette, Manuel F; Terry, Daniel S; Wasserman, Michael R; Altman, Roger B; Zhou, Zhou; Zhao, Hong; Blanchard, Scott C

    2016-04-01

    Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis. PMID:26878382

  1. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. II. From time Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Hu, Ming

    2015-11-01

    From a nanoscale heat transfer point of view, currently one of the most interesting and challenging tasks is to quantitatively analyze phonon mode specific transport properties in solid materials, which plays a vital role in many emerging and diverse technological applications. It has not been long that such information can be provided by the phonon spectral energy density (SED) or equivalently time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics (EMD) simulations. However, few methods have been developed for nonequilibrium molecular dynamics (NEMD) simulations [Phys. Rev. B 91, 115426 (2015), 10.1103/PhysRevB.91.115426], the other widely used computational method for calculating thermal transport of materials in addition to EMD. In this work, a computational scheme based on time Fourier transform of atomistic heat current, called the frequency domain direct decomposed method (FDDDM), is proposed to analyze the contributions of frequency dependent thermal conductivity in NEMD simulations. The FDDDM results of Lennard-Jones argon and Stillinger-Weber Si are compared with the TDNMA method from EMD simulation. Similar trends are found for both cases, which confirm the validity of our FDDDM approach. Benefiting from the inherent nature of NEMD and the theoretical formula that does not require any temperature assumption, the FDDDM can be directly used to investigate the size and temperature effect. Moreover, the unique advantage of FDDDM prior to previous methods (such as SED and TDNMA) is that it can be straightforwardly used to characterize the phonon frequency dependent thermal conductivity of disordered systems, such as amorphous materials. The FDDDM approach can also be a good candidate to be used to understand the phonon behaviors and thus provides useful guidance for designing efficient structures for advanced thermal management.

  2. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. I. From space Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Zhang, Xiaoliang; Hu, Ming

    2015-11-01

    Probing detailed spectral dependence of phonon transport properties in bulk materials is critical to improve the function and performance of structures and devices in a diverse spectrum of technologies. Currently, such information can only be provided by the phonon spectral energy density (SED) or equivalently, time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics simulations (EMD), but has not been realized in nonequilibrium molecular dynamics simulations (NEMD) so far. In this paper we generate a scheme directly based on NEMD and lattice dynamics theory, called the time domain direct decomposition method (TDDDM), to predict the phonon mode specific thermal conductivity. Two benchmark cases of Lennard-Jones (LJ) argon and Stillinger-Weber (SW) Si are studied by TDDDM to characterize contributions of individual phonon modes to overall thermal conductivity and the results are compared with that predicted using SED and TDNMA. Similar trends are found for both cases, which indicate that our TDDDM approach captures the major phonon properties in NEMD run. The biggest advantage of TDDDM is that it can be used to investigate the size effect of individual phonon modes in NEMD simulations, which cannot be tackled by SED and TDNMA in EMD simulations currently. We found that the phonon modes with mean free path larger than the system size are truncated in NEMD and contribute little to the overall thermal conductivity. The TDDDM provides direct physical origin for the well-known strong size effects in thermal conductivity prediction by NEMD. Moreover, the well-known common sense of the zero thermal conductivity contribution from the Γ point is rigorously proved by TDDDM. Since TDDDM inherently possesses the nature of both NEMD simulations and lattice dynamics, we anticipate that TDDDM is particularly useful for offering a deep understanding of phonon behaviors in nanostructures or under strong confinement, especially when the

  3. A general set of order parameters for molecular crystals

    NASA Astrophysics Data System (ADS)

    Santiso, Erik E.; Trout, Bernhardt L.

    2011-02-01

    Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.

  4. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  5. Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt

    NASA Astrophysics Data System (ADS)

    Kong, Bin

    2015-03-01

    Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.

  6. Photoinduced Ratchet-Like Rotational Motion of Branched Molecular Crystals.

    PubMed

    Zhu, Lingyan; Al-Kaysi, Rabih O; Bardeen, Christopher J

    2016-06-13

    Photomechanical molecular crystals can undergo a variety of light-induced motions, including expansion, bending, twisting, and jumping. The use of more complex crystal shapes may provide ways to turn these motions into useful work. To generate such shapes, pH-driven reprecipitation has been used to grow branched microcrystals of the anthracene derivative 4-fluoroanthracenecarboxylic acid. When these microcrystals are illuminated with light of λ=405 nm, an intermolecular [4+4] photodimerization reaction drives twisting and bending of the individual branches. These deformations drive a rotation of the overall crystal that can be repeated over multiple exposures to light. The magnitude and direction of this rotation vary because of differences in the crystal shape, but a typical branched crystal undergoes a 50° net rotation after 25 consecutive irradiations for 1 s. The ability of these crystals to undergo ratchet-like rotation is attributed to their chiral shape. PMID:27150819

  7. Quantum dissipative effects on non-equilibrium transport through a single-molecular transistor: The Anderson-Holstein-Caldeira-Leggett model

    NASA Astrophysics Data System (ADS)

    Raju, Ch. Narasimha; Chatterjee, Ashok

    2016-01-01

    The Anderson-Holstein model with Caldeira-Leggett coupling with environment is considered to describe the damping effect in a single molecular transistor (SMT) which comprises a molecular quantum dot (with electron-phonon interaction) mounted on a substrate (environment) and coupled to metallic electrodes. The electron-phonon interaction is first eliminated using the Lang-Firsov transformation and the spectral density function, charge current and differential conductance are then calculated using the non-equilibrium Keldysh Green function technique. The effects of damping rate, and electron-electron and electron-phonon interactions on the transport properties of SMT are studied at zero temperature.

  8. Quantum dissipative effects on non-equilibrium transport through a single-molecular transistor: The Anderson-Holstein-Caldeira-Leggett model.

    PubMed

    Raju, Ch Narasimha; Chatterjee, Ashok

    2016-01-01

    The Anderson-Holstein model with Caldeira-Leggett coupling with environment is considered to describe the damping effect in a single molecular transistor (SMT) which comprises a molecular quantum dot (with electron-phonon interaction) mounted on a substrate (environment) and coupled to metallic electrodes. The electron-phonon interaction is first eliminated using the Lang-Firsov transformation and the spectral density function, charge current and differential conductance are then calculated using the non-equilibrium Keldysh Green function technique. The effects of damping rate, and electron-electron and electron-phonon interactions on the transport properties of SMT are studied at zero temperature. PMID:26732725

  9. Quantum dissipative effects on non-equilibrium transport through a single-molecular transistor: The Anderson-Holstein-Caldeira-Leggett model

    PubMed Central

    Raju, Ch. Narasimha; Chatterjee, Ashok

    2016-01-01

    The Anderson-Holstein model with Caldeira-Leggett coupling with environment is considered to describe the damping effect in a single molecular transistor (SMT) which comprises a molecular quantum dot (with electron-phonon interaction) mounted on a substrate (environment) and coupled to metallic electrodes. The electron-phonon interaction is first eliminated using the Lang-Firsov transformation and the spectral density function, charge current and differential conductance are then calculated using the non-equilibrium Keldysh Green function technique. The effects of damping rate, and electron-electron and electron-phonon interactions on the transport properties of SMT are studied at zero temperature. PMID:26732725

  10. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    SciTech Connect

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  11. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

  12. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition.

    PubMed

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G; Mpourmpakis, Giannis; Asplin, John R; Rimer, Jeffrey D

    2016-08-25

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization--citrate and hydroxycitrate--exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation of

  13. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

    NASA Astrophysics Data System (ADS)

    Wang, Guan M.; Sandberg, William C.

    2007-04-01

    In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated

  14. Orientational disorder: A key to understand polarity of molecular crystals

    NASA Astrophysics Data System (ADS)

    Hulliger, J.; Brahimi, K.; Burgener, M.; Dulcevscaia, G.

    2014-12-01

    Polarity of molecular crystals is understood here as a result of 180° orientational disorder of asymmetrical building blocks. Symmetry arguments based on (i) a single rotational degree of freedom, (ii) the finite size of crystals and (iii) interactions in between asymmetrical molecules lead to the conclusion that such crystals should express a bi-polar (∞/∞m) average state of zero polarity. This basic property of molecular crystals is exemplified by forming solid solutions of 4-iodo-4‧-nitro-biphenyl (INBP) and symmetrical bi-phenyls (BP: A-π-A, D-π-D; A: acceptor; D: donor). Monte Carlo simulations based on a layer-by-layer growth model predict a reversal of the bi-polar state of pure INBP by forming a solid solution of (INBP)1-x(D-π-D)x. In the case of the addition of A-π-A reversal as found for pure INBP is promoted, i.e. needs less growth steps (layers) to be accomplished. Real crystals representing solid solutions were grown from 2-butanon solutions using symmetrical BPs. Scanning pyroelectric microscopy confirmed the qualitative behavior seen in Monte Carlo simulations. These findings represent an experimentum crucis supporting the general validity of the theory of stochastic polarity formation applied to single component or solid solution molecular crystals.

  15. Impact of heterocirculene molecular symmetry upon two-dimensional crystallization

    PubMed Central

    Xiao, W. D.; Zhang, Y. Y.; Tao, L.; Aït-Mansour, K.; Chernichenko, K. Y.; Nenajdenko, V. G.; Ruffieux, P.; Du, S. X.; Gao, H.-J.; Fasel, R.

    2014-01-01

    Despite the development of crystal engineering, it remains a great challenge to predict the crystal structure even for the simplest molecules, and a clear link between molecular and crystal symmetry is missing in general. Here we demonstrate that the two-dimensional (2D) crystallization of heterocirculenes on a Au(111) surface is greatly affected by the molecular symmetry. By means of ultrahigh vacuum scanning tunneling microscopy, we observe a variety of 2D crystalline structures in the coverage range from submonolayer to monolayer for D8h-symmetric sulflower (C16S8), whereas D4h-symmetric selenosulflower (C16S4Se4) forms square and rectangular lattices at submonolayer and monolayer coverages, respectively. No long-range ordered structure is observed for C1h-symmetric selenosulflower (C16S5Se3) self-assembling at submonolayer coverage. Such different self-assembly behaviors for the heterocirculenes with reduced molecular symmetries derive from the tendency toward close packing and the molecular symmetry retention in 2D crystallization due to van der Waals interactions. PMID:24957140

  16. Defect-induced solid state amorphization of molecular crystals

    NASA Astrophysics Data System (ADS)

    Lei, Lei; Carvajal, Teresa; Koslowski, Marisol

    2012-04-01

    We investigate the process of mechanically induced amorphization in small molecule organic crystals under extensive deformation. In this work, we develop a model that describes the amorphization of molecular crystals, in which the plastic response is calculated with a phase field dislocation dynamics theory in four materials: acetaminophen, sucrose, γ-indomethacin, and aspirin. The model is able to predict the fraction of amorphous material generated in single crystals for a given applied stress. Our results show that γ-indomethacin and sucrose demonstrate large volume fractions of amorphous material after sufficient plastic deformation, while smaller amorphous volume fractions are predicted in acetaminophen and aspirin, in agreement with experimental observation.

  17. Formation of ohmic contacts to perylene molecular crystals

    NASA Astrophysics Data System (ADS)

    Hiramoto, Masahiro; Tomioka, Akinori; Suemori, Kouji; Yokoyama, Masaaki

    2004-09-01

    Ohmic contacts to perylene molecular crystals were successfully formed at bromine-doped p-type crystal/platinum junctions and sodium-doped n-type crystal/aluminum junctions to enable hole and electron injection, respectively. Charge-carrier doping of the organic semiconductor surface that was in direct contact with the metal electrodes was revealed as being a requirement for fabricating organic/metal junctions that were ohmic in character. The fabrication of ohmic contacts would be applicable to carrier injection in organic electroluminescent devices and carrier extraction from organic solar cells.

  18. From crystal morphology to molecular and scale crystallography

    NASA Astrophysics Data System (ADS)

    Janner, A.; Janssen, T.

    2015-08-01

    A number of topics, ranging from morphology of aperiodic crystals to indexed enclosing forms of axial-symmetric proteins, nucleic acids and viruses, have been selected among those investigated by the authors in 50 years of research. The basic symmetries involved in fields like superspace, molecular and scale crystallography, are considered from a personal point of view in their time evolution. A number of specific subjects follow, chosen among a few highlights and presented according to the experience of the authors: snow crystals, calaverite {{AuTe}}2, the incommensurately modulated crystals {{Rb}}2{{ZnBr}}4, {[{N}{({{CH}}3)}4]}2{{ZnCl}}4 and the mitochondrial ferritin.

  19. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  20. Nonequilibrium kinetics of the electron–phonon sybsystem of a crystal in a strong electric field as a base of the electroplastic effect

    SciTech Connect

    Karas, V. I. Vlasenko, A. M.; Sokolenko, V. I.; Zakharov, V. E.

    2015-09-15

    We present the results of a kinetic analysis of nonequilibrium dynamics of the electron–phonon system of a crystal in a strong electric field based on the proposed method of numerically solving a set of Boltzmann equations for electron and phonon distribution functions without expanding the electron distribution function into a series in the phonon energy. It is shown that the electric field action excites the electron subsystem, which by transferring energy to the phonon subsystem creates a large amount of short-wave phonons that effectively influence the lattice defects (point, lines, boundaries of different phases), which results in a redistribution of and decrease in the lattice defect density, in damage healing, in a decrease in the local peak stress, and a decrease in the degradation level of the construction material properties.

  1. Molecular theory of liquid crystal thin films

    NASA Astrophysics Data System (ADS)

    Meng, Shihong

    A molecular theory has been developed to describe the isotropic-nematic transitoon of model nematogens in bulk and in thin films. The surfaces of thin films can be hard surfaces or coated with surfactant monolayers. The theory only includes hard body interactions between all molecule species: solvent, nematogens and surfactants. We have studied the influence of the separation between confining walls, concentration of nematogens, as well as the surface anchoring and areal density of surfactant at the interface upon the phases of nematogens. We have explained the possible existence of planar degenerate phase through entropic pictures and have confirmed close to the bulk isotropic-nematic transition point, the order of the phases of nematogens from isotropic to nematic then back to isotropic when varying the areal density of surfactant monolayers at interfaces. From the results obtained, we believe that we have captured the main competing interactions between surfactants and nematogens and our molecular level theory is capable of describing these two interactions of different natures. Our results can provide a guideline for molecular design of biosensors. We have modeled the molecular systems with as much simplification as possible while retaining the main features. The thesis is arranged into introduction, results on bulk, thin films confined between hard walls and between surfactant monolayers.

  2. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

  3. Molecular Dynamics Simulations of Spinodal-Assisted Polymer Crystallization

    SciTech Connect

    Gee, R H; Lacevic, N M; Fried, L

    2005-07-08

    Large scale molecular dynamics simulations of bulk melts of polar (poly(vinylidene fluoride) (pVDF)) polymers are utilized to study chain conformation and ordering prior to crystallization under cooling. While the late stages of polymer crystallization have been studied in great detail, recent theoretical and experimental evidence indicates that there are important phenomena occurring in the early stages of polymer crystallization that are not understood to the same degree. When the polymer melt is quenched from a temperature above the melting temperature to the crystallization temperature, crystallization does not occur instantaneously. This initial interval without crystalline order is characterized as an induction period. It has been thought of as a nucleation period in the classical theories of polymer crystallization, but recent experiments, computer simulations, and theoretical work suggest that the initial period in polymer crystallization is assisted by a spinodal decomposition type mechanism. In this study we have achieved physically realistic length scales to study early stages of polymer ordering, and show that spinodal-assisted ordering prior to crystallization is operative in polar polymers suggesting general applicability of this process.

  4. Modelling transient heat conduction in solids at multiple length and time scales: A coupled non-equilibrium molecular dynamics/continuum approach

    SciTech Connect

    Jolley, Kenny; Gill, Simon P.A.

    2009-10-20

    A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nose-Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.

  5. Electromagnetically induced grating in a crystal of molecular magnets system

    NASA Astrophysics Data System (ADS)

    Liu, Jibing; Liu, Na; Shan, Chuanjia; Liu, Tangkun; Li, Hong; Zheng, Anshou; Xie, Xiao-Tao

    2016-07-01

    We investigate the response of the molecular system to the magnetic field modulation. Molecular magnets are subjected to a strong standing ac magnetic field and a weak probe magnetic field. The transmission and absorption of the weak probe magnetic field can be changed due to quantum coherence and the spatially modulating of the standing field. And a electromagnetically induced grating is formed in the crystal of molecular magnets via electromagnetically induced transparency (EIT). The diffraction efficiency of the grating can be adjusted efficiently by tuning the intensity of the standing wave field and the single photon detuning.

  6. Fundamental gap of molecular crystals via constrained density functional theory

    NASA Astrophysics Data System (ADS)

    Droghetti, Andrea; Rungger, Ivan; Das Pemmaraju, Chaitanya; Sanvito, Stefano

    2016-05-01

    The energy gap of a molecular crystal is one of the most important properties since it determines the crystal charge transport when the material is utilized in electronic devices. This is, however, a quantity difficult to calculate and standard theoretical approaches based on density functional theory (DFT) have proven unable to provide accurate estimates. In fact, besides the well-known band-gap problem, DFT completely fails in capturing the fundamental gap reduction occurring when molecules are packed in a crystal structures. The failure has to be associated with the inability of describing the electronic polarization and the real space localization of the charged states. Here we describe a scheme based on constrained DFT, which can improve upon the shortcomings of standard DFT. The method is applied to the benzene crystal, where we show that accurate results can be achieved for both the band gap and also the energy level alignment.

  7. Two-dimensional van der Waals C60 molecular crystal

    PubMed Central

    Reddy, C. D.; Gen Yu, Zhi; Zhang, Yong-Wei

    2015-01-01

    Two-dimensional (2D) atomic crystals, such as graphene and transition metal dichalcogenides et al. have drawn extraordinary attention recently. For these 2D materials, atoms within their monolayer are covalently bonded. An interesting question arises: Can molecules form a 2D monolayer crystal via van der Waals interactions? Here, we first study the structural stability of a free-standing infinite C60 molecular monolayer using molecular dynamic simulations, and find that the monolayer is stable up to 600 K. We further study the mechanical properties of the monolayer, and find that the elastic modulus, ultimate tensile stress and failure strain are 55–100 GPa, 90–155 MPa, and 1.5–2.3%, respectively, depending on the stretching orientation. The monolayer fails due to shearing and cavitation under uniaxial tensile loading. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the monolayer are found to be delocalized and as a result, the band gap is reduced to only 60% of the isolated C60 molecule. Interestingly, this band gap can be tuned up to ±30% using strain engineering. Owing to its thermal stability, low density, strain-tunable semi-conducting characteristics and large bending flexibility, this van der Waals molecular monolayer crystal presents aplenty opportunities for developing novel applications in nanoelectronics. PMID:26183501

  8. Two-dimensional van der Waals C60 molecular crystal

    NASA Astrophysics Data System (ADS)

    Reddy, C. D.; Gen Yu, Zhi; Zhang, Yong-Wei

    2015-07-01

    Two-dimensional (2D) atomic crystals, such as graphene and transition metal dichalcogenides et al. have drawn extraordinary attention recently. For these 2D materials, atoms within their monolayer are covalently bonded. An interesting question arises: Can molecules form a 2D monolayer crystal via van der Waals interactions? Here, we first study the structural stability of a free-standing infinite C60 molecular monolayer using molecular dynamic simulations, and find that the monolayer is stable up to 600 K. We further study the mechanical properties of the monolayer, and find that the elastic modulus, ultimate tensile stress and failure strain are 55-100 GPa, 90-155 MPa, and 1.5-2.3%, respectively, depending on the stretching orientation. The monolayer fails due to shearing and cavitation under uniaxial tensile loading. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the monolayer are found to be delocalized and as a result, the band gap is reduced to only 60% of the isolated C60 molecule. Interestingly, this band gap can be tuned up to ±30% using strain engineering. Owing to its thermal stability, low density, strain-tunable semi-conducting characteristics and large bending flexibility, this van der Waals molecular monolayer crystal presents aplenty opportunities for developing novel applications in nanoelectronics.

  9. Molecular dynamics of polymer crystallization revisited: Crystallization from the melt and the glass in longer polyethylene

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takashi

    2013-08-01

    Molecular mechanisms of the steady-state growth of the chain folded lamella and the cold crystallization across the glass transition temperature Tg are investigated by molecular dynamics simulation for a system of long polyethylene (PE)-like polymers made of 512 united atoms C512. The present paper aims to reconsider results of our previous simulations for short PE-like polymers C100 by carrying out very long simulations up to 1 μs for more realistic systems of much longer chains, thereby to establish the firm molecular image of chain-folded crystallization and clarify the specific molecular process of cold crystallization. We observe that the chain-folded lamella shows fast thickening-growth keeping marked tapered growth front. Despite the fast growth in much longer chains, the fold-surface is found to be predominantly of adjacent-reentry. Detailed inspections of the molecular pathway give an insightful image that can explain the apparently contradicting results. In addition, the fold-structure with specific spatial heterogeneity is found to give rise to heterogeneous mobility within the crystalline region. On the other hand, investigations of the cold crystallization during slow heating of the glassy film across Tg is found to give a granular texture made of small crystallites. The crystallites are found to nucleate preferentially near the free surfaces having lower Tg, and to be dominantly edge-on showing a definite tendency to orient their chain axes parallel to the free surface.

  10. Theoretical characterization of charge transport in organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Sanchez-Carrera, Roel S.

    The rapid growth in the interest to explore new synthetic crystalline organic semiconductors and their subsequent device characterization has revived the debate on the development of theoretical models to better understand the intrinsic charge transport mechanisms in organic materials. At the moment, several charge-transport theories for organic molecular crystals have been proposed and have observed a comparable agreement with experimental results. However, these models are limited in scope and restricted to specific ranges of microscopic parameters and temperatures. A general description that is applicable in all parameter regimes is still unavailable. The first step towards a complete understanding of the problem associated with the charge transport in organic molecular crystals includes the development of a first-principles theoretical methodology to evaluate with high accuracy the main microscopic charge-transport parameters and their respective couplings with intra- and intermolecular vibrational degrees of freedom. In this thesis, we have developed a first-principles methodology to investigate the impact of electron-phonon interactions on the charge-carrier mobilities in organic molecular crystals. Well-known organic materials such as oligoacene and oligothienoacene derivatives were studied in detail. To predict the charge-transport phenomena in organic materials, we rely on the Marcus theory of electron-transfer reactions. Within this context, the nature of the intramolecular vibronic coupling in oligoacenes was studied using an approach that combines high-resolution gas-phase photo-electron spectroscopy measurements with first-principles quantum-mechanical calculations. This further led to investigation of the electron interactions with optical phonons in oligoacene single crystals. The lattice phonon modes were computed at both density functional theory (DFT) and empirical force field levels. The low-frequency optical modes are found to play a significant

  11. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    PubMed

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419

  12. Shear-strain-induced chemical reactivity of layered molecular crystals

    SciTech Connect

    M. M. Kuklja; Sergey N. Rashkeev

    2007-04-01

    A density-functional-theory study of shear-related dissociation of two molecular crystals, diamino-dinitroethylene (FOX-7) and triamino-trinitrobenzine (TATB), is presented. A detailed explanation is proposed for the fact that FOX-7 is more sensitive than TATB while their sensitivities to initiation of chemistry have been expected to be comparable. We suggest that shear plays a crucial role in dissociation of molecules in organic energetic crystals and may be imperative in providing specific recommendations on ways for materials design.

  13. Nonlinear Optical Investigations of Vibrational Relaxation in Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Decola, Philip Lawrence

    Experimental studies of four-wave mixing have been used to obtain novel spectroscopic information in molecular crystals. This work can be separated into singly resonant and multiresonant investigations. One effort was to exploit the frequency and time domain capabilities of singly resonant coherent anti-Stokes Raman spectroscopy (CARS) to study vibrational dynamics in naphthalene and benzene single crystals at liquid Helium temperatures. To a large extent vibrational energy is chemical energy, so to understand the flow of vibrational energy in molecules and molecular aggregates can enhance our understanding of chemical reaction rates and pathways. Some of the salient results are: (1) the existence of motional narrowing in molecular crystals makes it possible for lifetime (T _1) broadening to dominate the linewidth of the vibrational transition even when the intrinsic disorder width is much larger than 1/T_1, (2) relaxation in molecular crystals can be surprisingly slow, ranging from subnanosecond to nanosecond, (3) substantial mode dependent contribution to relaxation from ^{13}C impurities in benzene, and (4) evidence of mode specific energy relaxation observed in a systematic study of benzene Raman active modes. The results obtained here are applied to the problems of understanding the contributions to residual low-temperature vibron linewidths and of developing simple mechanical intuitions to explain systematically the kinetic pathways for vibrational relaxation in molecular crystals. These results are discussed in light of the current theories of excitation dynamics in condensed phases. The other area of study was multiresonant nonlinear spectroscopic investigations of mixed organic crystals. The first multiresonant CARS and its Stokes analogue (CSRS) have been obtained in a mixed crystal of pentacene in benzoic acid allowing the simultaneous observation of ground and excited state Raman spectra. These spectra contain lines that are much sharper than expected

  14. Controlling Molecular Growth between Fractals and Crystals on Surfaces.

    PubMed

    Zhang, Xue; Li, Na; Gu, Gao-Chen; Wang, Hao; Nieckarz, Damian; Szabelski, Paweł; He, Yang; Wang, Yu; Xie, Chao; Shen, Zi-Yong; Lü, Jing-Tao; Tang, Hao; Peng, Lian-Mao; Hou, Shi-Min; Wu, Kai; Wang, Yong-Feng

    2015-12-22

    Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpiński triangle (ST) fractals and 2D molecular crystals that were formed by 4,4″-dihydroxy-1,1':3',1″-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block. PMID:26502984

  15. High Throughput Profiling of Molecular Shapes in Crystals.

    PubMed

    Spackman, Peter R; Thomas, Sajesh P; Jayatilaka, Dylan

    2016-01-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. PMID:26908351

  16. Dispersion Interactions in High-Density Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Csernica, Peter; Maitra, Rahul; Distasio, Robert

    Dispersion interactions are ubiquitous quantum mechanical phenomena arising from correlated electron density fluctuations in molecules and materials. As a key component of non-bonded interactions, dispersion forces play a critical role in determining the structure and stability of molecular crystals. Due to the relative intermolecular separation in high-density molecular crystals, an accurate description of these non-bonded interactions requires the inclusion of terms beyond the asymptotic induced-dipole-induced-dipole (C6 /R6) contribution. In this work, we have developed a first principles based approach within the framework of Density Functional Theory (i.e., that only depends on the charge density n (r)) for capturing the higher-order induced multipolar contributions to the correlation energy. As a first application of this method, we have investigated the structure and stability of the high-density ice molecular crystal polymorphs at the ice VI--ice VII--ice VIII triple point (278K, 2.1GPa) using ab-initio molecular dynamics in the isobaric-isothermal (NpT) ensemble.

  17. High Throughput Profiling of Molecular Shapes in Crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Peter R.; Thomas, Sajesh P.; Jayatilaka, Dylan

    2016-02-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design.

  18. High Throughput Profiling of Molecular Shapes in Crystals

    PubMed Central

    Spackman, Peter R.; Thomas, Sajesh P.; Jayatilaka, Dylan

    2016-01-01

    Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. PMID:26908351

  19. Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Konnert, John H.; Pusey, Marc L.

    2000-01-01

    Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth

  20. Diffusion on (110) Surface of Molecular Crystal Pentaerythritol Tetranitrate

    SciTech Connect

    Wang, J; Golfinopoulos, T; Gee, R H; Huang, H

    2007-01-25

    Using classical molecular dynamics simulations, we investigate the diffusion mechanisms of admolecules on the (110) surface of molecular crystal pentaerythritol tetranitrate. Our results show that (1) admolecules are stable at off lattice sites, (2) admolecules diffuse along close-packed [1{bar 1}1] and [{bar 1}11] directions, and (3) admolecules detach from the surface at 350K and above. Based on the number of diffusion jumps as a function of temperature, we estimate the jump frequency to be v=1.14 x 10{sup 12} e{sup -0.08eV/kT} per second.

  1. Guest-Induced Breathing Effect in a Flexible Molecular Crystal.

    PubMed

    Sheng, Yujie; Chen, Qibin; Yao, Junyao; Lu, Yunxiang; Liu, Honglai; Dai, Sheng

    2016-03-01

    By introducing a flexible component into a molecular building block, we present an unprecedented alkyl-decorated flexible crystalline material with a breathing behavior. Its selective adsorption is derived from the breathing effect induced by a guest triggered alkyl transformation. This feature allows the crystal to take up 2.5 mmol g(-1) of chloroform with high adsorption selectivity (CHCl3 /EA >2000 for example), implying a potential application in sorption separation and chemical sensors. PMID:26836312

  2. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  3. NMR of small solutes in liquid crystals and molecular sieves

    NASA Astrophysics Data System (ADS)

    Ylihautala, Mika Petri

    The present thesis deals with the nuclear magnetic resonance (NMR) spectroscopy of small solutes applied to the studies of liquid crystals and molecular sieves. In this method, changes induced by the investigated environment to the static spectral parameters (i.e. nuclear shielding, indirect and direct spin-spin coupling and quadrupole coupling) of the solute are measured. The nuclear shielding of dissolved noble gases is utilized for the studies of thermotropic liquid crystals. The relation between the symmetry properties of mesophases and the nuclear shielding is described. The different interaction mechanisms perturbing the observed noble gas nuclear shielding are discussed, particularly, the role of long-range attractive van der Waals interactions is brought out. The suitability of the noble gas NMR spectroscopy to the studies of Iyotropic liquid crystals is investigated in terms of nuclear shielding and quadrupole coupling interactions. In molecular sieve systems, the effect of inter- and intracrystalline motions of solutes on their NMR spectra is discussed. A novel method for the measurement of the intracrystalline motions is developed. The distinctions in the 13C shielding of methane adsorbed in AlPO4-11 and SAPO-11, two structurally similar molecular sieves differing in composition, are indicated.

  4. Collective aspects of singlet fission in molecular crystals

    NASA Astrophysics Data System (ADS)

    Teichen, Paul E.; Eaves, Joel D.

    2015-07-01

    We present a model to describe collective features of singlet fission in molecular crystals and analyze it using many-body theory. The model we develop allows excitonic states to delocalize over several chromophores which is consistent with the character of the excited states in many molecular crystals, such as the acenes, where singlet fission occurs. As singlet states become more delocalized and triplet states more localized, the rate of singlet fission increases. We also determine the conditions under which the two triplets resulting from fission are correlated. Using the Bethe Ansatz and an entanglement measure for indistinguishable bipartite systems, we calculate the triplet-triplet entanglement as a function of the biexciton interaction strength. The biexciton interaction can produce bound biexciton states and provides a source of entanglement between the two triplets even when the triplets are spatially well separated. Significant entanglement between the triplet pair occurs well below the threshold for bound pair formation. Our results paint a dynamical picture that helps to explain why fission has been observed to be more efficient in molecular crystals than in their covalent dimer analogues and have consequences for photovoltaic efficiency models that assume that the two triplets can be extracted independently.

  5. Collective aspects of singlet fission in molecular crystals.

    PubMed

    Teichen, Paul E; Eaves, Joel D

    2015-07-28

    We present a model to describe collective features of singlet fission in molecular crystals and analyze it using many-body theory. The model we develop allows excitonic states to delocalize over several chromophores which is consistent with the character of the excited states in many molecular crystals, such as the acenes, where singlet fission occurs. As singlet states become more delocalized and triplet states more localized, the rate of singlet fission increases. We also determine the conditions under which the two triplets resulting from fission are correlated. Using the Bethe Ansatz and an entanglement measure for indistinguishable bipartite systems, we calculate the triplet-triplet entanglement as a function of the biexciton interaction strength. The biexciton interaction can produce bound biexciton states and provides a source of entanglement between the two triplets even when the triplets are spatially well separated. Significant entanglement between the triplet pair occurs well below the threshold for bound pair formation. Our results paint a dynamical picture that helps to explain why fission has been observed to be more efficient in molecular crystals than in their covalent dimer analogues and have consequences for photovoltaic efficiency models that assume that the two triplets can be extracted independently. PMID:26233118

  6. Collective aspects of singlet fission in molecular crystals

    SciTech Connect

    Teichen, Paul E.; Eaves, Joel D.

    2015-07-28

    We present a model to describe collective features of singlet fission in molecular crystals and analyze it using many-body theory. The model we develop allows excitonic states to delocalize over several chromophores which is consistent with the character of the excited states in many molecular crystals, such as the acenes, where singlet fission occurs. As singlet states become more delocalized and triplet states more localized, the rate of singlet fission increases. We also determine the conditions under which the two triplets resulting from fission are correlated. Using the Bethe Ansatz and an entanglement measure for indistinguishable bipartite systems, we calculate the triplet-triplet entanglement as a function of the biexciton interaction strength. The biexciton interaction can produce bound biexciton states and provides a source of entanglement between the two triplets even when the triplets are spatially well separated. Significant entanglement between the triplet pair occurs well below the threshold for bound pair formation. Our results paint a dynamical picture that helps to explain why fission has been observed to be more efficient in molecular crystals than in their covalent dimer analogues and have consequences for photovoltaic efficiency models that assume that the two triplets can be extracted independently.

  7. Communication: energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach.

    PubMed

    Liu, Zhen-Fei; Neaton, Jeffrey B

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals. PMID:25296777

  8. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    SciTech Connect

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-07

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  9. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  10. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    SciTech Connect

    Tanaka, Kouichi; Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki; Kitsunezuka, Masashi; Shinma, Atsushi

    2013-11-21

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  11. Unusually Large Young's Muduli of Amino Acid Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Azuri, Ido; Meirzadeh, Elena; Ehre, David; Cohen, Sidney R.; Rappe, Andrew M.; Lahav, Meir; Lubomirsky, Igor; Kronik, Leeor

    Young's moduli of selected amino acid molecular crystals were studied both experimentally and computationally using nanoindentation and dispersion-corrected density functional theory. The Young modulus is found to be strongly facet-dependent, with some facets exhibiting exceptionally high values (as large as 44 GPa). The magnitude of Young's modulus is strongly correlated with the relative orientation between the underlying hydrogen-bonding network and the measured facet. Furthermore, we show computationally that the Young modulus can be as large as 70-90 GPa if facets perpendicular to the primary direction of the hydrogen-bonding network can be stabilized. This value is remarkably high for a molecular solid and suggests the design of hydrogen-bond networks as a route for rational design of ultra-stiff molecular solids. Angew. Chem. Int. Ed.. doi: 10.1002/anie.201505813.

  12. Non-equilibrium Dynamics of DNA Nanotubes

    NASA Astrophysics Data System (ADS)

    Hariadi, Rizal Fajar

    Can the fundamental processes that underlie molecular biology be understood and simulated by DNA nanotechnology? The early development of DNA nanotechnology by Ned Seeman was driven by the desire to find a solution to the protein crystallization problem. Much of the later development of the field was also driven by envisioned applications in computing and nanofabrication. While the DNA nanotechnology community has assembled a versatile tool kit with which DNA nanostructures of considerable complexity can be assembled, the application of this tool kit to other areas of science and technology is still in its infancy. This dissertation reports on the construction of non-equilibrium DNA nanotube dynamic to probe molecular processes in the areas of hydrodynamics and cytoskeletal behavior. As the first example, we used DNA nanotubes as a molecular probe for elongational flow measurement in different micro-scale flow settings. The hydrodynamic flow in the vicinity of simple geometrical objects, such as a rigid DNA nanotube, is amenable to rigorous theoretical investigation. We measured the distribution of elongational flows produced in progressively more complex settings, ranging from the vicinity of an orifice in a microfluidic chamber to within a bursting bubble of Pacific ocean water. This information can be used to constrain theories on the origin of life in which replication involves a hydrodynamically driven fission process, such as the coacervate fission proposed by Oparin. A second theme of this dissertation is the bottom-up construction of a de novo artificial cytoskeleton with DNA nanotubes. The work reported here encompasses structural, locomotion, and control aspects of non-equilibrium cytoskeletal behavior. We first measured the kinetic parameters of DNA nanotube assembly and tested the accuracy of the existing polymerization models in the literature. Toward recapitulation of non-equilibrium cytoskeletal dynamics, we coupled the polymerization of DNA

  13. Thermomechanical coupling, heat conduction and director rotation in cholesteric liquid crystals studied by molecular dynamics simulation.

    PubMed

    Sarman, Sten; Laaksonen, Aatto

    2013-03-14

    The lack of a centre of inversion in a cholesteric liquid crystal allows linear cross couplings between thermodynamic forces and fluxes that are polar vectors and pseudovectors, respectively. This makes it possible for a temperature gradient parallel to the cholesteric axis to induce a torque that rotates the director, a phenomenon known as the Lehmann effect or thermomechanical coupling. The converse is also possible: a torque applied parallel to the cholesteric axis rotates the director and drives a heat flow. In order to study this phenomenon, nonequilibrium molecular dynamics simulation algorithms and Green-Kubo relations evaluated by equilibrium molecular dynamics simulation have been used to calculate the Leslie coefficient, i.e. the cross coupling coefficient between the temperature gradient and the director angular velocity, for a model system composed of soft prolate ellipsoids of revolution interacting via the Gay-Berne potential augmented by a chiral interaction potential causing the formation of a cholesteric phase. It is found that the Leslie coefficient is two orders of magnitudes smaller than other transport coefficients such as the heat conductivity and the twist viscosity, so that very long simulations are required to evaluate it. The Leslie coefficient decreases with the pitch but it has not been possible to determine the exact functional dependence of this coefficient on the pitch. Since very long simulations have been performed to evaluate the Leslie coefficient, very accurate values have been obtained for the twist viscosity and the heat conductivity as a by-product and it is found that they are very similar to the values of the corresponding quantities in the achiral nematic phase that arises when the pitch goes to infinity. PMID:23223192

  14. Thwarting Crystallization through Hydrogen Bonding in Triazine Molecular Glasses

    NASA Astrophysics Data System (ADS)

    Laventure, Audrey; Soldera, Armand; Lebel, Olivier; Pellerin, Christian

    2015-03-01

    Using irregular shaped molecules interacting weakly with each other is the most intuitive choice to generate amorphous molecular materials. In contrast, H-bonds are commonly used in crystal engineering to create predictable ordered and well-packed structures. In spite of this fact, Lebel et al. have demonstrated that H-bonds can be used efficiently to thwart crystallization by inducing the self-assembly of aggregates that pack poorly. Since 2006, libraries of triazine derivatives with a variety of different substituents capable of forming molecular glasses have been synthesized and studied. Their outstanding glass-forming ability (with critical cooling rates lower than 0.5 °C/min) and their wide range of Tg (from below ambient temperature up to 160 °C) make them an attractive amorphous model system to deepen our understanding of the relationship between microscopic features and macroscopic behavior of glasses. In this presentation, we will show that variable-temperature infrared spectroscopy is a tool of choice to probe the vitreous state of these compounds. We take advantage of the selectivity of this technique to correlate their molecular features to their thermal properties. Quantitative monitoring of hydrogen bonds during vitrification will be addressed.

  15. Excitonic couplings between molecular crystal pairs by a multistate approximation

    SciTech Connect

    Aragó, Juan Troisi, Alessandro

    2015-04-28

    In this paper, we present a diabatization scheme to compute the excitonic couplings between an arbitrary number of states in molecular pairs. The method is based on an algebraic procedure to find the diabatic states with a desired property as close as possible to that of some reference states. In common with other diabatization schemes, this method captures the physics of the important short-range contributions (exchange, overlap, and charge-transfer mediated terms) but it becomes particularly suitable in presence of more than two states of interest. The method is formulated to be usable with any level of electronic structure calculations and to diabatize different types of states by selecting different molecular properties. These features make the diabatization scheme presented here especially appropriate in the context of organic crystals, where several excitons localized on the same molecular pair may be found close in energy. In this paper, the method is validated on the tetracene crystal dimer, a well characterized case where the charge transfer (CT) states are closer in energy to the Frenkel excitons (FE). The test system was studied as a function of an external electric field (to explore the effect of changing the relative energy of the CT excited state) and as a function of different intermolecular distances (to probe the strength of the coupling between FE and CT states). Additionally, we illustrate how the approximation can be used to include the environment polarization effect.

  16. Excitonic couplings between molecular crystal pairs by a multistate approximation.

    PubMed

    Aragó, Juan; Troisi, Alessandro

    2015-04-28

    In this paper, we present a diabatization scheme to compute the excitonic couplings between an arbitrary number of states in molecular pairs. The method is based on an algebraic procedure to find the diabatic states with a desired property as close as possible to that of some reference states. In common with other diabatization schemes, this method captures the physics of the important short-range contributions (exchange, overlap, and charge-transfer mediated terms) but it becomes particularly suitable in presence of more than two states of interest. The method is formulated to be usable with any level of electronic structure calculations and to diabatize different types of states by selecting different molecular properties. These features make the diabatization scheme presented here especially appropriate in the context of organic crystals, where several excitons localized on the same molecular pair may be found close in energy. In this paper, the method is validated on the tetracene crystal dimer, a well characterized case where the charge transfer (CT) states are closer in energy to the Frenkel excitons (FE). The test system was studied as a function of an external electric field (to explore the effect of changing the relative energy of the CT excited state) and as a function of different intermolecular distances (to probe the strength of the coupling between FE and CT states). Additionally, we illustrate how the approximation can be used to include the environment polarization effect. PMID:25933752

  17. Absorbate-induced piezochromism in a porous molecular crystal.

    PubMed

    Hendon, Christopher H; Wittering, Kate E; Chen, Teng-Hao; Kaveevivitchai, Watchareeya; Popov, Ilya; Butler, Keith T; Wilson, Chick C; Cruickshank, Dyanne L; Miljanić, Ognjen Š; Walsh, Aron

    2015-03-11

    Atmospherically stable porous frameworks and materials are interesting for heterogeneous solid-gas applications. One motivation is the direct and selective uptake of pollutant/hazardous gases, where the material produces a measurable response in the presence of the analyte. In this report, we present a combined experimental and theoretical rationalization for the piezochromic response of a robust and porous molecular crystal built from an extensively fluorinated trispyrazole. The electronic response of the material is directly determined by analyte uptake, which provokes a subtle lattice contraction and an observable bathochromic shift in the optical absorption onset. Selectivity for fluorinated absorbates is demonstrated, and toluene is also found to crystallize within the pore. Furthermore, we demonstrate the application of electronic structure calculations to predict a physicochemical response, providing the foundations for the design of electronically tunable porous solids with the chemical properties required for development of novel gas-uptake media. PMID:25706577

  18. Micellar crystals in solution from molecular dynamics simulations

    SciTech Connect

    Anderson, J.; Lorenz, C.; Travesset, A.

    2008-05-14

    Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.

  19. Absorbate-Induced Piezochromism in a Porous Molecular Crystal

    PubMed Central

    2015-01-01

    Atmospherically stable porous frameworks and materials are interesting for heterogeneous solid–gas applications. One motivation is the direct and selective uptake of pollutant/hazardous gases, where the material produces a measurable response in the presence of the analyte. In this report, we present a combined experimental and theoretical rationalization for the piezochromic response of a robust and porous molecular crystal built from an extensively fluorinated trispyrazole. The electronic response of the material is directly determined by analyte uptake, which provokes a subtle lattice contraction and an observable bathochromic shift in the optical absorption onset. Selectivity for fluorinated absorbates is demonstrated, and toluene is also found to crystallize within the pore. Furthermore, we demonstrate the application of electronic structure calculations to predict a physicochemical response, providing the foundations for the design of electronically tunable porous solids with the chemical properties required for development of novel gas-uptake media. PMID:25706577

  20. Molecular Orientation of Liquid Crystals on Topographic Nanopatterns.

    PubMed

    Ryu, Seong Ho; Yoon, Dong Ki

    2016-07-13

    Controlling the orientation of building blocks in soft matter on the substrate has been a big challenge in material sciences. We have controlled the molecular orientation of liquid crystal (LC) materials on the porous anodic aluminum oxide (AAO) film having hexagonal pore arrays on the top surface. In our method, anchoring conditions can be varied by changing the pore size (Dp) and the porosity (P). As a proof-of-concept, the orientation of smectic A (SmA) structure at different anchoring conditions was successfully controlled in a sandwich cell consisting of AAO and a glass substrate, which has not been successfully controlled by conventional methods. PMID:27322013

  1. Study on Properties of Energy Spectra of the Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-Feng; Chen, Xiang-Rong

    The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

  2. Molecular-Level Understanding of Structural Changes of Organic Crystals Induced by Macroscopic Mechanical Stimulation.

    PubMed

    Seki, Tomohiro; Ito, Hajime

    2016-03-18

    Structural changes to molecular crystals upon mechanical stimulation have attracted attention for sensing, recording, and microactuation. Comprehensive structure information is required to understand relationships between the mechanical force applied, the crystal structure, and the bulk property changes in order to develop general design concepts for mechanoresponsive compounds. Unfortunately, mechanical stimulation of organic crystals typically deteriorates their integrity, preventing detailed structure analyses by single-crystal X-ray diffraction (XRD) methods. However, in the past three years, several interesting studies have been reported in which molecular crystals retain their integrity even after a mechanically induced crystalline structure change. These materials have allowed us to investigate how macroscopic mechanical forces affect the microscopic structures of molecular crystals by single-crystal XRD analyses. This Minireview summarizes current knowledge of mechanically induced structure changes in molecular crystals, which will facilitate research in this field. PMID:26748640

  3. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

    PubMed

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

    Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. PMID:21271625

  4. Alignment of liquid crystals using a molecular layer with patterned molecular density.

    PubMed

    Son, Jong-Ho; Zin, Wang-Cheol; Takezoe, Hideo; Song, Jang-Kun

    2012-11-27

    The surface of self-constructed molecular density modulation (SDM) exhibits a wide range of liquid crystal alignment capabilities including planar, tilted, and homeotropic alignments, disclination-free uniform and heterogeneous alignments, and even spatially varying alignments through the single non-contact process. Alignment defects are eliminated by temporary lowering the frictional energy barrier via the open-boundary elastic stabilization (OES) treatment. PMID:22945601

  5. Nonequilibrium thermodynamics of an interface

    NASA Astrophysics Data System (ADS)

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics.

  6. Nonequilibrium thermodynamics of an interface.

    PubMed

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics. PMID:27300960

  7. Molecular dynamics simulations of alkyl substituted nanographene crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, Orestis George; Theodorou, Doros Nicolas

    2015-09-01

    Discotic polyaromatic molecules, similar to nanometric graphene flakes, constitute an interesting class of materials for organic electronic applications. Grafting flexible side chains around the periphery of such molecules enhances their processability and gives rise to diverse behaviours, such as the manifestation of liquid-crystalline character and anisotropic mechanical response. In this work, we examine by means of molecular dynamics simulations the properties of molecular crystals comprised of alkyl-substituted hexa-peri-hexabenzocoronene mesogens. Pristine and mono-substituted systems by hydrogen or iodine atoms are modelled, with variable side chain length. A general structural and mechanical robustness to peripheral substitution is reported, with the mesogens forming tightly packed molecular wires even at elevated temperature and pressure. In their discotic ordering, the molecules present relatively low translational mobility, a beneficial phenomenon for charge transport. A thermotropic dependence of the mechanical response is identified, with the systems behaving differently in their room-temperature crystalline phase and in their liquid-crystalline phase at elevated temperatures. The melting process is also examined, elucidating an initial negative expansion along a high symmetry direction and the existence of a metastable state, before falling into the final liquid-crystalline state. Dedicated to Professor Jean-Pierre Hansen, with deepest appreciation of his outstanding contributions to liquid and soft matter theory.

  8. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    NASA Astrophysics Data System (ADS)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  9. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    PubMed

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio

  10. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    SciTech Connect

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-06-05

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the <100> direction form intersecting stacking faults by slippage along {l_brace}111{r_brace} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the <111> case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the <110> direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society.

  11. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    SciTech Connect

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  12. The crystal and molecular structure of triethanol-ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Bracuti, A. J.

    1992-12-01

    The liquid propellant used in the 155-mm regenerative liquid propellant gun is XM46. XM46 is a solution of 60 percent hydroxyl ammonium nitrate (HAN), 20 percent triethanolammonium nitrate (TEAN), and 20 percent water. This material exhibits rather unusual liquid properties that have been attributed to its being a 'molten eutectic' of fused salts rather than a normal aqueous solution of two different nitrate salts. A hydrogen-bonded liquid structure for eutectic LP1946 was proposed previously based on the known structures of neat HAN and water and a best-guess estimate of the TEAN structure. To verify this estimate, the molecular structure of neat TEAN was recently determined. This investigation revealed TEAN has very unusual and interesting bifurcated intermolecular and trifurcated intramolecular hydrogen bonding configurations within the crystal. If these hydrogen bonding configurations are retained in aqueous solution, they could be responsible in some part to the observed unusual liquid properties of liquid propellant XM46.

  13. InPBi Single Crystals Grown by Molecular Beam Epitaxy

    PubMed Central

    Wang, K.; Gu, Y.; Zhou, H. F.; Zhang, L. Y.; Kang, C. Z.; Wu, M. J.; Pan, W. W.; Lu, P. F.; Gong, Q.; Wang, S. M.

    2014-01-01

    InPBi was predicted to be the most robust infrared optoelectronic material but also the most difficult to synthesize within In-VBi (V = P, As and Sb) 25 years ago. We report the first successful growth of InPBi single crystals with Bi concentration far beyond the doping level by gas source molecular beam epitaxy. The InPBi thin films reveal excellent surface, structural and optical qualities making it a promising new III–V compound family member for heterostructures. The Bi concentration is found to be 2.4 ± 0.4% with 94 ± 5% Bi atoms at substitutional sites. Optical absorption indicates a band gap of 1.23 eV at room temperature while photoluminescence shows unexpectedly strong and broad light emission at 1.4–2.7 μm which can't be explained by the existing theory. PMID:24965260

  14. Development of Crystal Al MKIDs by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Naruse, M.; Sekimoto, Y.; Noguchi, T.; Miyachi, A.; Nitta, T.; Uzawa, Y.

    2011-11-01

    We report here the effect of film qualities in superconductors on the properties of Microwave Kinetic Inductance Detectors (MKIDs). The sensitivity of MKIDs between crystal aluminum films and amorphous aluminum films is compared. The good quality and crystallized aluminum films have been prepared by using molecular beam epitaxy. We have confirmed that epitaxial Al(111) films were grown on Si(111) substrates with X-ray diffraction and in-situ reflection high-energy electron diffraction measurements. The amorphous aluminum films on the Si(111) wafers have been deposited by electron beam evaporation. We have measured transmission losses of MKIDs, noise spectrum and relaxation time against optical pulses, changing MKIDs' bath temperature from 0.11 K to 0.55 K in a dilution refrigerator. Despite of the improvement in normal resistivity, the quasiparticle decay time of both films are equivalent and 450 μs at 0.11 K. The electrical noise equivalent power of the both MKIDs are also comparable and around 10^{-17} W/sqrt{Hz}. Fabrication details and performance data of both films are presented.

  15. The heat conductivity of liquid crystal phases of a soft ellipsoid string-fluid evaluated by molecular dynamics simulation.

    PubMed

    Sarman, Sten; Laaksonen, Aatto

    2011-04-01

    We have applied a nonequilibrium molecular dynamics heat flow algorithm to calculate the heat conductivity of a molecular model system, which forms uniaxial and biaxial nematic liquid crystals. The model system consists of a soft ellipsoid string-fluid where the ellipsoids interact according to a repulsive version of the Gay-Berne potential. On compression, this system forms discotic or calamitic uniaxial nematic phases depending on the dimensions of the molecules, and on further compression a biaxial nematic phase is formed. In the discotic nematic phase, the heat conductivity has two components, one parallel and one perpendicular to the director, where the last mentioned component is the largest one. This order of magnitudes is reversed in the calamitic nematic phase. In the biaxial nematic phase there are three components of the heat conductivity, one in the direction around which the long axes of the molecules are oriented, this is the largest component, another one in the direction around which the normals of the broadsides of the molecules are oriented, this is the smallest component, and one in the direction perpendicular to these two directions with a magnitude in between those of the first mentioned components. The relative magnitudes of the components of the heat conductivity span a fairly wide interval so it should be possible to use the model to parameterise experimental data. PMID:21336361

  16. Exciton dynamics in organic molecular crystals and nanostructures

    NASA Astrophysics Data System (ADS)

    Bardeen, Chris

    2014-03-01

    The photophysical behavior of organic semiconductors is governed by their excitonic states. In this talk, we classify the three different exciton types (Frenkel singlet, Frenkel triplet, and charge-transfer) typically encountered in organic semiconductors. The availability of several different exciton bands provides the possibility of interband processes. One such process is singlet fission, where an initially excited singlet exciton can spontaneously split into a pair of spin-entangled triplet excitons. We analyze this phenomenon in detail, emphasizing the role of spin state coherence and magnetic fields in studying singlet <-- --> triplet pair interconversion. Singlet fission provides an example of how all three types of excitons (triplet, singlet, and charge-transfer) interact to generate unique nonlinear excitonic processes in molecular systems. These processes may be useful for applications like solar energy conversion, where the generation of two excitons per absorbed photon could lead to significant enhancements in the efficiency of single junction photovoltaic cells. Finally, we will briefly describe how excitons can also be used to initiate photochemical reactions in molecular crystal nanostructures, resulting in large shape changes and deformations.

  17. Nonlinearity and slip behavior of n-hexadecane in large amplitude oscillatory shear flow via nonequilibrium molecular dynamic simulation

    NASA Astrophysics Data System (ADS)

    Wang, Chen-Chieh; Chang, Rong-Yeu

    2012-03-01

    Molecular dynamic simulation is used to investigate the viscoelastic properties of n-hexadecane under oscillatory shear flow. Rheometric simulations of an ultra-thin molecular film are studied and compared with the results of a bulk simulation. Strain amplitude sweep tests at a fixed frequency show that strain thinning (the dynamic modulus monotonically decreases with increasing strain amplitude) exists at extreme strain for both bulk and thin film systems. Fourier analysis is performed to characterize the nonlinear behavior of the viscoelasticity. No even harmonic was found in our study even though wall slip occurs. Furthermore, we show that a Fourier series with odd harmonics can be used to perfectly describe the simulation results by plotting Lissajous loops. Shear wave propagation appears when the frequency is larger than a certain value. Moreover, the molecular orientation and molecular potential energies, including those for bonding potential, intra- and intermolecular van der Waals interactions are plotted against the strain amplitude to examine the changes in the microscopic structures with respect to the macroscopic thermodynamic states.

  18. Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Monk, J.; Yang, Y.; Mendelev, M. I.; Asta, M.; Hoyt, J. J.; Sun, D. Y.

    2010-01-01

    The generation and dissipation of latent heat at the moving solid-liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose-Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid-liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a kinetic

  19. Influence of longitudinal isotope substitution on the thermal conductivity of carbon nanotubes: Results of nonequilibrium molecular dynamics and local density functional calculations

    SciTech Connect

    Leroy, Frédéric Böhm, Michael C.; Schulte, Joachim; Balasubramanian, Ganesh

    2014-04-14

    We report reverse nonequilibrium molecular dynamics calculations of the thermal conductivity of isotope substituted (10,10) carbon nanotubes (CNTs) at 300 K. {sup 12}C and {sup 14}C isotopes both at 50% content were arranged either randomly, in bands running parallel to the main axis of the CNTs or in bands perpendicular to this axis. It is found that the systems with randomly distributed isotopes yield significantly reduced thermal conductivity. In contrast, the systems where the isotopes are organized in patterns parallel to the CNTs axis feature no reduction in thermal conductivity when compared with the pure {sup 14}C system. Moreover, a reduction of approximately 30% is observed in the system with the bands of isotopes running perpendicular to the CNT axis. The computation of phonon dispersion curves in the local density approximation and classical densities of vibrational states reveal that the phonon structure of carbon nanotubes is conserved in the isotope substituted systems with the ordered patterns, yielding high thermal conductivities in spite of the mass heterogeneity. In order to complement our conclusions on the {sup 12}C-{sup 14}C mixtures, we computed the thermal conductivity of systems where the {sup 14}C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

  20. Imatinib (Gleevec@) conformations observed in single crystals, protein-Imatinib co-crystals and molecular dynamics: Implications for drug selectivity

    NASA Astrophysics Data System (ADS)

    Golzarroshan, B.; Siddegowda, M. S.; Li, Hong qi; Yathirajan, H. S.; Narayana, B.; Rathore, R. S.

    2012-06-01

    Structure and dynamics of the Leukemia drug, Imatinib, were examined using X-ray crystallography and molecular dynamics studies. Comparison of conformations observed in single crystals with several reported co-crystals of protein-drug complexes suggests existence of two conserved conformations of Imatinib, extended and compact (or folded), corresponding to two binding modes of interaction with the receptor. Furthermore, these conformations are conserved throughout a dynamics simulation. The present study attempts to draw a parallel on conformations and binding patterns of interactions, obtained from small-molecule single-crystal and macromolecule co-crystal studies, and provides structural insights for understanding the high selectivity of this drug molecule.

  1. Quantitative analysis of molecular-level DNA crystal growth on a 2D surface

    PubMed Central

    Lee, Junwye; Hamada, Shogo; Hwang, Si Un; Amin, Rashid; Son, Junyoung; Dugasani, Sreekantha Reddy; Murata, Satoshi; Park, Sung Ha

    2013-01-01

    Crystallization is an essential process for understanding a molecule's aggregation behavior. It provides basic information on crystals, including their nucleation and growth processes. Deoxyribonucleic acid (DNA) has become an interesting building material because of its remarkable properties for constructing various shapes of submicron-scale DNA crystals by self-assembly. The recently developed substrate-assisted growth (SAG) method produces fully covered DNA crystals on various substrates using electrostatic interactions and provides an opportunity to observe the overall crystallization process. In this study, we investigated quantitative analysis of molecular-level DNA crystallization using the SAG method. Coverage and crystal size distribution were studied by controlling the external parameters such as monomer concentration, annealing temperature, and annealing time. Rearrangement during crystallization was also discussed. We expect that our study will provide overall picture of the fabrication process of DNA crystals on the charged substrate and promote practical applications of DNA crystals in science and technology. PMID:23817625

  2. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed

    Karle, J M; Karle, I L

    1989-07-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  3. Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach.

    PubMed

    Fang, Tao; Jia, Junteng; Li, Shuhua

    2016-05-01

    The generalized energy-based fragmentation (GEBF) approach for molecular crystals with periodic boundary condition (PBC) (denoted as PBC-GEBF) is extended to allow vibrational spectra of molecular crystals to be easily computed at various theory levels. Within the PBC-GEBF approach, the vibrational frequencies of a molecular crystal can be directly evaluated from molecular quantum chemistry calculations on a series of nonperiodic molecular systems. With this approach, the vibrational spectra of molecular crystals can be calculated with much reduced computational costs at various theory levels, as compared to those required by the methods based on periodic electronic structure theory. By testing the performance of the PBC-GEBF method for two molecular crystals (CO2 and imidazole), we demonstrate that the PBC-GEBF approach can reproduce the results of the methods based on periodic electronic structure theory in predicting vibrational spectra of molecular crystals. We apply the PBC-GEBF method at second-order Møller-Plesset perturbation theory (PBC-GEBF-MP2 in short) to investigate the vibrational spectra of the urea and ammonia borane crystals. Our results show that the PBC-GEBF-MP2 method can provide quite accurate descriptions for the observed vibrational spectra of the two systems under study. PMID:27076120

  4. Computer simulation of nonequilibrium processes

    SciTech Connect

    Wallace, D.C.

    1985-07-01

    The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed.

  5. Nonequilibrium diagnostics of plasma thrusters

    SciTech Connect

    Eddy, T.L.; Grandy, J.D.

    1990-01-01

    This paper describes possible techniques by which the state of plasma thruster operation for space propulsion can be determined from a minimum set of experimental data in the laboratory. The kinetic properties of the nonequilibrium plasma plume usually can not be directly related to the observed radiation; hence, appropriate nonequilibrium diagnostic techniques must be employed. A newly developed multithermal, multichemical equilibrium method is discussed that uses measured line emission intensities and N equations to solve for N unknowns. The effect of arbitrarily changing the number of selected N unknowns and how one determines the optimum (minimum) number to be used for a given composition is also presented. The chemical nonequilibrium aspects and the application to molecular species have not yet been published. The important conclusions are that (1) complete thermodynamic systems in nonequilibrium can be described by relatively few variables if appropriate choices and filtering methods are used, (2) a few radiation measurements can yield valid kinetic properties, and (3) the major question in the relations to be used is in the form of the law of mass action. The results are substantiated in the laboratory by additional alternative methods of measurement of some of the kinetic properties. 13 refs., 1 fig.

  6. Molecular simulation of chevrons in confined smectic liquid crystals

    NASA Astrophysics Data System (ADS)

    Webster, Richard E.; Mottram, Nigel J.; Cleaver, Douglas J.

    2003-08-01

    Chevron structures adopted by confined smectic liquid crystals are investigated via molecular dynamics simulations of the Gay-Berne model. The chevrons are formed by quenching nematic films confined between aligning planar substrates whose easy axes have opposing azimuthal components. When the substrates are perfectly smooth, the chevron formed migrates rapidly towards one of the confining walls to yield a tilted layer structure. However, when substrate roughness is included, by introducing a small-amplitude modulation to the particle-substrate interaction well depth, a symmetric chevron is formed which remains stable over sufficiently long run times for detailed structural information, such as the relevant order parameters and director orientation, to be determined. For both smooth and rough boundaries, the smectic order parameter remains nonzero across the entire chevron, implying that layer identity is maintained across the chevron tip. Also, when the surface-stabilized chevron does eventually revert to a tilted layer structure, it does so via surface slippage, such that layer integrity is maintained throughout the chevron to tilted layer relaxation process.

  7. Molecular crystals as precursors for poly-nitrogen

    NASA Astrophysics Data System (ADS)

    Borstad, Gustav; Ciezak-Jenkins, Jennifer

    The application of pressure to matter results in dramatic modifications of its properties. The compression of molecular crystals first eliminates ``empty'' space between the molecules. It then alters the electron density distribution, favoring the increase of atomic coordination and the formation of polymers. The polymerization of low-Z compounds into covalently-bonded networks in three dimensions tend to generate materials characterized by superconductivity, super-hardness, and high-energy density.1 Poly-nitrogen (analogous to diamond) has been synthesized under extreme conditions above 100 GPa and 2000 K in diamond anvil cells, but could not be recovered to ambient conditions.2 A useful form of poly-nitrogen would have to be synthesized at low-pressure with enhanced stability at ambient conditions. The changes in the intermolecular and intramolecular interactions with pressure play a crucial role in the synthesizing and stabilizing of the structure as well as in tuning its properties. In this talk, we provide Raman and x-ray diffraction data on nitrogen-containing compound biuret and compare it to work on other possible poly-nitrogen precursors. During this project, coauthor GB was supported in part by an appointment to the Postdoctoral Research Program at the US Army Research Laboratory administered by the Oak Ridge Associated Universities.

  8. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    NASA Astrophysics Data System (ADS)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  9. Thermodynamic stability and crystallization behavior of molecular complexes with TEP host

    NASA Astrophysics Data System (ADS)

    Fijiwara, Atsushi; Kitamura, Mitsutaka

    2013-06-01

    In the crystallization of molecular complex (co-crystal, clathrate complex), polymorphism in regard to the host structure frequently appears. Previously, we studied the release process of the biocide, CMI (5-chloro-2-methyl-4-isothiazolin-3-one) from the molecular complex with TEP (1,1,2,2-tetrakis(4-hydroxyphenyl)ethane) (TEP·2CMI) in methanol-water mixed solvents. It was clear that the release process of the biocide (CMI) is composed of the transformation from the TEP·2CMI crystal to a more stable molecular complex crystal with solvent. In this work, the crystallization was performed in the methanol solutions including TEP and CMI at constant temperature (298 K and 308 K). It appeared that two kinds of TEP molecular complexes (TEP·2CMI and TEP·2MeOH) crystallize competitively. The crystallization zone of each molecular complex was shown in the map using the coordinates of initial concentrations of TEP and CMI. In the boundary zone both molecular complexes appeared and the transformation from TEP·2CMI to TEP·2MeOH was observed, indicating that the stable form is TEP·2MeOH. Without the boundary zone the corresponding stable form crystallized in each zone. The value of the initial concentration ratio of CMI/TEP for the selective crystallization of TEP·2CMI was higher at 298 K (1.54) than that (1.36) at 308 K. The equilibrium concentrations of TEP and CMI in the presence of two molecular complexes were expressed using the dissociation constants of the molecular complexes and it was indicated that the dissociation of TEP·2CMI highly increases with temperature

  10. Polarised photoselection and molecular dynamics in liquid crystals and proteins

    NASA Astrophysics Data System (ADS)

    Bryant, Jason

    Time resolved fluorescence polarisation studies of probe motion in a liquid crystal and protein matrix are presented. In this work, the dynamics and orientational properties of four common laser dyes (Oxazine 1, Oxazine 4, Rhodamine 6G and Rhodamine B) are determined in the liquid crystal 5CB. These studies provide the first direct measurement of θ and φ diffusion (hitherto unobserved) of molecular probes in a nematic host. A distinct anisotropy in θ and φ motion is observed, θ diffusion dynamics show a conventional Arrhenius temperature dependence in the approach to T NI. In contrast, φ motion is largely temperature independent and shows some evidence of slowing in the vicinity of the phase transition. From constructing the orientational distribution function P(θ), it is revealed that the dyes are aligned in pockets between the flexible tails of the host (θ ~ 38°) and conventional models assuming a cylindrical potential are shown to be non-applicable. These effects are most pronounced in Oxazine 4 whose alignment correlates strongly with that of the alkyl tails in 5CB. Here θ and φ diffusion dynamics are highly anisotropic with the ratio of τ20/τ22 in the region of 5:1. In the approach to TNI τ22 is seen to increase by c.a. 50% whilst τ20 shows a c.a 70% decrease. Measurements of Oxazine 4 motion in the Isotropic phase of 5CB indicate that the dye remains strongly correlated with the liquid crystal. Two diffusion times are observed consistent with restricted rotational diffusion within a more slowly diffusing arrangement (domain) of solvent molecules. The domain motion is seen to exhibit a Landau-de Gennes type temperature dependence whilst probe motion within the domains is seen to be largely temperature independent, similar behaviour having been recently reported for diffusion in pure 5CB. A central portion of the work concerns the development of a wholly new approach to polarised photoselection. A novel 3 beam photoselection technique in which

  11. Molecular reorientation of a nematic liquid crystal by thermal expansion

    PubMed Central

    Kim, Young-Ki; Senyuk, Bohdan; Lavrentovich, Oleg D.

    2012-01-01

    A unique feature of nematic liquid crystals is orientational order of molecules that can be controlled by electromagnetic fields, surface modifications and pressure gradients. Here we demonstrate a new effect in which the orientation of nematic liquid crystal molecules is altered by thermal expansion. Thermal expansion (or contraction) causes the nematic liquid crystal to flow; the flow imposes a realigning torque on the nematic liquid crystal molecules and the optic axis. The optical and mechanical responses activated by a simple temperature change can be used in sensing, photonics, microfluidic, optofluidic and lab-on-a-chip applications as they do not require externally imposed gradients of temperature, pressure, surface realignment, nor electromagnetic fields. The effect has important ramifications for the current search of the biaxial nematic phase as the optical features of thermally induced structural changes in the uniaxial nematic liquid crystal mimic the features expected of the biaxial nematic liquid crystal. PMID:23072803

  12. Nonequilibrium thermodynamics of an interface

    NASA Astrophysics Data System (ADS)

    Savin, Thierry; Schweizer, Marco; Öttinger, Hans Christian

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the ``dividing surface,'' as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a ``thermometer,'' and can be significantly different from the temperatures of the adjacent phases.

  13. Molecular dynamics study of the crystallization of nitromethane from the melt

    NASA Astrophysics Data System (ADS)

    Siavosh-Haghighi, Ali; Sewell, Thomas D.; Thompson, Donald L.

    2010-11-01

    The crystallization of nitromethane, CH3NO2, from the melt on the (100), (010), (001), and (110) crystal surfaces at 170, 180, 190, 200, 210, and 220 K has been investigated using constant-volume and -temperature (NVT) molecular dynamics simulations with a realistic, fully flexible force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The crystallization process and the nature of the solid-liquid interface have been investigated by computing the molecular orientations, density, and radial distribution functions as functions of time and location in the simulation cell. During crystallization the translational motion of the molecules ceases first, after which molecular rotation ceases as the molecules assume proper orientations in the crystal lattice. The methyl groups are hindered rotors in the liquid; hindrance to rotation is reduced upon crystallization. The width of the solid-liquid interface varies between 6 and 13 Å (about two to five molecular layers) depending on which crystal surface is exposed to the melt and which order parameter is used to define the interface. The maximum rate of crystallization varies from 0.08 molecules ns-1 Å-2 for the (010) surface at 190 K to 0.41 molecules ns-1 Å-2 for the (001) surface at 220 K.

  14. A reconstruction strategy to synthesize mesoporous SAPO molecular sieve single crystals with high MTO catalytic activity.

    PubMed

    Wang, Chan; Yang, Miao; Li, Mingrun; Xu, Shutao; Yang, Yue; Tian, Peng; Liu, Zhongmin

    2016-05-11

    Mesoporous SAPO-34 single crystals with tunable porosity and Si content have been fast synthesized within 4 hours by a reconstruction strategy, which show excellent hydrothermal stability and MTO catalytic activity. This new strategy is further proven to be applicable to prepare other mesoporous SAPO molecular sieve single crystals. PMID:27101359

  15. Plasmonic Photopatterning of Complex Molecular Orientations in Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Guo, Yubing; Jiang, Miao; Peng, Chenhui; Sun, Kai; Yaroshchuk, Oleg; Lavrentovich, Oleg; Wei, Qi-Huo

    Aligning liquid crystal (LC) molecules in spatially non-uniform patterns are highly demanded for applications such as programmable origami and liquid crystal enabled nonlinear electrokinetics. We developed a high resolution projection photoalignment technique for patterning arbitrary LC alignment fields. The photoalignment is based on carefully engineered metasurfaces, or dubbed as plasmonic metamasks (PMMs). When illuminated by light, the PMMs generate patterns of both light intensity and polarization. By projecting the light transmitted through the PMMs onto liquid crystal cells coated with photosensitive materials, alignment patterns predesigned in polarization patterns of the PMMs can be imposed in liquid crystals. This technique makes the liquid crystal alignment a repeatable and scalable process similar to conventional photolithography, promising various applications. National Science Foundation CMMI-1436565.

  16. Molecular Basis of Urolithiasis: Role of Crystal Retention

    NASA Astrophysics Data System (ADS)

    Koul, Hari K.; Koul, Sweaty

    2008-09-01

    Urolithiasis is a multifactorial disorder, and it is unlikely that a single cause is responsible for entire spectrum of this disorder. Nonetheless, increased concentrations of various urinary constituents (e.g., calcium and/or oxalate) have been associated with a majority of stone formers. Irrespective of the underlying metabolic conditions, crystal precipitation and crystal retention along the urinary tract are two essential pre-requisites for urinary tract stone formation. In this chapter we summarize underlying metabolic abnormalities associated with various subsets of stone formers. We will also present evidence in support of our hypothesis that crystal formation is a normal physiological process of eliminating toxic wastes as solid complexes, and that pathological events begin with crystal retention. In the end we present evidence supporting various mechanisms of crystal retention.

  17. The director and molecular dynamics of the field-induced alignment of a Gay-Berne nematic phase: An isothermal-isobaric nonequilibrium molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Luckhurst, Geoffrey R.; Satoh, Katsuhiko

    2010-05-01

    Isothermal-isobaric molecular dynamics simulations have been performed for the generic Gay-Berne (GB) mesogen, GB(4.4, 20.0, 1, 1), to investigate director and molecular rotational motion during the field-induced alignment of a nematic. The alignment process for the director is discussed within the context of a hydrodynamic analysis based on the Ericksen-Leslie theory and this is found to predict the simulated behavior well. The dependence of the relaxation time for the alignment on the field strength is also in good accord with the theory. The rotational viscosity coefficient estimated from the simulation is smaller than that typically observed for real nematics and the possible reasons for this are discussed. However, the simulation results are found to follow not only the theory but also the experiments, at least qualitatively. No significant variation in the local and long-range structure of the nematic phase is found during the field-induced alignment process. In addition, we have explored the molecular dynamics in the nematic phase in the presence of the field using the first- and second-rank time autocorrelation functions. More importantly we are able to show that the director relaxation time is longer than that for molecular rotation. It is also possible to use the two orientational correlation times to explore the relationship between the rotational viscosity coefficient and the rotational diffusion constant. The diffusion constants determined from the orientational correlation times, based on the short-time expansion of the autocorrelation functions, are found to be significantly different. In consequence it is not possible to test, unambiguously, the relationship between the rotational viscosity coefficient and the rotational diffusion constant. However, it would seem that the second-rank rotational correlation time provides the most reliable route to the rotational viscosity coefficient.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  19. Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystals.

    PubMed

    Turner, Michael J; Thomas, Sajesh P; Shi, Ming W; Jayatilaka, Dylan; Spackman, Mark A

    2015-03-01

    We present an approach to understanding crystal packing via 'energy frameworks', that combines efficient calculation of accurate intermolecular interaction energies with a novel graphical representation of their magnitude. In this manner intriguing questions, such as why some crystals bend with an applied force while others break, and why one polymorph of a drug exhibits exceptional tabletability compared to others, can be addressed in terms of the anisotropy of the topology of pairwise intermolecular interaction energies. This approach is applied to a sample of organic molecular crystals with known bending, shearing and brittle behaviour, to illustrate its use in rationalising their mechanical behaviour at a molecular level. PMID:25525647

  20. Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Perozzo, Mary A.; Konnert, John H.; Nadarajan, Arunan; Pusey, Marc L.

    1998-01-01

    Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

  1. Crystallization kinetics and molecular mobility of an amorphous active pharmaceutical ingredient: A case study with Biclotymol.

    PubMed

    Schammé, Benjamin; Couvrat, Nicolas; Malpeli, Pascal; Delbreilh, Laurent; Dupray, Valérie; Dargent, Éric; Coquerel, Gérard

    2015-07-25

    The present case study focuses on the crystallization kinetics and molecular mobility of an amorphous mouth and throat drug namely Biclotymol, through differential scanning calorimetry (DSC), temperature resolved X-ray powder diffraction (TR-XRPD) and hot stage microscopy (HSM). Kinetics of crystallization above the glass transition through isothermal and non-isothermal cold crystallization were considered. Avrami model was used for isothermal crystallization process. Non-isothermal cold crystallization was investigated through Augis and Bennett model. Differences between crystallization processes have been ascribed to a site-saturated nucleation mechanism of the metastable form, confirmed by optical microscopy images. Regarding molecular mobility, a feature of molecular dynamics in glass-forming liquids as thermodynamic fragility index m was determined through calorimetric measurements. It turned out to be around m=100, describing Biclotymol as a fragile glass-former for Angell's classification. Relatively long-term stability of amorphous Biclotymol above Tg was analyzed indirectly by calorimetric monitoring to evaluate thermodynamic parameters and crystallization behavior of glassy Biclotymol. Within eight months of storage above Tg (T=Tg+2°C), amorphous Biclotymol does not show a strong inclination to crystallize and forms a relatively stable glass. This case study, involving a multidisciplinary approach, points out the importance of continuing looking for stability predictors. PMID:26003417

  2. Computational study of the structure and mechanical properties of the molecular crystal rdx

    NASA Astrophysics Data System (ADS)

    Munday, Lynn

    Molecular crystals constitute a class of materials commonly used as active pharmaceutical ingredients, energetic and high explosive materials. Like simpler crystalline materials, they possess a repeating lattice structure. However, the complexity of the structure -- due to having several entire molecules instead of atoms at each lattice site -- significantly complicates the relationship between the crystal structure and mechanical properties. Of particular interest to molecular crystals are the mechanically activated processes initiated by large deformations. These include polymorph transitions, slip deformation, cleavage fracture, or the transition to disordered states. Activation of slip systems is generally the preferred mode of deformation in molecular crystals because the long range order of the crystal and its associated properties are maintained. These processes change the crystal structure and affect the physiological absorption of advanced pharmaceutical ingredients and the decomposition of high explosives. This work used molecular dynamics to study the energetic molecule RDX, C3H6N6O6, as a model molecular crystal that is a commonly used military high explosive. Molecular dynamics is used to determine the crystal response to deformation by determination of elastic constants, polymorph transitions, cleavage properties, and energy barriers to slip. The cleavage and the free surface energy are determined through interface decohesion simulations and the attachment energy method. The energy barriers to slip are determined through the generalized stacking fault (GSF) procedure. To account for the steric contributions and elastic shearing due to the presence of flexible molecules, a modified calculation procedure for the GSF energy is proposed that enables the distinction of elastic shear energy from the energy associated with the interfacial displacement discontinuity at the slip plane. The unstable stacking fault energy from the GSF simulations is compared to

  3. Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study.

    PubMed

    Murugan, N Arul

    2005-09-01

    Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle. PMID:16164354

  4. Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations.

    PubMed

    Zhao, Yinghe; Wu, Qisheng; Chen, Qian; Wang, Jinlan

    2015-11-19

    van der Waals (vdW) epitaxy of ultrathin organic films on two-dimensional (2D) atomic crystals has become a sovereign area because of their unique advantages in organic electronic devices. However, the dynamic mechanism of the self-assembly remains elusive. Here, we visualize the nanoscale self-assembly of organic molecules on graphene and boron nitride monolayer from a disordered state to a 2D lattice via molecular dynamics simulation for the first time. It is revealed that the assembly toward 2D ordered structures is essentially the minimization of the molecule-molecule interaction, that is, the vdW interaction in nonpolar systems and the vdW and Coulomb interactions in polar systems that are the decisive factors for the formation of the 2D ordering. The role of the substrate is mainly governing the array orientation of the adsorbates. The mechanisms unveiled here are generally applicable to a broad class of organic thin films via vdW epitaxy. PMID:26523464

  5. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  6. Long-range orientational order, local-field anisotropy, and mean molecular polarizability in liquid crystals

    SciTech Connect

    Aver'yanov, E. M.

    2009-01-15

    The problems on the relation of the mean effective molecular polarizability {gamma}-bar to the long-range orientational order of molecules (the optical anisotropy of the medium) in uniaxial and biaxial liquid crystals, the local anisotropy on mesoscopic scales, and the anisotropy of the Lorentz tensor L and the local-field tensor f are formulated and solved. It is demonstrated that the presence of the long-range orientational order of molecules in liquid crystals imposes limitations from below on the molecular polarizability {gamma}-bar, which differs for uniaxial and biaxial liquid crystals. The relation between the local anisotropy and the molecular polarizability {gamma}-bar is investigated for calamitic and discotic uniaxial liquid crystals consisting of lath- and disk-shaped molecules. These liquid crystals with identical macroscopic symmetry differ in the local anisotropy and the relationships between the components L{sub parallel} < L{sub perpendicular} , f{sub parallel} < f{sub perpendicular} (calamitic) and L{sub parallel} > L{sub perpendicular} , f{sub parallel} > f{sub perpendicular} (discotic) for an electric field oriented parallel and perpendicular to the director. The limitations from below and above on the molecular polarizability {gamma}-bar due to the anisotropy of the tensors L and f are established for liquid crystals of both types. These limitations indicate that the molecular polarizability {gamma}-bar depends on the phase state and the temperature. The factors responsible for the nonphysical consequences of the local-field models based on the approximation {gamma}-bar = const are revealed. The theoretical inferences are confirmed by the experimental data for a number of calamitic nematic liquid crystals with different values of birefringence and the discotic liquid crystal Col{sub ho}.

  7. REVIEW ARTICLE: Effects of light on molecular orientation of liquid crystals

    NASA Astrophysics Data System (ADS)

    Simoni, F.; Francescangeli, O.

    1999-10-01

    A review of basic physical phenomena underlying the light-induced molecular reorientation in nematic liquid crystals is presented. A detailed description of the mechanisms of direct optical torque, photoisomerization and photorefractivity and of their effect on the macroscopic order of liquid crystals is reported. The first part of the article deals with the study of reorientation effects in transparent liquid crystalline materials. Here, the effects of photo-induced molecular reorientation are fully interpreted within the framework of classical electrodynamics and standard continuum theory of liquid crystals. We investigate the peculiar properties related to the macroscopic anisotropy and the collective behaviour of liquid crystals that result in extraordinarily large nonlinear optical response. Afterwards, the behaviour of liquid crystals in the presence of light absorption is considered and the related reorientation effects are discussed. We give a review of the wide phenomenology which is met in liquid crystals when doped with absorbing azo-dye molecules. The photoisomerization process that in this case drives the evolution of the dye-liquid crystal mixture consequent to the interaction with the light is discussed in detail. Finally, the relatively new field of photorefractivity in liquid crystals as a source of molecular reorientation is considered. We describe the different mechanisms contributing to the creation of a space-charge field such as conductivity anisotropy, dielectric anisotropy and photocharge production. A theoretical discussion of the fundamental mechanisms regulating the dc-field-assisted optically induced space-charge fields and the optical molecular reorientation in nematic liquid crystal films is also given.

  8. High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

    SciTech Connect

    Hu, Ting-Chou; Korczyńska, Justyna; Smith, David K.; Brzozowski, Andrzej Marek

    2008-09-01

    High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization. Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here.

  9. Molecular polarity in tropomyosin-troponin T co-crystals.

    PubMed Central

    Cabral-Lilly, D; Tobacman, L S; Mehegan, J P; Cohen, C

    1997-01-01

    New features of the structure and interactions of troponin T and tropomyosin have been revealed by electron microscopy of so-called double-diamond co-crystals. These co-crystals were formed using rabbit alpha2 tropomyosin complexed with troponin T from either skeletal or cardiac muscle, which have different lengths in the amino-terminal region, as well as a bacterially expressed skeletal muscle troponin T fragment of 190 residues that lacks the amino-terminal region. Differences in the images of the co-crystals have allowed us to establish the polarities of both the troponin T subunit and tropomyosin in the projected lattice. Moreover, in agreement with their sequences, the amino-terminal region of a bovine cardiac muscle troponin T isoform appears to be longer than that from the rabbit skeletal muscle troponin T isoform and to span more of the amino terminus of tropomyosin at the head-to-tail filament joints. Images of crystals tilted relative to the electron beam also reveal the supercoiling of the tropomyosin filaments in this lattice. Based on these results, a three-dimensional model of the double-diamond lattice has been constructed. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:9336171

  10. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  11. Molecular Surface Chemistry by Metal Single Crystals and Nanoparticles from Vacuum to High Pressure.

    SciTech Connect

    Somorjai, Gabor A.; Park, Jeong Y.

    2008-04-05

    Model systems for studying molecular surface chemistry have evolved from single crystal surfaces at low pressure to colloidal nanoparticles at high pressure. Low pressure surface structure studies of platinum single crystals using molecular beam surface scattering and low energy electron diffraction techniques probe the unique activity of defects, steps and kinks at the surface for dissociation reactions (H-H, C-H, C-C, O{double_bond}O bonds). High-pressure investigations of platinum single crystals using sum frequency generation vibrational spectroscopy have revealed the presence and the nature of reaction intermediates. High pressure scanning tunneling microscopy of platinum single crystal surfaces showed adsorbate mobility during a catalytic reaction. Nanoparticle systems are used to determine the role of metal-oxide interfaces, site blocking and the role of surface structures in reactive surface chemistry. The size, shape and composition of nanoparticles play important roles in determining reaction activity and selectivity.

  12. Molecular Interactions in Monolayers οf Azo Dye/Liquid Crystal Mixtures at Interfaces

    NASA Astrophysics Data System (ADS)

    Bauman, D.; Płóciennik, A.; Inglot, K.

    2009-08-01

    Full Text PDF A study of azo dye/liquid crystal mixtures in monolayers formed at an air-water interface (the Langmuir films) and at a solid surface (the Langmuir-Blodgett films) has been performed. Five azo dyes with various molecular structure and the liquid crystal 4-octyl-4' cyanobiphenyl (8CB) have been used. The dyes have been added to the liquid crystal at various molar fractions. Surface pressure and surface potential versus mean molecular area isotherms for the Langmuir films have been recorded and information about intermolecular interactions at the air-water interface has been obtained. On the basis of electronic absorption measurements for the Langmuir and Langmuir-Blodgett films the conclusions about the ability of dyes molecules to form self aggregates at the interfaces have been drawn. The influence of the dye molecular structure and its concentration on aggregates' geometry has been found.

  13. Active porous transition towards spatiotemporal control of molecular flow in a crystal membrane.

    PubMed

    Takasaki, Yuichi; Takamizawa, Satoshi

    2015-01-01

    Fluidic control is an essential technology widely found in processes such as flood control in land irrigation and cell metabolism in biological tissues. In any fluidic control system, valve function is the key mechanism used to actively regulate flow and miniaturization of fluidic regulation with precise workability will be particularly vital in the development of microfluidic control. The concept of crystal engineering is alternative to processing technology in microstructure construction, as the ultimate microfluidic devices must provide molecular level control. Consequently, microporous crystals can instantly be converted to microfluidic devices if introduced in an active transformability of porous structure and geometry. Here we show that the introduction of a stress-induced martensitic transition mechanism converts a microporous molecular crystal into an active fluidic device with spatiotemporal molecular flow controllability through mechanical reorientation of subnanometre channels. PMID:26568441

  14. Computational Protocol for Modeling Thermochromic Molecular Crystals: Salicylidene Aniline As a Case Study.

    PubMed

    Presti, Davide; Labat, Fréderic; Pedone, Alfonso; Frisch, Michael J; Hratchian, Hrant P; Ciofini, Ilaria; Menziani, Maria Cristina; Adamo, Carlo

    2014-12-01

    A computational protocol that combines periodic and QM/QM' calculations has been applied to investigate the structural (geometrical and electronic) and photophysical absorption properties of the salicylidene aniline (SA) thermochromic molecular crystal. The protocol consists of three different steps, namely (i) the description of the molecular crystal using a periodic approach taking into account dispersion interactions, (ii) the identification of reliable finite models (clusters), and (iii) the calculation of vertical transition energies including environmental effects through the use of an electronic embedding model (QM/QM' ONIOM approach). The encouraging results obtained in this work for the β polymorph of SA, both in terms of accuracy and computational cost, open the way to the simulation and the prediction of the photophysical behavior of other molecular crystals, especially those much less well characterized experimentally. PMID:26583240

  15. Active porous transition towards spatiotemporal control of molecular flow in a crystal membrane

    NASA Astrophysics Data System (ADS)

    Takasaki, Yuichi; Takamizawa, Satoshi

    2015-11-01

    Fluidic control is an essential technology widely found in processes such as flood control in land irrigation and cell metabolism in biological tissues. In any fluidic control system, valve function is the key mechanism used to actively regulate flow and miniaturization of fluidic regulation with precise workability will be particularly vital in the development of microfluidic control. The concept of crystal engineering is alternative to processing technology in microstructure construction, as the ultimate microfluidic devices must provide molecular level control. Consequently, microporous crystals can instantly be converted to microfluidic devices if introduced in an active transformability of porous structure and geometry. Here we show that the introduction of a stress-induced martensitic transition mechanism converts a microporous molecular crystal into an active fluidic device with spatiotemporal molecular flow controllability through mechanical reorientation of subnanometre channels.

  16. Active porous transition towards spatiotemporal control of molecular flow in a crystal membrane

    PubMed Central

    Takasaki, Yuichi; Takamizawa, Satoshi

    2015-01-01

    Fluidic control is an essential technology widely found in processes such as flood control in land irrigation and cell metabolism in biological tissues. In any fluidic control system, valve function is the key mechanism used to actively regulate flow and miniaturization of fluidic regulation with precise workability will be particularly vital in the development of microfluidic control. The concept of crystal engineering is alternative to processing technology in microstructure construction, as the ultimate microfluidic devices must provide molecular level control. Consequently, microporous crystals can instantly be converted to microfluidic devices if introduced in an active transformability of porous structure and geometry. Here we show that the introduction of a stress-induced martensitic transition mechanism converts a microporous molecular crystal into an active fluidic device with spatiotemporal molecular flow controllability through mechanical reorientation of subnanometre channels. PMID:26568441

  17. Molecular mechanism of crystallization impacting calcium phosphate cements

    SciTech Connect

    Giocondi, J L; El-Dasher, B S; Nancollas, G H; Orme, C A

    2009-05-31

    In summary, SPM data has shown that (1) Mg inhibits growth on all steps but relatively high Mg/Ca ratios are needed. Extracting the mechanism of interaction requires more modeling of the kinetic data, but step morphology is consistent with incorporation. (2) Citrate has several effects depending on the citrate/Ca ratio. At the lowest concentrations, citrate increases the step free energy without altering the step kinetics; at higher concentrations, the polar step is slowed. (3) Oxalate also slows the polar step but additionally stabilizes a new facet, with a [100]{sub Cc} step. (4) Etidronate has the greatest kinetic impact of the molecules studied. At 7{micro}M concentrations, the polar step slows by 60% and a new polar step appears. However, at the same time the [10-1]{sub Cc} increases by 67%. It should be noted that all of these molecules complex calcium and can effect kinetics by altering the solution supersaturation or the Ca to HPO{sub 4}{sup 2-} ratio. For the SPM data shown, this effect was corrected for to distinguish the effect of the molecule at the crystal surface from the effect of the molecule on the solution speciation. The goal of this paper is to draw connections between fundamental studies of atomic step motion and potential strategies for materials processing. It is not our intent to promote the utility of SPM for investigating processes in cement dynamics. The conditions are spectacularly different in many ways. The data shown in this paper are fairly close to equilibrium (S=1.6) whereas the nucleation of cements is initiated at supersaturation ratios in the thousands to millions. Of course, after the initial nucleation phase, the growth will occur at more modest supersaturations and as the cement evolves towards equilibrium certainly some of the growth will occur in regimes such as shown here. In addition to the difference in supersaturation, cements tend to have lower additive to calcium ratios. As an example, the additive to Ca ratio is

  18. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    NASA Astrophysics Data System (ADS)

    Melnikov, V. V.

    2015-06-01

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H2 in Si, and the obtained dispersion law is analyzed.

  19. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    SciTech Connect

    Melnikov, V. V.

    2015-06-15

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H{sub 2} in Si, and the obtained dispersion law is analyzed.

  20. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  1. Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

    NASA Astrophysics Data System (ADS)

    Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

    2004-10-01

    Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

  2. A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals.

    PubMed

    Özpınar, Gül Altınbaş; Beierlein, Frank R; Peukert, Wolfgang; Zahn, Dirk; Clark, Timothy

    2012-08-01

    Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules. PMID:22281810

  3. Molecular structures and crystal packings of 2-styrylquinoline and its derivatives

    SciTech Connect

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2011-07-15

    The crystal and molecular structures of five styrylheterocycles of the quinoline series are studied. All molecules are planar. The double bond in the ethylene fragment is essentially localized. In the molecule of 2-(4-methylstyryl)quinoline, the ethylene fragment is disordered by the bicycle-pedal pattern. In four of the five compounds, the crystal packings do not contain stacking dimers prearranged for the [2+2] photocycloaddition (PCA) reaction. In the crystal of 2-(3-nitrostyryl)quinoline, pairs of crystallographically independent molecules form stacking dimers. In a dimer, the ethylene fragments have a twist orientation, which is incompatible with the PCA reaction. An attempt to initiate a temperature-dependent process of bicyclepedal isomerization in the crystal and, as a consequence, the PCA reaction by means of simultaneous irradiation and heating of a single crystal is unsuccessful.

  4. Drug-polymer interactions at water-crystal interfaces and implications for crystallization inhibition: molecular dynamics simulations of amphiphilic block copolymer interactions with tolazamide crystals.

    PubMed

    Gao, Yi; Olsen, Kenneth W

    2015-07-01

    A diblock copolymer, poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA), modulates the crystal growth of tolazamide (TLZ), resulting in a crystal morphology change from needles to plates in aqueous media. To understand this crystal surface drug-polymer interaction, we conducted molecular dynamics simulations on crystal surfaces of TLZ in water containing PEG-b-PLA. A 130-ns simulation of the polymer in a large water box was run before initiating 50 ns simulations with each of the crystal surfaces. The simulations demonstrated differentiated drug-polymer interactions that are consistent with experimental studies. Interaction of PEG-b-PLA with the (001) face occurred more rapidly (≤10 ns) and strongly (total interaction energy of -121.1 kJ/mol/monomer) than that with the (010) face (∼35 ns, -85.4 kJ/mol/monomer). There was little interaction with the (100) face. Hydrophobic and van der Waals (VDW) interactions were the dominant forces, accounting for more than 90% of total interaction energies. It suggests that polymers capable of forming strong hydrophobic and VDW interactions might be more effective in inhibiting crystallization of poorly water-soluble and hydrophobic drugs in aqueous media (such as gastrointestinal fluid) than those with hydrogen-bonding capacities. Such in-depth analysis and understanding facilitate the rational selection of polymers in designing supersaturation-based enabling formulations. PMID:26045147

  5. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    PubMed

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide. PMID:27365051

  6. Crystal and molecular structure of perindopril erbumine salt

    NASA Astrophysics Data System (ADS)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  7. Equilibrium sampling by reweighting nonequilibrium simulation trajectories

    NASA Astrophysics Data System (ADS)

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  8. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    PubMed

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems. PMID:27078486

  9. Spatial distribution of defects and the kinetics of nonequilibrium charge carriers in GaN wurtzite crystals doped with Sm, Eu, Er, Tm, and supplementary Zn impurities

    SciTech Connect

    Mezdrogina, M. M. Krivolapchuk, V. V.; Kozhanova, Yu. V.

    2008-02-15

    By analyzing time-resolved and steady-state photoluminescence spectra, it is established that the spatial distribution of rare-earth ion dopants in wurtzite GaN crystals doped with Sm, Eu, Er, or Tm is governed by the type and concentration of defects in the initial semiconductor matrix as well as by the type of the impurity (its capacity for segregation). Doping with multicharged rare-earth impurities and additionally introduced Zn impurity leads to an intensification of emission. The effect of intensification of emission in the case of n-and p-GaN crystals is considered with the use of the model of isoelectronic traps.

  10. Crystal and mol-ecular structure of aflatrem.

    PubMed

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabi-cyclo-[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1). PMID:26594569

  11. Orientational Order of Molecular Assemblies on Inorganic Crystals

    NASA Astrophysics Data System (ADS)

    Chun, Jaehun; Saville, Dudley; Li, Je-Luen; Schniepp, Hannes; Car, Roberto; Aksay, Ilhan

    2006-03-01

    Surfactant micelles form oriented arrays on crystalline substrates such as HOPG (Highly Ordered Pyrolytic Graphite) although registration is unexpected since the template unit cell is small compared to the size of a rod-like micelle. In addition, with atomic force microscopy, we show that orientational ordering is a dynamic, multi-molecule process. Interaction energy calculations based on molecular simulations reveal that orientational energy differences on a molecular scale are too small to explain matters. However, treating the cooperative processes as a balance between van der Waals torque on a large, rod-like micellar assembly and Brownian motion shows that orientation is favored. Our study provides a physical insight on regulation of self-assembly structures at small length scale.

  12. Spin-Crossover Molecular Solids Beyond Rigid Crystal Approximation.

    PubMed

    Gudyma, Iurii V; Ivashko, Victor V

    2016-12-01

    The qualitative analysis of the spin-crossover molecular solid with distortion effect is presented. A spin-crossover solid with effect of distortion is studied in the framework of the Ising-like model with two-order parameters under statistical approach, where the effect of elastic strain on inter-ion interaction is considered. These considerations lead to examination of the relation between the primary and secondary order parameters during temperature and pressure changes. PMID:27075338

  13. Spin-Crossover Molecular Solids Beyond Rigid Crystal Approximation

    NASA Astrophysics Data System (ADS)

    Gudyma, Iurii V.; Ivashko, Victor V.

    2016-04-01

    The qualitative analysis of the spin-crossover molecular solid with distortion effect is presented. A spin-crossover solid with effect of distortion is studied in the framework of the Ising-like model with two-order parameters under statistical approach, where the effect of elastic strain on inter-ion interaction is considered. These considerations lead to examination of the relation between the primary and secondary order parameters during temperature and pressure changes.

  14. Crystal morphology prediction of 1,3,3-trinitroazetidine in ethanol solvent by molecular dynamics simulation.

    PubMed

    Shi, Wenyan; Chu, Yuting; Xia, Mingzhu; Lei, Wu; Wang, Fengyun

    2016-03-01

    In order to understand the mechanism of the effect of solvent on the crystal morphology of explosives, and be convenient for the choice of crystallization solvent, the attachment energy (AE) model was performed to predict the growth morphology and the main crystal faces of 1,3,3-trinitroazetidine (TNAZ) in vacuum. The molecular dynamics simulation was applied to investigate the interactions of TNAZ crystal faces and ethanol solvent, and the growth habit of TNAZ in ethanol solvent was predicted using the modified AE model. The results indicate that the morphology of TNAZ crystal in vacuum is dominated by the six faces of [021], [112], [002], [102], [111] and [020], and the crystal shape is similar to polyhedron. In ethanol solvent, The binding strength of ethanol with TNAZ faces changes in the order of [021]>[112]>[002]>[102]>[111]>[020], which causes that [111] and [020] faces disappear and the crystal morphology becomes more regular. The radial distribution function analysis shows that the interactions between solvent and crystal faces mainly consist of coulomb interaction, van der Waals force and hydrogen bonds. PMID:26811871

  15. Determination of screened Coulomb repulsion energies in organic molecular crystals: A real space approach

    NASA Astrophysics Data System (ADS)

    Cano-Cortés, Laura; Dolfen, Andreas; Merino, Jaime; Koch, Erik

    2010-06-01

    We present a general method for determining screened Coulomb parameters in molecular assemblies, in particular organic molecular crystals. This allows us to calculate the interaction parameters used in a generalized Hubbard model description of correlated organic materials. In such a model only the electrons in levels close to the Fermi level are included explicitly, while the effect of all other electrons is included as a renormalization of the model parameters. For the Coulomb integrals this renormalization is mainly due to screening. For molecular materials we can split the screening into intra- and inter-molecular screening. Here we demonstrate how the inter-molecular screening can be calculated by modeling the molecules by distributed point-polarizabilities and solving the resulting self-consistent electrostatic screening problem in real space. For the example of the quasi one-dimensional molecular metal TTF-TCNQ we demonstrate that the method gives remarkably accurate results.

  16. A molecular dynamics study of the effect of thermal boundary conductance on thermal transport of ideal crystal of n-alkanes with different number of carbon atoms

    NASA Astrophysics Data System (ADS)

    Rastgarkafshgarkolaei, Rouzbeh; Zeng, Yi; Khodadadi, J. M.

    2016-05-01

    Phase change materials such as n-alkanes that exhibit desirable characteristics such as high latent heat, chemical stability, and negligible supercooling are widely used in thermal energy storage applications. However, n-alkanes have the drawback of low thermal conductivity values. The low thermal conductivity of n-alkanes is linked to formation of randomly oriented nano-domains of molecules in their solid structure that is responsible for excessive phonon scattering at the grain boundaries. Thus, understanding the thermal boundary conductance at the grain boundaries can be crucial for improving the effectiveness of thermal storage systems. The concept of the ideal crystal is proposed in this paper, which describes a simplified model such that all the nano-domains of long-chain n-alkanes are artificially aligned perfectly in one direction. In order to study thermal transport of the ideal crystal of long-chain n-alkanes, four (4) systems (C20H42, C24H50, C26H54, and C30H62) are investigated by the molecular dynamics simulations. Thermal boundary conductance between the layers of ideal crystals is determined using both non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. Both NEMD and EMD simulations exhibit no significant change in thermal conductance with the molecular length. However, the values obtained from the EMD simulations are less than the values from NEMD simulations with the ratio being nearly three (3) in most cases. This difference is due to the nature of EMD simulations where all the phonons are assumed to be in equilibrium at the interface. Thermal conductivity of the n-alkanes in three structures including liquid, solid, and ideal crystal is investigated utilizing NEMD simulations. Our results exhibit a very slight rise in thermal conductivity values as the number of carbon atoms of the chain increases. The key understanding is that thermal transport can be significantly altered by how the molecules and the

  17. Crystallographic approaches for the investigation of molecular materials: structure property relationships and reverse crystal engineering.

    PubMed

    Macchi, Piero

    2014-01-01

    This article discusses the connection between crystallography and material science. It sheds light on some of the research opportunities that are currently available and it critically reviews the directions taken by the scientific community in the field of crystal engineering. The focus is on materials formed by the assembly of organic and organometallic molecular building blocks. PMID:24801694

  18. The calculation of electrostatic interactions and their role in determining the energies and geometries of explosive molecular crystals

    SciTech Connect

    Ritchie, J.P.; Kober, E.M.; Copenhaver, A.S.

    1993-01-01

    Three different procedures were used to calculate electrostatic interactions in explosive molecular crystals. The use of Potential Derived Charges (PDC's) and atom-centered multipole expansions (ACME's) provides reasonable fits of the molecular electrostatic potential. The ability of these approaches to reproduce observed crystal structures was also evaluated.

  19. Energy Minimization of Molecular Features Observed on the (110) Face of Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Perozzo, Mary A.; Konnert, John H.; Li, Huayu; Nadarajah, Arunan; Pusey, Marc

    1999-01-01

    Molecular dynamics and energy minimization have been carried out using the program XPLOR to check the plausibility of a model lysozyme crystal surface. The molecular features of the (110) face of lysozyme were observed using atomic force microscopy (AFM). A model of the crystal surface was constructed using the PDB file 193L, and was used to simulate an AFM image. Molecule translations, van der Waals radii, and assumed AFM tip shape were adjusted to maximize the correlation coefficient between the experimental and simulated images. The highest degree of 0 correlation (0.92) was obtained with the molecules displaced over 6 A from their positions within the bulk of the crystal. The quality of this starting model, the extent of energy minimization, and the correlation coefficient between the final model and the experimental data will be discussed.

  20. Nonequilibrium viscosity of glass

    NASA Astrophysics Data System (ADS)

    Mauro, John C.; Allan, Douglas C.; Potuzak, Marcel

    2009-09-01

    Since glass is a nonequilibrium material, its properties depend on both composition and thermal history. While most prior studies have focused on equilibrium liquid viscosity, an accurate description of nonequilibrium viscosity is essential for understanding the low temperature dynamics of glass. Departure from equilibrium occurs as a glass-forming system is cooled through the glass transition range. The glass transition involves a continuous breakdown of ergodicity as the system gradually becomes trapped in a subset of the available configurational phase space. At very low temperatures a glass is perfectly nonergodic (or “isostructural”), and the viscosity is described well by an Arrhenius form. However, the behavior of viscosity during the glass transition range itself is not yet understood. In this paper, we address the problem of glass viscosity using the enthalpy landscape model of Mauro and Loucks [Phys. Rev. B 76, 174202 (2007)] for selenium, an elemental glass former. To study a wide range of thermal histories, we compute nonequilibrium viscosity with cooling rates from 10-12 to 1012K/s . Based on these detailed landscape calculations, we propose a simplified phenomenological model capturing the essential physics of glass viscosity. The phenomenological model incorporates an ergodicity parameter that accounts for the continuous breakdown of ergodicity at the glass transition. We show a direct relationship between the nonequilibrium viscosity parameters and the fragility of the supercooled liquid. The nonequilibrium viscosity model is validated against experimental measurements of Corning EAGLE XG™ glass. The measurements are performed using a specially designed beam-bending apparatus capable of accurate nonequilibrium viscosity measurements up to 1016Pas . Using a common set of parameters, the phenomenological model provides an accurate description of EAGLE XG™ viscosity over the full range of measured temperatures and fictive temperatures.

  1. Crystal Structures of Precise Functional Copolymers: Atomistic Molecular Dynamics Simulations and Comparisons with Experiments

    NASA Astrophysics Data System (ADS)

    Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.

    Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.

  2. Molecular dynamics simulation of fast particle irradiation on the single crystal CeO2

    NASA Astrophysics Data System (ADS)

    Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

    2013-11-01

    We used a molecular dynamics method to simulate structural relaxation caused by the high-energy-ion irradiation of single crystal CeO2. As the initial condition, we assumed high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order diameter located in the center of the single crystal. The potential proposed by Inaba et al. was utilized to calculate interactions between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it was dissipated in the crystal. We compared the obtained results with those of computer simulations for UO2 and found that CeO2 was more stable than UO2 when supplied with high thermal energy.

  3. Molecular mechanisms of crystallization impacting calcium phosphate cements

    PubMed Central

    Giocondi, Jennifer L.; El-Dasher, Bassem S.; Nancollas, George H.; Orme, Christine A.

    2010-01-01

    The biomineral calcium hydrogen phosphate dihydrate (CaHPO4·2H2O), known as brushite, is a malleable material that both grows and dissolves faster than most other calcium minerals, including other calcium phosphate phases, calcium carbonates and calcium oxalates. Within the body, this ready formation and dissolution can play a role in certain diseases, such as kidney stone and plaque formation. However, these same properties, along with brushite’s excellent biocompatibility, can be used to great benefit in making resorbable biomedical cements. To optimize cements, additives are commonly used to control crystallization kinetics and phase transformation. This paper describes the use of in situ scanning probe microscopy to investigate the role of several solution parameters and additives in brushite atomic step motion. Surprisingly, this work demonstrates that the activation barrier for phosphate (rather than calcium) incorporation limits growth kinetics and that additives such as magnesium, citrate and bisphosphonates each influence step motion in distinctly different ways. Our findings provide details of how, and where, molecules inhibit or accelerate kinetics. These insights have the potential to aid in designing molecules to target specific steps and to guide synergistic combinations of additives. PMID:20308110

  4. Putting pressure on aromaticity along with in situ experimental electron density of a molecular crystal

    NASA Astrophysics Data System (ADS)

    Casati, Nicola; Kleppe, Annette; Jephcoat, Andrew P.; Macchi, Piero

    2016-03-01

    When pressure is applied, the molecules inside a crystal undergo significant changes of their stereoelectronic properties. The most interesting are those enhancing the reactivity of systems that would be otherwise rather inert at ambient conditions. Before a reaction can occur, however, a molecule must be activated, which means destabilized. In aromatic compounds, molecular stability originates from the resonance between two electronic configurations. Here we show how the resonance energy can be decreased in molecular crystals on application of pressure. The focus is on syn-1,6:8,13-Biscarbonyl[14]annulene, an aromatic compound at ambient conditions that gradually localizes one of the resonant configurations on compression. This phenomenon is evident from the molecular geometries measured at several pressures and from the experimentally determined electron density distribution at 7.7 GPa the observations presented in this work are validated by periodic DFT calculations.

  5. Putting pressure on aromaticity along with in situ experimental electron density of a molecular crystal

    PubMed Central

    Casati, Nicola; Kleppe, Annette; Jephcoat, Andrew P.; Macchi, Piero

    2016-01-01

    When pressure is applied, the molecules inside a crystal undergo significant changes of their stereoelectronic properties. The most interesting are those enhancing the reactivity of systems that would be otherwise rather inert at ambient conditions. Before a reaction can occur, however, a molecule must be activated, which means destabilized. In aromatic compounds, molecular stability originates from the resonance between two electronic configurations. Here we show how the resonance energy can be decreased in molecular crystals on application of pressure. The focus is on syn-1,6:8,13-Biscarbonyl[14]annulene, an aromatic compound at ambient conditions that gradually localizes one of the resonant configurations on compression. This phenomenon is evident from the molecular geometries measured at several pressures and from the experimentally determined electron density distribution at 7.7 GPa; the observations presented in this work are validated by periodic DFT calculations. PMID:26979750

  6. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel S.; Bukusoglu, Emre; de Pablo, Juan J.; Abbott, Nicholas L.

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  7. Nonequilibrium thermal entanglement

    SciTech Connect

    Quiroga, Luis; Rodriguez, Ferney J.; Ramirez, Maria E.; Paris, Roberto

    2007-03-15

    Results on heat current, entropy production rate, and entanglement are reported for a quantum system coupled to two different temperature heat reservoirs. By applying a temperature gradient, different quantum states can be found with exactly the same amount of entanglement but different purity degrees and heat currents. Furthermore, a nonequilibrium enhancement-suppression transition behavior of the entanglement is identified.

  8. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  9. Unoccupied electronic structure and molecular orientation of rubrene; from evaporated films to single crystals

    NASA Astrophysics Data System (ADS)

    Ueba, T.; Park, J.; Terawaki, R.; Watanabe, Y.; Yamada, T.; Munakata, T.

    2016-07-01

    Two-photon photoemission (2PPE) spectroscopy and ultraviolet photoemission spectroscopy (UPS) have been performed for rubrene single crystals and evaporated thin films on highly oriented pyrolytic graphite (HOPG). The changes in the 2PPE intensity from the single crystals by the polarization of the light and by the angle of the light incident plane against the crystalline axes indicate that the molecular arrangement on the surface is similar to that in the bulk crystal. On the other hand, in the case of evaporated films, the polarization dependence of 2PPE indicates that the tetracene backbone becomes standing upright as the thickness increases. In spite of the alignment of molecules, the broadened 2PPE spectral features for thick films suggest that the films are amorphous and molecules are in largely different environments. The film structures are confirmed by scanning tunneling microscopy (STM). The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) derived levels of the single crystal are shifted by + 0.18 and - 0.20 eV, respectively, from those of the 0.8 ML film. The shifts are attributed to the packing density of molecules. It is shown that the unoccupied electronic structure is more sensitively affected by the film structure than the occupied electronic structure.

  10. Study of silicon crystal surface formation based on molecular dynamics simulation results

    NASA Astrophysics Data System (ADS)

    Barinovs, G.; Sabanskis, A.; Muiznieks, A.

    2014-04-01

    The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.