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Sample records for crystal nonequilibrium molecular

  1. Electrophoresis in Protein Crystal: Nonequilibrium Molecular Dynamics Simulations

    PubMed Central

    Hu, Zhongqiao; Jiang, Jianwen

    2008-01-01

    Electrophoresis of a mixture of NaCl and CaCl2 in a lysozyme crystal is investigated using nonequilibrium molecular dynamics (MD) simulations. Upon exposure to an electric field, the stability of lysozyme is found to decrease slightly. This finding is demonstrated by increases in the root mean-square deviations of the heavy atoms of lysozyme, in the solvent-accessible surface area of hydrophobic residues, and in the number of hydrogen bonds between lysozyme and water. The solvent-accessible surface area of hydrophilic residues changes marginally, and the number of hydrogen bonds between lysozyme molecules decreases. Water molecules tend to align preferentially parallel to the electric field, and the dipole moment along the pore axis increases linearly with increasing field strength. Two pronounced layered structures are observed for Na+ and Ca2+ in the vicinity of protein surface, but only one enriched layer is observed for Cl−. The number distributions of all ions are nearly independent of the electric field. The water coordination numbers of all ions are smaller in the crystal than in aqueous bulk solution; however, the reverse is found for the Cl− coordination numbers of cations. Both the water and the Cl− coordination numbers are insensitive to the electric field. Ion diffusivities in the crystal are ∼2 orders of magnitude smaller than those in aqueous bulk solution. The drift velocities of ions increase proportionally to the electric field, particularly at high strengths, and depend on ionic charge and coordination with oppositely charged ions. Electrical current exhibits a linear relationship with the field strength. The zero-field electrical conductivity is estimated to be 0.56 S/m, which is very close to 0.61 S/m as predicted by the Nernst-Einstein equation. PMID:18641079

  2. Non-equilibrium molecular dynamics simulations of spall in single crystal tantalum

    NASA Astrophysics Data System (ADS)

    Hahn, Eric N.; Germann, Timothy C.; Ravelo, Ramon J.; Hammerberg, James E.; Meyers, Marc A.

    2017-01-01

    Ductile tensile failure of tantalum is examined through large scale non-equilibrium molecular dynamics simulations. Several loading schemes including flyer plate impact, decaying shock loading via a frozen piston, and quasi-isentropic (constant strain-rate) expansion are employed to span tensile strain-rates of 108 to 1014 per second. Single crystals of <001> orientation are specifically evaluated to eliminate grain boundary effects. Heterogeneous void nucleation occurs principally at the intersection of deformation twins in single crystals. At high strain rates, multiple spall events occur throughout the material and voids continue to nucleate until relaxation waves arrive from adjacent events. At ultra-high strain rates, those approaching or exceeding the atomic vibrational frequency, spall strength saturates near the maximum theoretical spall strength.

  3. 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.

  4. Thermal conductance at the interface between crystals using equilibrium and nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Merabia, Samy; Termentzidis, Konstantinos

    2012-09-01

    In this article, we compare the results of nonequilibrium (NEMD) and equilibrium (EMD) molecular dynamics methods to compute the thermal conductance at the interface between solids. We propose to probe the thermal conductance using equilibrium simulations measuring the decay of the thermally induced energy fluctuations of each solid. We also show that NEMD and EMD give generally speaking inconsistent results for the thermal conductance: Green-Kubo simulations probe the Landauer conductance between two solids which assumes phonons on both sides of the interface to be at equilibrium. On the other hand, we show that NEMD give access to the out-of-equilibrium interfacial conductance consistent with the interfacial flux describing phonon transport in each solid. The difference may be large and reaches typically a factor 5 for interfaces between usual semiconductors. We analyze finite size effects for the two determinations of the interfacial thermal conductance, and show that the equilibrium simulations suffer from severe size effects as compared to NEMD. We also compare the predictions of the two above-mentioned methods—EMD and NEMD—regarding the interfacial conductance of a series of mass mismatched Lennard-Jones solids. We show that the Kapitza conductance obtained with EMD can be well described using the classical diffuse mismatch model (DMM). On the other hand, NEMD simulation results are consistent with an out-of-equilibrium generalization of the acoustic mismatch model (AMM). These considerations are important in rationalizing previous results obtained using molecular dynamics, and help in pinpointing the physical scattering mechanisms taking place at atomically perfect interfaces between solids, which is a prerequisite to understand interfacial heat transfer across real interfaces.

  5. Non-Equilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro

    Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and non-equilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws and the microscopic expressions for the transport properties that enter the constitutive relations. If the system is displaced far from equilibrium, no fully general theory exists to treat such systems. By restricting consideration to a class of non-equilibrium states which arise from perturbations (linear or non-linear) of an equilibrium state, methods can be developed to treat non-equilibrium states. Furthermore, non-equilibrium molecular dynamics (NEMD) simulation methods can be devised to provide estimates for the transport properties of these systems.

  6. Nonequilibrium transport through a disordered molecular nanowire

    NASA Astrophysics Data System (ADS)

    Thiessen, P.; Díaz, E.; Römer, R. A.; Domínguez-Adame, F.

    2017-05-01

    We investigate the nonequilibrium transport properties of a disordered molecular nanowire. The nanowire is regarded as a quasi-one-dimensional organic crystal composed of self-assembled molecules. One orbital and a single random energy are assigned to each molecule while the intermolecular coupling does not fluctuate. Consequently, electronic states are expected to be spatially localized. We consider the regime of strong localization, namely, the localization length is smaller than the length of the molecular wire. Electron-vibron interaction, taking place at each single molecule, is also considered. We investigate the interplay between static disorder and electron-vibron interaction in response to either an applied electric bias or a temperature gradient. To this end, we calculate the electric and heat currents when the nanowire is connected to leads, using the Keldysh nonequilibrium Green's function formalism. At intermediate temperature, scattering by disorder dominates both charge and heat transport. We find that the electron-vibron interaction enhances the effect of the disorder on the transport properties due to the decrease of the coherent electron tunneling among molecules.

  7. Nonequilibrium quantum thermodynamics in Coulomb crystals

    NASA Astrophysics Data System (ADS)

    Cosco, F.; Borrelli, M.; Silvi, P.; Maniscalco, S.; De Chiara, G.

    2017-06-01

    We present an in-depth study of the nonequilibrium statistics of the irreversible work produced during sudden quenches in proximity to the structural linear-zigzag transition of ion Coulomb crystals in 1+1 dimensions. By employing both an analytical approach based on a harmonic expansion and numerical simulations, we show the divergence of the average irreversible work in proximity to the transition. We show that the nonanalytic behavior of the work fluctuations can be characterized in terms of the critical exponents of the quantum Ising chain. Due to the technological advancements in trapped-ion experiments, our results can be readily verified.

  8. 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.

  9. 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.

  10. Correlation between thermal conductivity and bond length alternation in carbon nanotubes: a combined reverse nonequilibrium molecular dynamics--crystal orbital analysis.

    PubMed

    Alaghemandi, Mohammad; Schulte, Joachim; Leroy, Frédéric; Müller-Plathe, Florian; Böhm, Michael C

    2011-01-15

    The thermal conductivity (λ) of carbon nanotubes (CNTs) with chirality indices (5,0), (10,0), (5,5), and (10,10) has been studied by reverse nonequilibrium molecular dynamics (RNEMD) simulations as a function of different bond length alternation patterns (Δr(i) ). The Δr(i) dependence of the bond force constant (k(rx) ) in the molecular dynamics force field has been modeled with the help of an electronic band structure approach. These calculations show that the Δr(i) dependence of k(rx) in tubes with not too small a diameter can be mapped by a simple linear bond length-bond order correlation. A bond length alternation with an overall reduction in the length of the nanotube causes an enhancement of λ, whereas an alternation scheme leading to an elongation of the tube is coupled to a decrease of the thermal conductivity. This effect is more pronounced in carbon nanotubes with larger diameters. The formation of a polyene-like structure in the direction of the longitudinal axis has a negligible influence on λ. A comparative analysis of the RNEMD and crystal orbital results indicates that Δr(i) -dependent modifications of λ and the electrical conductivity are uncorrelated. This behavior is in-line with a heat transfer that is not carried by electrons. Modifications of λ as a function of the bond alternation in the (10,10) nanotube are explained with the help of power spectra, which provide access to the density of vibrational states. We have suggested longitudinal low-energy modes in the spectra that might be responsible for the Δr(i) dependence of λ. Copyright © 2010 Wiley Periodicals, Inc.

  11. Non-equilibrium Reaction Kinetics in Molecular Solids

    NASA Astrophysics Data System (ADS)

    Wood, Mitchell; Strachan, Alejandro

    We explore the possibility of non-statistical chemical reactions in condense-phase energetic materials via reactive molecular dynamics (MD) simulations. We characterize the response of three unique high energy density molecular crystals to different types of insults: electric fields of various frequencies (100-4000cm-1) and strengths and direct heating at various rates. We find that non-equilibrium states can be created for short timescales when energy input targets specific vibrations through the electric fields, and that equilibration eventually occurs even while the insults remain present. Interestingly, for strong fields these relaxation timescales are comparable to those of the initial chemical decomposition of the molecules. Details of how this vibrational energy localization affects the preferred uni- or multi-molecular reactions are discussed. These results provide insight into non-equilibrium or coherent initiation of chemistry in the condensed phase that would of interest in fields ranging from catalysis to explosives.

  12. Flow and plasticity via nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G.

    1984-06-11

    The viscous flow of fluids and the plastic flow of solids, such as metals, are interesting from both the practical and the theoretical points of view. Atomistic molecular dynamics simulations provide a way of visualizing and understanding these flows in a detailed microscopic way. Simulations are necessarily carried out at relatively high rates of strain. For this reason they are ideally suited to the study of nonlinear flow phenomena: normal stresses induced by shear deformation, stress rotation, and the coupling of stress with heat flow, for instance. The simulations require appropriate boundary conditions, forces, and equations of motion. Newtonian mechanics is relatively inefficient for this simulation task. A modification, Nonequilibrium Molecular Dynamics, has been developed to simulate nonequilibrium flows. By now, many high-strain-rate rheological studies of flowing (viscous) fluids and (plastic) solids have been carried out. Here I describe the new methods used in the simulations and some results obtained in this way. A three-body shear-flow exercise is appended to make these ideas more concrete.

  13. 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.

  14. Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.

    2006-04-01

    Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.

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

    PubMed Central

    Liu, Shuanglong; Nurbawono, Argo; Zhang, Chun

    2015-01-01

    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. PMID:26472080

  16. Nonequilibrium molecular motion in a hypersonic shock wave

    NASA Technical Reports Server (NTRS)

    Pham-Van-diep, G.; Erwin, D.; Muntz, E. P.

    1989-01-01

    Molecular velocities have been measured inside a hypersonic, normal shock wave, where the gas experiences rapid changes in its macroscopic properties. As first hypothesized by Mott-Smith, but never directly observed, the molecular velocity distribution exhibits a qualitatively bimodal character that is derived from the distribution functions on either side of the shock. Quantitatively correct forms of the molecular velocity distribution function in highly nonequilibrium flows can be calculated, by means of the Direct Simulation Monte Carlo technique.

  17. Nonequilibrium molecular motion in a hypersonic shock wave.

    PubMed

    Pham-Van-Diep, G; Erwin, D; Muntz, E P

    1989-08-11

    Molecular velocities have been measured inside a hypersonic, normal shock wave, where the gas experiences rapid changes in its macroscopic properties. As first hypothesized by Mott-Smith, but never directly observed, the molecular velocity distribution exhibits a qualitatively bimodal character that is derived from the distribution functions on either side of the shock. Quantitatively correct forms of the molecular velocity distribution function in highly nonequilibrium flows can be calculated, by means of the Direct Simulation Monte Carlo technique.

  18. On the theory of steady-state crystallization with a non-equilibrium mushy layer

    NASA Astrophysics Data System (ADS)

    Alexandrov, D. V.; Alexandrova, I. V.; Ivanov, A. A.

    2016-12-01

    Complete analytical solutions of nonlinear equations describing the steady-state directional crystallization of binary melts with a nonequilibrium mushy layer, where the processes of nucleation and growth of crystals occur, are constructed.

  19. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    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.

  20. 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.

  1. 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

  2. Non-equilibrium phase transitions in a liquid crystal.

    PubMed

    Dan, K; Roy, M; Datta, A

    2015-09-07

    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

  3. 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.

  4. On determining continuum quantities of non-equilibrium processes via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Fu, Yao

    In this dissertation, a high-fidelity atomistic-to-continuum link for highly non-equilibrium processes has been established by making several modifications to Hardy's theory. Although Hardy's thermomechanical quantities were derived analytically to conserve mass, momentum and energy, they have not been rigorously tested and validated numerically in the past. Hence the first task was to investigate the effectiveness of ensemble averaging in removing thermal fluctuations and compare with conventional time averaging for fcc crystals simulated using both equilibrium and non-equilibrium molecular dynamics (MD) simulations, where the non-equilibrium process was introduced by a shock impact. It has been found that the ensemble averaging has better convergence than time averaging due to the statistical independence of the thermomechanical quantities computed using ensemble averaging. The second task was to test the validity of Hardy's theory by checking if it is able to conserve mass, momentum and energy numerically. A few highly non-equilibrium processes were simulated using MD, including Gaussian wave and shock impact propagation in 1D and 3D fcc crystals. Based on the test results, a new normalization rule has been proposed so that the computed thermomechanical quantities can conserve the fundamental properties more accurately. To a large extent, Hardy's theory has been found to be valid regardless of the width of the localization function, the interatomic potential and crystal structure, and with and without ensemble averaging. To further test the validity of Hardy's theory for more complex non-equilibrium processes, where plastic deformation is accomplished through dislocation glide and slip band emission, a crack propagation problem in iron crystal with a pre-created center crack is simulated using MD. The computed Hardy's thermomechanical quantities can generally conserve mass, momentum and energy. Exceptions have been found around the crack region, where the

  5. Molecular Simulation Of Nonequilibrium Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Schwartzentruber, T. E.; Valentini, P.; Tump, P.

    2011-05-01

    Large-scale conventional time-driven molecular dynamics (MD) simulations of normal shock waves are performed for monatomic argon and argon-helium mixtures. For pure argon, near perfect agreement between MD and direct simulation Monte Carlo (DSMC) results using the variable-hard-sphere model are found for density and temperature profiles as well as for velocity distribution functions throughout the shock. MD simulation results for argon are also in excellent agreement with experimental shock thickness data. Preliminary MD simulation results for argon-helium mixtures are in qualitative agreement with experimental density and temperature profile data, where separation between argon and helium density profiles due to disparate atomic mass is observed. Since conventional time-driven MD simulation of dilute gases is computationally inefficient, a combined Event-Driven/Time-Driven MD algorithm is presented. The ED/TD-MD algorithm computes impending collisions and advances molecules directly to their next collision while evaluating the collision using conventional time-driven MD with an arbitrary interatomic potential. The method timestep thus approaches the mean-collision- time in the gas, while also detecting and simulating multi-body collisions with a small approximation. Extension of the method to diatomic and small polyatomic molecules is detailed, where center-of-mass velocities and extended cutoff radii are used to advance molecules to impend- ing collisions. Only atomic positions are integrated during collisions and molecule sorting algorithms are em- ployed to determine if atoms are bound in a molecule after a collision event. Rotational relaxation to equilibrium for a low density diatomic gas is validated by comparison with large-scale conventional time-driven MD simulation, where the final rotational distribution function is verified to be the correct Boltzmann rotational energy distribution.

  6. 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.

  7. Vibrational energy transfer in shocked molecular crystals.

    PubMed

    Hooper, Joe

    2010-01-07

    We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state.

  8. 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

  9. Shock and Laser Induced Non-Equilibrium Chemistry in Molecular Energetics

    NASA Astrophysics Data System (ADS)

    Wood, Mitchell; Cherukara, Mathew; Kober, Edward; Strachan, Alejandro

    2015-06-01

    In this study, we have used large scale reactive molecular dynamics (MD) simulations to study how contrasting initiation mechanisms from either shock or electromagnetic insults compare to traditional thermal initiation. We will show how insults of equal strength but different character can yield vastly different reaction profiles and thus the evolution of hot-spots. For shocked RDX (Up = 2km/s), we find that the collapse of a cylindrical 40 nm diameter pore leads to a significant amount of non-equilibrium reactions followed by the formation of a sustained deflagration wave. In contrast, a hot spot that is seeded into a statically compressed crystal with matching size and temperature will quench over the same timescale, highlighting the importance of insult type. Furthermore, MD simulations of electromagnetic insults coupled to intramolecular vibrations have shown, in some cases, mode specific initial chemistry and altered kinetics of the subsequent decomposition. By leveraging spectroscopic and chemical information gathered in our MD simulations, we have been able to identify and track non-equilibrium vibrational states of these materials and correlate them to these observed changes. Implications of insult dependent reactivity and non-equilibrium chemistry will be discussed.

  10. Mesoscopic non-equilibrium thermodynamic analysis of molecular motors.

    PubMed

    Kjelstrup, S; Rubi, J M; Pagonabarraga, I; Bedeaux, D

    2013-11-28

    We show that the kinetics of a molecular motor fueled by ATP and operating between a deactivated and an activated state can be derived from the principles of non-equilibrium thermodynamics applied to the mesoscopic domain. The activation by ATP, the possible slip of the motor, as well as the forward stepping carrying a load are viewed as slow diffusion along a reaction coordinate. Local equilibrium is assumed in the reaction coordinate spaces, making it possible to derive the non-equilibrium thermodynamic description. Using this scheme, we find expressions for the velocity of the motor, in terms of the driving force along the spacial coordinate, and for the chemical reaction that brings about activation, in terms of the chemical potentials of the reactants and products which maintain the cycle. The second law efficiency is defined, and the velocity corresponding to maximum power is obtained for myosin movement on actin. Experimental results fitting with the description are reviewed, giving a maximum efficiency of 0.45 at a myosin headgroup velocity of 5 × 10(-7) m s(-1). The formalism allows the introduction and test of meso-level models, which may be needed to explain experiments.

  11. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    SciTech Connect

    Radak, Brian K.; Roux, Benoît

    2016-10-07

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  12. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    DOE PAGES

    Radak, Brian K.; Roux, Benoît

    2016-10-07

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance.more » An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.« less

  13. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Radak, Brian K.; Roux, Benoît

    2016-10-01

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  14. Plasticity induced by shock waves in nonequilibrium molecular-dynamics simulations

    PubMed

    Holian; Lomdahl

    1998-06-26

    Nonequilibrium molecular-dynamics simulations of shock waves in three-dimensional 10-million atom face-centered cubic crystals with cross-sectional dimensions of 100 by 100 unit cells show that the system slips along all of the available 111 slip planes, in different places along the nonplanar shock front. Comparison of these simulations with earlier ones on a smaller scale not only eliminates the possibility that the observed slippage is an artifact of transverse periodic boundary conditions, but also reveals the richness of the nanostructure left behind. By introducing a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, it is shown that for weaker shock waves (below the perfect-crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  16. 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

  17. 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.

  18. Non-equilibrium phase behavior and friction of confined molecular films under shear: A non-equilibrium molecular dynamics study.

    PubMed

    Maćkowiak, Sz; Heyes, D M; Dini, D; Brańka, A C

    2016-10-28

    The phase behavior of a confined liquid at high pressure and shear rate, such as is found in elastohydrodynamic lubrication, can influence the traction characteristics in machine operation. Generic aspects of this behavior are investigated here using Non-equilibrium Molecular Dynamics (NEMD) simulations of confined Lennard-Jones (LJ) films under load with a recently proposed wall-driven shearing method without wall atom tethering [C. Gattinoni et al., Phys. Rev. E 90, 043302 (2014)]. The focus is on thick films in which the nonequilibrium phases formed in the confined region impact on the traction properties. The nonequilibrium phase and tribological diagrams are mapped out in detail as a function of load, wall sliding speed, and atomic scale surface roughness, which is shown can have a significant effect. The transition between these phases is typically not sharp as the external conditions are varied. The magnitude of the friction coefficient depends strongly on the nonequilibrium phase adopted by the confined region of molecules, and in general does not follow the classical friction relations between macroscopic bodies, e.g., the frictional force can decrease with increasing load in the Plug-Slip (PS) region of the phase diagram owing to structural changes induced in the confined film. The friction coefficient can be extremely low (∼0.01) in the PS region as a result of incommensurate alignment between a (100) face-centered cubic wall plane and reconstructed (111) layers of the confined region near the wall. It is possible to exploit hysteresis to retain low friction PS states well into the central localization high wall speed region of the phase diagram. Stick-slip behavior due to periodic in-plane melting of layers in the confined region and subsequent annealing is observed at low wall speeds and moderate external loads. At intermediate wall speeds and pressure values (at least) the friction coefficient decreases with increasing well depth of the LJ potential

  19. Non-equilibrium phase behavior and friction of confined molecular films under shear: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Maćkowiak, Sz.; Heyes, D. M.; Dini, D.; Brańka, A. C.

    2016-10-01

    The phase behavior of a confined liquid at high pressure and shear rate, such as is found in elastohydrodynamic lubrication, can influence the traction characteristics in machine operation. Generic aspects of this behavior are investigated here using Non-equilibrium Molecular Dynamics (NEMD) simulations of confined Lennard-Jones (LJ) films under load with a recently proposed wall-driven shearing method without wall atom tethering [C. Gattinoni et al., Phys. Rev. E 90, 043302 (2014)]. The focus is on thick films in which the nonequilibrium phases formed in the confined region impact on the traction properties. The nonequilibrium phase and tribological diagrams are mapped out in detail as a function of load, wall sliding speed, and atomic scale surface roughness, which is shown can have a significant effect. The transition between these phases is typically not sharp as the external conditions are varied. The magnitude of the friction coefficient depends strongly on the nonequilibrium phase adopted by the confined region of molecules, and in general does not follow the classical friction relations between macroscopic bodies, e.g., the frictional force can decrease with increasing load in the Plug-Slip (PS) region of the phase diagram owing to structural changes induced in the confined film. The friction coefficient can be extremely low (˜0.01) in the PS region as a result of incommensurate alignment between a (100) face-centered cubic wall plane and reconstructed (111) layers of the confined region near the wall. It is possible to exploit hysteresis to retain low friction PS states well into the central localization high wall speed region of the phase diagram. Stick-slip behavior due to periodic in-plane melting of layers in the confined region and subsequent annealing is observed at low wall speeds and moderate external loads. At intermediate wall speeds and pressure values (at least) the friction coefficient decreases with increasing well depth of the LJ potential

  20. Nonequilibrium transport on a quantum molecular chain in terms of the complex Liouvillian spectrum.

    PubMed

    Tanaka, Satoshi; Kanki, Kazuki; Petrosky, Tomio

    2011-05-01

    The transport process in a molecular chain in a nonequilibrium stationary state is theoretically investigated. The molecule is interacting at both ends with thermal baths of different temperatures, while no dissipation mechanism is contained inside the molecular chain. We have first obtained the nonequilibrium stationary state outside the Hilbert space in terms of the complex spectral representation of Liouvillian. The nonequilibrium stationary state is obtained as an eigenstate of the Liouvillian, which is constructed through the collision invariant of the kinetic equation. The eigenstate of the Liouvillian contains information on the spatial correlation between the molecular chain and the thermal baths. While energy flow in the nonequilibrium state which is due to the first-order correlation can be described by the Landauer formula, the particle current due to the second-order correlation cannot be described by the Landauer formula. The present method provides a simple way to evaluate the energy transport in a molecular chain in a nonequilibrium situation.

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

    PubMed

    Alavi, Saman; Ripmeester, J A

    2010-04-14

    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.

  2. 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.

  3. Spectral analysis of nonequilibrium molecular dynamics: Spectral phonon temperature and local nonequilibrium in thin films and across interfaces

    NASA Astrophysics Data System (ADS)

    Feng, Tianli; Yao, Wenjun; Wang, Zuyuan; Shi, Jingjing; Li, Chuang; Cao, Bingyang; Ruan, Xiulin

    2017-05-01

    Although extensive experimental and theoretical works have been conducted to understand the ballistic and diffusive phonon transport in nanomaterials recently, direct observation of temperature and thermal nonequilibrium of different phonon modes has not been realized. Herein, we have developed a method within the framework of molecular dynamics to calculate the temperatures of phonons in both real and phase spaces. Taking silicon thin film and graphene as examples, we directly obtained the spectral phonon temperature (SPT) and observed the local thermal nonequilibrium between the ballistic and diffusive phonons. Such nonequilibrium also generally exists across interfaces and is surprisingly large, and it provides a significant additional thermal interfacial resistance mechanism besides phonon reflection. Our SPT results directly show that the vertical thermal transport across the dimensionally mismatched graphene-substrate interface is through the coupling between flexural acoustic phonons of graphene and the longitudinal phonons in the substrate with mode conversion. In the dimensionally matched interfaces, e.g., graphene-graphene junction and graphene-boron nitride planar interfaces, strong coupling occurs between the acoustic phonon modes on both sides, and the coupling decreases with interfacial mixing. The SPT method together with the spectral heat flux can eliminate the size effect of the thermal conductivity prediction induced from ballistic transport.

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

    SciTech Connect

    Bjorgaard, Josiah August; Velizhanin, Kirill A.; Tretiak, Sergei

    2016-04-15

    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 paper, 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. Finally, molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  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. Molecular-Based Optical Diagnostics for Hypersonic Nonequilibrium Flows

    NASA Technical Reports Server (NTRS)

    Danehy, Paul; Bathel, Brett; Johansen, Craig; Winter, Michael; O'Byrne, Sean; Cutler, Andrew

    2015-01-01

    This presentation package consists of seven different talks rolled up into one. These talks are all invited orals presentations in a special session at the Aviation 2015 conference and represent contributions that were made to a recent AIAA book that will be published entitled 'Hypersonic Nonequilibrium Flows: Fundamentals and Recent Advances'. Slide 5 lists the individual presentations that will be given during the special session.

  8. Emergence of an enslaved phononic bandgap in a non-equilibrium pseudo-crystal

    NASA Astrophysics Data System (ADS)

    Bachelard, Nicolas; Ropp, Chad; Dubois, Marc; Zhao, Rongkuo; Wang, Yuan; Zhang, Xiang

    2017-08-01

    Material systems that reside far from thermodynamic equilibrium have the potential to exhibit dynamic properties and behaviours resembling those of living organisms. Here we realize a non-equilibrium material characterized by a bandgap whose edge is enslaved to the wavelength of an external coherent drive. The structure dynamically self-assembles into an unconventional pseudo-crystal geometry that equally distributes momentum across elements. The emergent bandgap is bestowed with lifelike properties, such as the ability to self-heal to perturbations and adapt to sudden changes in the drive. We derive an exact analytical solution for both the spatial organization and the bandgap features, revealing the mechanism for enslavement. This work presents a framework for conceiving lifelike non-equilibrium materials and emphasizes the potential for the dynamic imprinting of material properties through external degrees of freedom.

  9. 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.

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

    PubMed

    Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan

    2015-02-09

    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.

  11. 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

  12. Microwave-driven zeolite-guest systems show athermal effects from nonequilibrium molecular dynamics.

    PubMed

    Blanco, Cristian; Auerbach, Scott M

    2002-06-05

    Nonequilibrium molecular dynamics simulations show that steady-state systems obtained by microwave heating are qualitatively different from those at thermal equilibrium. This difference arises because energy transfer from hotter to colder species is not efficient enough to equilibrate the distribution of energy. Under nonequilibrium conditions, we found that microwave radiation can selectively heat methanol in a binary mixture of methanol-benzene adsorbed in faujasite zeolite. The difference in steady-state temperatures follows the trend Tmethanol > Tbenzene > Tzeolite, which is qualitatively consistent with recent experimental results.

  13. Ultrasonic attenuation in molecular crystals

    NASA Astrophysics Data System (ADS)

    Perrin, Bernard

    1981-11-01

    It is now well established from an experimental point of view that, concerning the ultrasonic attenuation, molecular crystals exhibit a specific behavior among dielectric crystals. This fact suggests the presence of a relaxation process. Liebermann, who has introduced this field, has proposed a way to analyze this problem and in particular has given an expression for the ultrasonic absorption coefficient in terms of a relaxation time and some thermodynamic quantities. In contrast to Liebermann's approach, a solid-state viewpoint is presented here, and it is shown that this ultrasonic relaxation can be taken into account in the framework of Akhieser's theory. A general expression of the ultrasonic absorption coefficient is calculated in terms of the phonon collision operator using the Boltzmann-equation approach of Woodruff and Ehrenreich. The collision-time approximation widely used in dielectric crystals fails in molecular crystals for which the presence of slow relaxation times in the collision operator prevents the thermalization of the whole set of phonons and gives rise to an ultrasonic relaxation. Thus a more suitable approximation is suggested here, which leads to a new expression of the ultrasonic attenuation valid in molecular crystals. Different forms of this expression are discussed, and comparison with Liebermann's expression used in most of the previous papers shows that the present treatment takes better account of the anisotropy of the solid state. The fit of experimental results obtained for some ionic-molecular crystals also shows that the expression derived here gives better agreement than does Liebermann's. Finally, it is shown that in the framework of the present treatment and under rather general conditions, the anisotropy affects primarily the magnitude of the ultrasonic absorption due to the molecular relaxation, but it does not affect its frequency dependence.

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

    DOE PAGES

    Bjorgaard, Josiah August; Velizhanin, Kirill A.; Tretiak, Sergei

    2016-04-15

    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 paper, 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. Finally, molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibriummore » due to photoexcitation and emission.« less

  15. Nonequilibrium Molecular Switching of Chiral Helicene Oligomers in Double-Helix Formation.

    PubMed

    Shigeno, Masanori

    2016-01-01

    Molecular switching is the phenomenon in which a molecular structural change occurs reversibly in response to an external stimulus or energy. It plays an important role in biology, in which it is used for sensing environmental changes. In contrast to well-studied equilibrium molecular switching involving thermodynamically stable states, nonequilibrium molecular switching involving a metastable state is a notable chemical phenomenon and is the theme of this study. Sulfonamido- and aminomethylenehelicene oligomers show a reversible structural change from a double helix to a random coil in dilute solution. A metastable state consisting of random coils can be generated by heating, which shows various nonequilibrium thermodynamic properties. Molecular phenomena including molecular thermal hysteresis, molecular memory effect, and one-directional three-state molecular structural change occur, none of which is observed in an equilibrium molecular switching system. They can be applied to sensing environmental changes such as temperature increases/decreases, temperature change rates, and concentration increases, and for counting the numbers 1 and 2.

  16. Nonequilibrium molecular dynamics simulations of heat flow in one-dimensional lattices

    PubMed

    Zhang; Isbister; Evans

    2000-04-01

    We study the use of the Evans nonequilibrium molecular dynamics (NEMD) heat flow algorithm for the computation of the heat conductivity in one-dimensional lattices. For the well-known Fermi-Pasta-Ulam model, it is shown that when the heat field strength is greater than a certain critical value (which depends on the system size) solitons can be generated in molecular dynamics simulations starting from random initial conditions. Such solitons are stable and travel with supersonic speeds. For smaller heat fields, no solitons are generated in the molecular dynamics simulations; the heat conductivity obtained via the NEMD algorithm increases monotonically with the size of the system.

  17. Nanoscopic spontaneous motion of liquid trains: Nonequilibrium molecular dynamics simulation.

    PubMed

    Bahrami, Amir Houshang; Jalali, Mir Abbas

    2010-01-14

    Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in submicron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less than a critical value.

  18. Nonequilibrium chemistry in shocked molecular clouds. [interstellar gases

    NASA Technical Reports Server (NTRS)

    Iglesias, E. R.; Silk, J.

    1978-01-01

    The gas-phase chemistry is studied behind a 10-km/s shock propagating into a dense molecular cloud. The principal conclusions are that: the concentrations of certain molecules (CO, NH3, HCN, N2) are unperturbed by the shock; other molecules (H2CO, CN, HCO(+)) are greatly decreased in abundance; and substantial amounts of H2O, HCO, and CH4 are produced. Approximately 1 million yr (independent of the density) must elapse after shock passage before chemical equilibrium is attained.

  19. Classical molecular dynamics simulations for non-equilibrium correlated plasmas

    NASA Astrophysics Data System (ADS)

    Ferri, S.; Calisti, A.; Talin, B.

    2017-03-01

    A classical molecular dynamics model was recently extended to simulate neutral multi-component plasmas where various charge states of the same atom and electrons coexist. It is used to investigate the plasma effects on the ion charge and on the ionization potential in dense plasmas. Different simulated statistical properties will show that the concept of isolated particles is lost in such correlated plasmas. The charge equilibration is discussed for a carbon plasma at solid density and investigation on the charge distribution and on the ionization potential depression (IPD) for aluminum plasmas is discussed with reference to existing experiments.

  20. Temperature control in molecular dynamic simulations of non-equilibrium processes

    NASA Astrophysics Data System (ADS)

    Toton, Dawid; Lorenz, Christian D.; Rompotis, Nikolaos; Martsinovich, Natalia; Kantorovich, Lev

    2010-02-01

    Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic

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

    PubMed

    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.

  2. 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.

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

    PubMed Central

    2016-01-01

    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

  4. Non-equilibrium conformational dynamics in the function of molecular chaperones.

    PubMed

    Barducci, Alessandro; De Los Rios, Paolo

    2015-02-01

    Why do chaperones need ATP hydrolysis to help proteins reach their native, functional states? In this review, we highlight the most recent experimental and theoretical evidences suggesting that ATP hydrolysis allows molecular chaperones to escape the bounds imposed by equilibrium thermodynamics. We argue here that energy consumption must be fully taken into account to understand the mechanism of these intrinsically non-equilibrium machines and we propose a novel perspective in the way the relation between function and ATP hydrolysis is viewed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity

    NASA Astrophysics Data System (ADS)

    Müller-Plathe, Florian

    1997-04-01

    A nonequilibrium molecular dynamics method for calculating the thermal conductivity is presented. It reverses the usual cause and effect picture. The "effect," the heat flux, is imposed on the system and the "cause," the temperature gradient is obtained from the simulation. Besides being very simple to implement, the scheme offers several advantages such as compatibility with periodic boundary conditions, conservation of total energy and total linear momentum, and the sampling of a rapidly converging quantity (temperature gradient) rather than a slowly converging one (heat flux). The scheme is tested on the Lennard-Jones fluid.

  6. 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.

  7. Molecular dynamics simulation of crystal growth in Al50Ni50: The generation of defects

    NASA Astrophysics Data System (ADS)

    Kuhn, Philipp; Horbach, Jürgen

    2013-01-01

    The ordering processes in the interface of a solidifying binary alloy (Al50Ni50) are studied by molecular dynamics computer simulation. At various temperatures below the melting point, inhomogeneous systems with planar crystal-melt interfaces in (100) orientation are prepared. The growth of a new crystalline Al or Ni layer proceeds through different time-delayed ordering processes. Before the onset of crystallization, there is a segregation process of Al and Ni atoms in the region where a new layer forms. We show that the interplay between segregation and crystallization supports the formation of a high nonequilibrium concentration of point defects.

  8. On the effect of confined fluid molecular structure on nonequilibrium phase behaviour and friction.

    PubMed

    Ewen, J P; Gattinoni, C; Zhang, J; Heyes, D M; Spikes, H A; Dini, D

    2017-07-21

    A detailed understanding of the behaviour of confined fluids is critical to a range of industrial applications, for example to control friction in engineering components. In this study, a combination of tribological experiments and confined nonequilibrium molecular dynamics simulations has been used to investigate the effect of base fluid molecular structure on nonequilibrium phase behaviour and friction. An extensive parameter study, including several lubricant and traction fluid molecules subjected to pressures (0.5-2.0 GPa) and strain rates (10(4)-10(10) s(-1)) typical of the elastohydrodynamic lubrication regime, reveals clear relationships between the friction and flow behaviour. Lubricants, which are flexible, broadly linear molecules, give low friction coefficients that increase with strain rate and pressure in both the experiments and the simulations. Conversely, traction fluids, which are based on inflexible cycloaliphatic groups, give high friction coefficients that only weakly depend on strain rate and pressure. The observed differences in friction behaviour can be rationalised through the stronger shear localisation which is observed for the traction fluids in the simulations. Higher pressures lead to more pronounced shear localisation, whilst increased strain rates lead to a widening of the sheared region. The methods utilised in this study have clarified the physical mechanisms of important confined fluid behaviour and show significant potential in both improving the prediction of elastohydrodynamic friction and developing new molecules to control it.

  9. Verification of Onsager's reciprocal relations for evaporation and condensation using non-equilibrium molecular dynamics.

    PubMed

    Xu, J; Kjelstrup, S; Bedeaux, D; Røsjorde, A; Rekvig, L

    2006-07-01

    Non-equilibrium molecular dynamic (NEMD) simulations have been used to study heat and mass transfer across a vapor-liquid interface for a one-component system using a Lennard-Jones spline potential. It was confirmed that the relation between the surface tension and the surface temperature in the non-equilibrium system was the same as in equilibrium (local equilibrium). Interfacial transfer coefficients were evaluated for the surface, which expressed the heat and mass fluxes in temperature and chemical potential differences across the interfacial region (film). In this analysis it was assumed that the Onsager reciprocal relations were valid. In this paper we extend the number of simulations such that we can calculate all four interface film transfer coefficients along the whole liquid-vapor coexistence curve. We do this analysis both for the case where we use the measurable heat flux on the vapor side and for the case where we use the measurable heat flux on the liquid side. The most important result we found is that the coupling coefficients within the accuracy of the calculation are equal. This is the first verification of the validity of the Onsager relations for transport through a surface using molecular dynamics. The interfacial film transfer coefficients are found to be a function of the surface temperature alone. New expressions are given for the kinetic theory values of these coefficients which only depend on the surface temperature. The NEMD values were found to be in good agreement with these expressions.

  10. Molecular theory of thermomechanical coupling in cholesteric liquid crystals

    NASA Astrophysics Data System (ADS)

    Sarman, Sten

    1999-06-01

    A cholesteric liquid crystal lacks a center of inversion and it is consequently different from its mirror image. The low symmetry allows linear cross couplings between thermodynamic forces and fluxes that are polar vectors and pseudovectors, respectively. This makes it possible for a temperature gradient, which is a polar vector to induce a director angular velocity, which is a pseudovector. The reverse is also possible; the torque conjugate to the director angular velocity can drive a heat current. This is the basis for the Lehman effect where a temperature gradient parallel to the cholesteric axis causes the local director to rotate. We use linear response theory to derive Green-Kubo relations and nonequilibrium molecular dynamics simulation algorithms for the transport coefficient that couples the temperature gradient and the director angular velocity. The theory is completely general and can consequently be used to find relations for any linear cross coupling coefficient between a polar vector and a pseudovector.

  11. Melting of superheated molecular crystals

    NASA Astrophysics Data System (ADS)

    Cubeta, Ulyana; Bhattacharya, Deepanjan; Sadtchenko, Vlad

    2017-07-01

    Melting dynamics of micrometer scale, polycrystalline samples of isobutane, dimethyl ether, methyl benzene, and 2-propanol were investigated by fast scanning calorimetry. When films are superheated with rates in excess of 105 K s-1, the melting process follows zero-order, Arrhenius-like kinetics until approximately half of the sample has transformed. Such kinetics strongly imply that melting progresses into the bulk via a rapidly moving solid-liquid interface that is likely to originate at the sample's surface. Remarkably, the apparent activation energies for the phase transformation are large; all exceed the enthalpy of vaporization of each compound and some exceed it by an order of magnitude. In fact, we find that the crystalline melting kinetics are comparable to the kinetics of dielectric α-relaxation in deeply supercooled liquids. Based on these observations, we conclude that the rate of non-isothermal melting for superheated, low-molecular-weight crystals is limited by constituent diffusion into an abnormally dense, glass-like, non-crystalline phase.

  12. 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.

  13. 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.

  14. 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.

  15. Nonequilibrium processes.

    PubMed

    Polanyi, J C

    1971-08-01

    Nonequilibrium phenomena have been studied for over half a century, particularly as a means to understanding the mechanism of energy transfer. Application of the insights and techniques of molecular physics to chemistry has resulted in a view of chemistry as constituting an aspect of the study of strong collisions, and chemical reaction as a special type of energy transfer. Increasing use has been made in experimental work of nonequilibrium environments for the study of chemical processes. The nature and purpose of such experiments are reviewed here, very briefly, and an attempt is made to point to areas that appear ripe for development over the coming decade.

  16. Mesoscale modeling of dislocations in molecular crystals

    NASA Astrophysics Data System (ADS)

    Lei, Lei; Koslowski, Marisol

    2011-02-01

    Understanding the inelastic deformation of molecular crystals is of fundamental importance to the modeling of the processing of drugs in the pharmaceutical industry as well as to the initiation of detonation in high energy density materials. In this work, we present dislocation dynamics simulations of the deformation of two molecular crystals of interest in the pharmaceutical industry, sucrose and paracetamol. The simulations calculate the yield stress of sucrose and paracetamol in good agreement with experimental observation and predict the anisotropy in the mechanical response observed in these materials. Our results show that dislocation dynamics is an effective tool to study plastic deformation in molecular crystals.

  17. Molecular tectonics: from crystals to crystals of crystals.

    PubMed

    Marinescu, Gabriela; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2013-12-11

    The in situ combination of M(II) cations (Co, Ni, Cu or Zn) with 2,4,6-pyridinetricarboxylic acid as a ligand, a bisamidinium dication as a H-bond donor tecton and NaOH leads to the formation of anionic metal complexes ML2(2-) and their interconnection into isomorphous 3D H-bonded networks displaying different colours which were used as preformed seed crystals for the formation of crystals of crystals by 3D epitaxial growth.

  18. Negative Ion Crystal Formation in Nonequilibrium Dusty Plasma at a Gas Evacuation from Technological Devices for Vacuum Support

    NASA Astrophysics Data System (ADS)

    Azarenkov, Nikolai A.; Egorov, Alexei M.; Maslov, Vasyl I.; Onishchenko, Ivan N.; Frolova, Darya Yu.

    2002-11-01

    Plasma crystal formation (or so called ion crystal formation) are investigated now intensively (see, for example, [1-5]). In particular, the formation of the plasma crystals has been observed in experiments at providing of nonequilibrium state. If in equilibrium dusty plasma there was no plasma crystal but at providing of nonequilibrium state at a gas evacuation from devices for vacuum support in a dusty plasma in experiment an ion crystal has been formed. In this case at gas evacuation the plasma flow has been appeared due to gradient of the pressure. The flow excites the perturbations of large amplitudes. The generalised equation is derived for the spatial distribution of field of any amplitude. It is shown that these perturbations of large amplitude lead to spatial ordering of heavy negative ions. It is shown that the crystal is almost motionless, because heavy negative ions are trapped by chain of perturbations formed due to instability development on generalised dusty-ion-acoustic mode with velocity equal almost zero. 1.H.M.Thomas, G.E. Morfill. Nature. 379 (1996) 806. 2.R.K.Varma, P.K.Shukla. Physica Scripta. 51 (1995) 522. 3.M.Nambu, S.V.Vladimirov, P.K.Shukla. Phys. Lett. A. 203 (1995) 40. 4.A.Melzer, A.Piel et al. Proc. Int. Top. Conf. on Plasma Physics. Trieste. Italy. 2000. 5.V.E.Fortov, A.P.Nefedov et al. Proc. Int. Conf. on Plasma Physics. Trieste. Italy. 2000. 6.D.A.Law, B.M.Annaratone, J.E.Allen et al. Dust Particle Interaction in RF Plasma Sheaths.

  19. Influence of Al content on non-equilibrium solidification behavior of Ni-Al-Ta model single crystal alloys

    NASA Astrophysics Data System (ADS)

    Ai, Cheng; Zhou, Jian; Zhang, Heng; Zhao, Xinbao; Pei, Yanling; Li, Shusuo; Gong, Shengkai

    2016-01-01

    The non-equilibrium solidification behaviors of five Ni-Al-Ta ternary model single crystal alloys with different Al contents were investigated by experimental analysis and theoretical calculation (by JMatPro) in this study. These model alloys respectively represented the γ' phase with various volume fractions (100%, 75%, 50%, 25% and 0%) at 900 °C. It was found that with decreasing Al content, liquidus temperature of experimental alloys first decreased and then increased. Meanwhile, the solidification range showed a continued downward trend. In addition, with decreasing Al content, the primary phases of non-equilibrium solidified model alloys gradually transformed from γ' phase to γ phase, and the area fraction of which first decreased and then increased. Moreover, the interdendritic/intercellular precipitation of model alloys changed from β phase (for 100% γ') to (γ+γ')Eutectic (for 75% γ'), (γ+γ')Eutectic+γ' (for 50% γ' and 25% γ') and none interdendritic precipitation (for 0% γ'), and the last stage non-equilibrium solidification sequence of model alloys was determined by the nominal Al content and different microsegregation behaviors of Al element.

  20. Molecular dynamics on nonequilibrium motion of a colloidal particle driven by an external torque

    NASA Astrophysics Data System (ADS)

    Yoo, Donghwan; Jung, Youngkyun; Kwon, Chulan

    2017-03-01

    We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use molecular dynamics simulation as an alternative to the Langevin dynamics. We prepare a heat bath composed of thousands of particles interacting with each other through the Lennard–Jones potential and impose the Langevin thermostat to maintain the heat bath in equilibrium. We consider a single colloidal particle interacting with with the particles of the heat bath also by the Lennard–Jones potential, without applying any types of dissipative or fluctuating forces used in Langevin dynamics. We set up simulation protocol fit for the overdamped limit as in real experiments, by increasing the size and mass of the colloidal particle. We study nonequilibrium fluctuations for work and heat produced incessantly in time and compare the results with those obtained from the previous studies via the overdamped Langevin dynamics. We confirm the Gallavotti–Cohen symmetry and the fluctuation theorem.

  1. Thermal diode in gas-filled nanogap with heterogeneous surfaces using nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Avanessian, T.; Hwang, G.

    2016-10-01

    A thermal diode serves as a basic building block to design advanced thermal management systems in energy-saving applications. However, the main challenges of existing thermal diodes are poor steady-state performance, slow transient response, and/or extremely difficult manufacturing. In this study, the thermal diode is examined by employing an argon gas-filled nanogap with heterogeneous surfaces in the Knudsen regime, using nonequilibrium molecular dynamics simulation. The asymmetric gas pressure and thermal accommodation coefficients changes are found due to asymmetric adsorptions onto the heterogeneous nanogap with respect to the different temperature gradient directions, and these in turn result in the thermal diode. The maximum degree of diode (or rectification) is Rmax ˜ 7, at the effective gas-solid interaction ratio between the two surfaces of ɛ*= 0.75. This work could pave the way to designing advanced thermal management systems such as thermal switches (transistors).

  2. A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise

    NASA Astrophysics Data System (ADS)

    Terao, Takamichi; Müller-Plathe, Florian

    2005-02-01

    We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81Wm-1K-1. It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.

  3. A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise.

    PubMed

    Terao, Takamichi; Müller-Plathe, Florian

    2005-02-22

    We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81 W m(-1) K(-1). It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.

  4. A uniform source-and-sink scheme for calculating thermal conductivity by nonequilibrium molecular dynamics.

    PubMed

    Cao, Bing-Yang; Li, Yuan-Wei

    2010-07-14

    A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.

  5. A uniform source-and-sink scheme for calculating thermal conductivity by nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Cao, Bing-Yang; Li, Yuan-Wei

    2010-07-01

    A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.

  6. Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

    NASA Astrophysics Data System (ADS)

    Chung, Pil Seung; Song, Wonyup; Biegler, Lorenz T.; Jhon, Myung S.

    2017-05-01

    During the operation of hard disk drive (HDD), the perfluoropolyether (PFPE) lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″) by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

  7. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    PubMed

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  8. 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.

  9. Engineering crystals by the strategy of molecular tectonics.

    PubMed

    Wuest, James D

    2005-12-21

    Detailed structures of molecular crystals cannot yet be predicted with consistent accuracy, but the strategy of molecular tectonics offers crystal engineers a powerful tool for designing molecules that are predisposed to form crystals with particular structural features and properties.

  10. Equilibrium and nonequilibrium molecular dynamics simulations of thermal conductance at solid-gas interfaces.

    PubMed

    Liang, Zhi; Evans, William; Keblinski, Pawel

    2013-02-01

    The thermal conductance at solid-gas interfaces with different interfacial bonding strengths is calculated through Green-Kubo equilibrium molecular dynamics (EMD) simulations. Due to the finite size of the simulation system, the long-time integral of the time correlation function of heat power across the solid-gas interface exhibits an exponential decay, which contains the information on interfacial thermal conductance. If an adsorbed gas layer is formed on the solid surface, it is found that the solid-gas interface needs to be defined at a plane outside the adsorbed layer so as to obtain the correct result from the Green-Kubo formula. The EMD simulation result agrees very well with that obtained from nonequilibrium molecular dynamics simulations. By calculating the average solid-gas interaction time as a function of solid-gas interaction strength, we find the incident gas atoms thermalize with the metal surface much more rapidly when the surface is covered by adsorbed gas molecules.

  11. Slip length of water on graphene: limitations of non-equilibrium molecular dynamics simulations.

    PubMed

    Kannam, Sridhar Kumar; Todd, B D; Hansen, J S; Daivis, Peter J

    2012-01-14

    Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is "not practical, if not impossible" based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.

  12. Water Flow inside Polamide Reverse Osmosis Membranes: A Non-Equilibrium Molecular Dynamics Study.

    PubMed

    Song, Yang; Xu, Fang; Wei, Mingjie; Wang, Yong

    2017-02-23

    Water flow inside polyamide (PA) reverse osmosis (RO) membranes is studied by steady state nonequilibrium molecular dynamics (NEMD) simulations in this work. The PA RO membrane is constructed with the all-atom model, and the density and average pore size obtained thereby are consistent with the latest experimental results. To obtain the time-independent water flux, a steady state NEMD method is used under various pressure drops. The water flux in our simulations, which is calculated under higher pressure drops, is in a linear relation with the pressure drops. Hence, the water flux in lower pressure drops can be reliably estimated, which could be compared with the experimental results. The molecular details of water flowing inside the membrane are considered. The radial distribution function and residence time of water around various groups of polyamide are introduced to analyze the water velocities around these groups, and we find that water molecules flow faster around benzene rings than around carboxyl or amino groups in the membrane, which implies that the main resistance of mass transport of water molecules comes from the carboxyl or amino groups inside the membranes. This finding is in good consistency with experimental results and suggests that less free carboxyl or amino groups should be generated inside RO membranes to enhance water permeance.

  13. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure.

    PubMed

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

    2012-07-28

    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.

  14. 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.

  15. Nanoindentation in crystal engineering: quantifying mechanical properties of molecular crystals.

    PubMed

    Varughese, Sunil; Kiran, M S R N; Ramamurty, Upadrasta; Desiraju, Gautam R

    2013-03-04

    Nanoindentation is a technique for measuring the elastic modulus and hardness of small amounts of materials. This method, which has been used extensively for characterizing metallic and inorganic solids, is now being applied to organic and metal-organic crystals, and has also become relevant to the subject of crystal engineering, which is concerned with the design of molecular solids with desired properties and functions. Through nanoindentation it is possible to correlate molecular-level properties such as crystal packing, interaction characteristics, and the inherent anisotropy with micro/macroscopic events such as desolvation, domain coexistence, layer migration, polymorphism, and solid-state reactivity. Recent developments and exciting opportunities in this area are highlighted in this Minireview.

  16. 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.

  17. Molecular-weight-dependent changes in morphology of solution-grown polyethylene single crystals.

    PubMed

    Zhang, Bin; Chen, Jingbo; Baier, Moritz C; Mecking, Stefan; Reiter, Renate; Mülhaupt, Rolf; Reiter, Günter

    2015-01-01

    Polymer single crystals consisting of folded chains are always in a nonequilibrium state, even if they are faceted with a well-defined envelope reflecting the parameters of the crystal unit cell. Heterogeneities like small variations in the degree of chain folding within such crystals are responsible for a rather broad range in melting temperature. Consequently, upon annealing at a given temperature, some parts may be above and some below their respective melting temperatures, inducing a lamellar thickening process, which may vary locally. To emphasize such variations, controlled annealing experiments are performed at comparatively low temperatures and for long times. For single crystals of low-molecular-weight polyethylene, the formation of the well-known "Swiss-cheese"-like morphology with randomly distributed holes of varying sizes within the annealed single crystal is observed. However, for high-molecular-weight polyethylene, a regular pattern appeared upon annealing, characterized by branches of equal width that are oriented perpendicular to the crystal edge. All branches end at the nucleation site. Interestingly, the resulting pattern depends sensitively on both crystallization and annealing conditions. These thermally induced regular patterns within a single crystal are attributed to a stable crystalline framework formed within polyethylene single crystals in the course of growth. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Computationally efficient dielectric calculations of molecular crystals

    SciTech Connect

    Schwarz, Kathleen A.; Sundararaman, Ravishankar; Arias, T. A.

    2015-06-07

    The microscopic dielectric response is a key quantity for electronic materials such as organic semiconductors. Calculations of this response for molecular crystals are currently either expensive or rely on extreme simplifications such as multipole expansions which lack microscopic detail. We present an alternate approach using a microscopic analogue of the Clausius-Mossotti equation, which constructs the dielectric response of a crystal from an eigenvalue decomposition of the dielectric response of individual molecules. This method can potentially be used to examine the effects of defects, disorder, and surfaces on the dielectric properties of molecular solids.

  19. 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.

  20. Habit of long-chain molecular crystals

    NASA Astrophysics Data System (ADS)

    Egorov, V. M.; Marikhin, V. A.

    2016-11-01

    The quantitative analysis of the temperature dependence of the heat capacity of molecular crystals with chains of different lengths was performed using the theory of diffuse first-order phase transitions. The same chemical structure of the "core" of molecular crystals of {CH3(CH2) n CH3} normal paraffins, {COH(CH2) n COH} diols, {CH3(CH2) n COH} normal alcohols, and {CH3(CH2) n COOH} saturated carboxylic and {COOH(CH2) n COOH} dicarboxylic acids enabled the comparative analysis of phase transition parameters.

  1. Nonequilibrium Molecular Dynamics Simulations of Steady-State Heat and Mass Transport in Condensation. II. Transfer Coefficients.

    PubMed

    Røsjorde, A.; Kjelstrup, S.; Bedeaux, D.; Hafskjold, B.

    2001-08-01

    We present coefficients for transfer of heat and mass across the liquid-vapor interface of a one-component fluid. The coefficients are defined for the Gibbs surface from nonequilibrium thermodynamics and determined by nonequilibrium molecular dynamics simulations. The main conductivity coefficients are found to become large near the critical point, consistent with the disappearance of the surface in this limit. The resistivities of transfer found by molecular dynamics simulations are compared to the values predicted by kinetic theory. The main resistivity to heat transfer is found to agree from the triple point to about halfway to the critical point. The resistivity to mass transfer was used to determine the condensation coefficient, which was found to be practically constant with a value of about 0.82. The resistivity coupling coefficient predicted by simulations also agrees with values predicted by kinetic theory from the triple point until about halfway to the critical point. Copyright 2001 Academic Press.

  2. 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.

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

    PubMed

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

    2013-03-28

    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.

  4. Thermal resistance of twist boundaries in silicon nanowires by nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bohrer, Jan K.; Schröer, Kevin; Brendel, Lothar; Wolf, Dietrich E.

    2017-04-01

    The thermal boundary resistance (Kapitza resistance) of (001) twist boundaries in silicon is investigated by nonequilibrium molecular dynamics simulations. In order to enable continuous adjustment of the mismatch angle, a cylindrical geometry with fixed atomic positions at the boundaries is devised. The influence of the boundary conditions on the Kapitza resistance is removed by means of a finite size analysis. Due to the diamond structure of silicon, twist boundaries with mismatch angles ϕ and 90 ° - ϕ are not equivalent, whereas those with ± ϕ or with 90 ° ± ϕ are. The Kapitza resistance increases with mismatch angle up to 45 ° , where it reaches a plateau around 1.56 ± 0.05 K m 2 / GW . Between 80 ° and the 90 ° Σ 1 grain boundary it drops by about 30%. Surprisingly, lattice coincidence at other angles ( Σ 5 , Σ 13 , Σ 27 , Σ 25 ) has no noticable effect on the Kapitza resistance. However, there is a clear correlation between the Kapitza resistance and the width of a non-crystalline layer at the twist boundaries.

  5. Calculations of thermal conductivity of complex (dusty) plasmas using homogenous nonequilibrium molecular simulations

    NASA Astrophysics Data System (ADS)

    Shahzad, Aamir; He, Mao-Gang

    2015-09-01

    The heat conductivity of three-dimensional Yukawa dusty plasma liquids (YDPLs) has been investigated by employing a homogenous nonequilibrium molecular dynamics (HNEMD) technique at a low normalized force field strength (F*). The obtained results for plasma heat conductivity with suitable normalizations are measured over a wide range of various plasma states of the Coulomb coupling (Γ) and screening length (κ) in a canonical ensemble (NVT). The calculations for lattice correlations (Ψ) show that our YDPLs system remains in a nonideal strongly coupled regime for a complete range of Γ. It has been shown that the presented Yukawa system obeys a simple analytical temperature demonstration of λ0 with a normalized Einstein frequency. The employed HNEMD algorithm is found to have a more efficient method than that of different earlier numerical methods and it gives more satisfactory results for lower to intermediate Γ with small system sizes at low F*. The obtained simulation results at nearly equilibrium F* (= 0.002) are in reasonable agreement with different earlier numerical results and with the present reference set of data showed deviations within less than ±15% for most of the present data points and generally underpredicted the λ0 by 2-22%, depending on (Γ, κ).

  6. 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.

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

    PubMed

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

    2015-06-28

    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.

  8. 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.

  9. On the domain size effect of thermal conductivities from equilibrium and nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Zuyuan; Ruan, Xiulin

    2017-01-01

    Equilibrium molecular dynamics (EMD) simulations with the Green-Kubo formula and nonequilibrium molecular dynamics (NEMD) simulations with the Fourier's Law are two widely used methods for calculating thermal conductivities of materials. It is well known that both methods suffer from domain size effects, especially for NEMD. But the underlying mechanisms and their comparison have not been much quantitatively studied before. In this paper, we investigate their domain size effects by using crystalline silicon at 1000 K, graphene at 300 K, and silicene at 300 K as model material systems. The thermal conductivity of silicon from EMD simulations increases normally with the increasing domain size and converges at a size of around 4 ×4 ×4 nm3 . The converging trend agrees well with the wavelength-accumulated thermal conductivity. The thermal conductivities of graphene and silicene from EMD simulations decrease abnormally with the increasing domain size and converge at a size of around 10 ×10 nm2 . We ascribe the anomalous size effect to the fact that as the domain size increases, the effect of more phonon scattering processes (particularly the flexural phonons) dominates over the effect of more phonon modes contributing to the thermal conductivity. The thermal conductivities of the three material systems from NEMD simulations all show normal domain size effects, although their dependences on the domain size differ. The converging trends agree with the mean free path accumulation of thermal conductivity. This study provides new insights that other than some exceptions, the domain size effects of EMD and NEMD are generally associated with wavelength and mean free path accumulations of thermal conductivity, respectively. Since phonon wavelength spans over a much narrower range than mean free path, EMD usually has less significant domain size effect than NEMD.

  10. Nonequilibrium ab initio molecular dynamics determination of Ti monovacancy migration rates in B 1 TiN

    NASA Astrophysics Data System (ADS)

    Gambino, D.; Sangiovanni, D. G.; Alling, B.; Abrikosov, I. A.

    2017-09-01

    We use the color diffusion (CD) algorithm in nonequilibrium (accelerated) ab initio molecular dynamics simulations to determine Ti monovacancy jump frequencies in NaCl-structure titanium nitride (TiN), at temperatures ranging from 2200 to 3000 K. Our results show that the CD method extended beyond the linear-fitting rate-versus-force regime [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016), 10.1103/PhysRevB.93.094305] can efficiently determine metal vacancy migration rates in TiN, despite the low mobilities of lattice defects in this type of ceramic compound. We propose a computational method based on gamma-distribution statistics, which provides unambiguous definition of nonequilibrium and equilibrium (extrapolated) vacancy jump rates with corresponding statistical uncertainties. The acceleration-factor achieved in our implementation of nonequilibrium molecular dynamics increases dramatically for decreasing temperatures from 500 for T close to the melting point Tm, up to 33 000 for T ≈0.7 Tm .

  11. 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.

  12. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  13. Preferential Enrichment of DL-Leucine Using Cocrystal Formation With Oxalic Acid Under Nonequilibrium Crystallization Conditions.

    PubMed

    Manoj, Kochunnoonny; Takahashi, Hiroki; Morita, Yoko; Gonnade, Rajesh G; Iwama, Sekai; Tsue, Hirohito; Tamura, Rui

    2015-07-01

    By utilizing the preferential enrichment (PE) technique, we achieved an improved enantiomeric resolution of DL-leucine (Leu) using a 1:1 cocrystal (DL-) of DL-Leu and oxalic acid. The crystal structure analysis of DL- indicated the occurrence of a novel type of phase transition and subsequent preferential redissolution of one enantiomer from the resulting crystals into solution.

  14. 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.

  15. 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.

  16. Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

    Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, Rg2 and φ, respectively. In addition, a specific orientational order Sx defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of Rg2, while their shape and order barely vary with an infinite value of φ and Sx. It is important to note that

  17. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ngo, Son Tung; Nguyen, Minh Tung; Nguyen, Minh Tho

    2017-05-01

    The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. The calculated free energy difference terms help clarifying the nature of the binding. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The paradigm used is able to rank two inhibitors having the maximum difference of ∼1.5 kcal/mol in absolute binding free energies.

  18. Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics.

    PubMed

    Palla, Pier Luca; Pierleoni, Carlo; Ciccotti, Giovanni

    2008-08-01

    Nonequilibrium molecular dynamics (NEMD) calculations of the bulk viscosity of the triple point Lennard-Jones fluid are performed with the aim of investigating the origin of the observed disagreement between Green-Kubo estimates and previous NEMD data. We show that a careful application of the Doll's perturbation field, the dynamical NEMD method, the instantaneous form of the perturbation and the "subtraction technique" provides a NEMD estimate of the bulk viscosity at zero field in full agreement with the value obtained by the Green-Kubo formula. As previously reported for the shear viscosity, we find that the bulk viscosity exhibits a large linear regime with the field intensity.

  19. A study of some non-equilibrium driven models and their contribution to the understanding of molecular motors

    NASA Astrophysics Data System (ADS)

    Mazilu, Irina; Gonzalez, Joshua

    2008-03-01

    From the point of view of a physicist, a bio-molecular motor represents an interesting non-equilibrium system and it is directly amenable to an analysis using standard methods of non-equilibrium statistical physics. We conduct a rigorous Monte Carlo study of three different driven lattice gas models that retain the basic behavior of three types of cytoskeletal molecular motors. Our models incorporate novel features such as realistic dynamics rules and complex motor-motor interactions. We are interested to have a deeper understanding of how various parameters influence the macroscopic behavior of these systems, what is the density profile and if the system undergoes a phase transition. On the analytical front, we computed the steady-state probability distributions exactly for the one of the models using the matrix method that was established in 1993 by B. Derrida et al. We also explored the possibilities offered by the ``Bethe ansatz'' method by mapping some well studied spin models into asymmetric simple exclusion models (already analyzed using computer simulations), and to use the results obtained for the spin models in finding an exact solution for our problem. We have exhaustive computational studies of the kinesin and dynein molecular motor models that prove to be very useful in checking our analytical work.

  20. Diffusion behavior in a liquid-liquid interfacial crystallization by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kitayama, Akira; Yamanaka, Shinya; Kadota, Kazunori; Shimosaka, Atsuko; Shirakawa, Yoshiyuki; Hidaka, Jusuke

    2009-11-01

    Interfacial crystallization, such as surface crystallization in solution (solid-liquid) and liquid-liquid crystallization, gives us an asymmetric reaction field and is a technique for morphology control of crystals. In the liquid-liquid crystallization, the concentration distribution of solute ions and solvent molecules at the liquid-liquid interface directly relates to nucleation, crystal growth, and crystal morphology. Nonequilibrium molecular dynamics (MD) simulations have been performed at interfaces in NaCl solution/1-butanol and KCl solution/1-butanol system in order to clarify diffusion behavior of solute ions and solvent molecules. As simulation results, the hydrated solute ions were dehydrated with the diffusion of water from solution phase into 1-butanol phase. The different dehydration behaviors between NaCl and KCl solution can be also obtained from MD simulation results. Aggregated ions or clusters were formed by the dehydration near the solution/1-butanol interface. By comparison on the normalized number of total solute ions, the size and number of generated cluster in KCl solution/1-butanol interface are larger than those in the NaCl system. This originates in the difference hydration structures in the each solute ion.

  1. Bacteria as self-propelled liquid crystals: non-equilibrium clustering, polar order, collective motion, and aggregation

    NASA Astrophysics Data System (ADS)

    Peruani, Fernando

    2014-03-01

    Bacteria exhibit fascinating collective phenomena such as collective motion and aggregation. It is usually believed that such kind of collective effects require cells to coordinate their motion via chemotactic signaling. Despite of this common belief, I will show that in experiments with myxobacteria such collective effects emerge in absence of biochemical regulation, and even hydrodynamic interactions, and result from simple physical interaction among the motile bacteria. As proof of principle, I will show that collective phenomena such as collective motion and aggregation naturally emerge in models of simple self-propelled rods that interact by volume exclusion. Combining experiments and theoretical models, we will explain that the interplay of bacterial self-propulsion and steric interactions among the elongated bacteria leads to an effective velocity alignment mechanism (VAM). Such VAM allows cells to display a non-equilibrium clustering transition that marks the onset of collective motion. I will argue that even though the symmetry of the resulting VAM is clearly nematic, it induces, counter intuitively, polar order. Finally, I will show that by increasing the cell density, or alternatively the aspect ratio of bacteria, collective motion patterns become unstable, and cells form aggregates. In short, our results indicate that for bacteria moving on surfaces, the cell shape plays a crucial role in the bacterial self-organization process. By thinking of bacteria as self-propelled liquid crystals, we can explain complex behaviors such as collective motion and aggregation.

  2. Supersaturation and crystallization: non-equilibrium dynamics of amorphous solid dispersions for oral drug delivery.

    PubMed

    Kawakami, Kohsaku

    2017-06-01

    Amorphous solid dispersions (ASDs) are one of the key formulation technologies that aid the development of poorly soluble candidates. However, their dynamic behaviors, including dissolution and crystallization processes, are still full of mystery. Further understanding of these processes should enhance their wider use. Areas covered: The first part of this review describes the current understanding of the dissolution of ASDs, where phase separation behavior is frequently involved and attempts to develop appropriate dissolution tests to achieve an in vitro-in vivo correlation are examined. The second part of this review discusses crystallization of the drug molecule with the eventual aim of establishing an accelerated testing protocol for predicting its physical stability. Expert opinion: The phase separation behavior from the supersaturated state during the dissolution test must be understood, and its relevance to the oral absorption behavior needs to be clarified. Research efforts should focus on the differences between the phase behavior in in vitro and in vivo situations. Initiation time of the crystallization was shown to be predicted only from storage and glass transition temperatures. This finding should encourage the establishment of testing protocol of the physical stability of ASDs.

  3. Non-equilibrium molecular simulations of simple fluid transport at fluid-solid interfaces and fluidic behaviors at nanoscale

    NASA Astrophysics Data System (ADS)

    Yong, Xin

    Nano fluidics has shown promising potential for applications that could significantly impact our daily life, such as energy harvest, lab on a chip, desalination, etc. Current techniques to realize nano fluidic ideas are still very limited due to manufacturing technology. Although sub-micron fabrication techniques are undergoing rapid development recently, scientists and engineers are still not able to access actual nanometric systems. This reason prompts the development of computational tools to reveal physical principles underlying nano fluidic phenomena. Among various numerical approaches ranging from macroscopic to microscopic, molecular dynamics stands out because of its ability to faithfully model both equilibrium and non-equilibrium nanosystems by involving an appropriate amount of molecular details. The results from molecular dynamics simulations could elucidate essential physics and benefit designs of practical nano fluidic systems. This thesis attempts to provide the theoretical foundation for modeling nano fluidic systems, by investigating nanoscale fluid behaviors and nanoscale fluid-solid interfacial physics and transport for simple fluids via molecular dynamics simulations. Boundary-driven-shear, homogeneous-shear and reverse non-equilibrium molecular dynamics methods are implemented to generate non-equilibrium systems. The fundamental fluid behaviors such as velocity profile, temperature distribution and rheological material functions under steady planar shear are explored comprehensively by each method corresponding to different perspectives. The influences of nanoscale confinement are analyzed from the comparison among these methods. The advantages and disadvantages of each method are clarified, which provide guidance to conduct appropriate molecular dynamics simulations for nano fluidics. Further studies on the intrinsic slip of smooth solid surfaces is realized by the boundary-driven-shear method. Inspired by previous hypothesis of momentum

  4. Modeling magma flow in volcanic conduit with non-equilibrium crystallization

    NASA Astrophysics Data System (ADS)

    Yulia, Tsvetkova

    2010-05-01

    Modeling magma flow in volcanic conduit including with non -equilibrium crystallization There is a set of models of magma flow in volcanic conduits which predicts oscillations in magma discharge during extrusion of lava domes. These models neglect heating of surrounding rocks and use 1D approximation of the flow in the conduit. Here magma flow is investigated with an account of heat exchange between surrounding rocks and magma and different dependences viscosity on temperature and crystal concentration. Stick-slip conditions were applied at the wall. The flow is assumed to be quasi-static and quasi 1D. Only vertical component of velocity vector is present, thus, we do not consider horizontal momentum balance. At the top of the conduit the pressure is assumed to be fixed, chamber pressure changes according with magma influx and outflux. First set of simulation was made for the viscosity that depends on cross-section average crystal concentration and parabolic velocity profile. In earlier models that account for crystal growth kinetics the temperature was allowed to change only due to the release of latent heat of crystallization. Heat transfer leads to cooling of the outer parts of the conduit leading to high crystal contents and high magma viscosities. Changes in viscosity result in changes in discharge rate. For the non-isothermal case there is no motion during most part of the cycle and a portion of magma solidifies at the top of the conduit forming a plug. During repose period chamber pressure is growing due to influx of fresh magma, and magma discharge rate starts to increase. Influx of hot magma into the conduit leads to decrease in friction resulting in a jump in discharge rate that lead to depressurization of magma chamber. Discharge rate decreases and magma solidifies again. For isothermal model with the same parameters discharge rate monotonically tends to the value of Qin. Simulation reveal that crystal content changes significantly across the conduit

  5. Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Derreumaux, Philippe; Stock, Gerhard

    2009-07-09

    A nonequilibrium molecular dynamics (MD) study of the temperature-induced energy flow in a RNA-ligand complex is presented, which employs extensive all-atom explicit solvent MD simulations of the aptamer domain of the guanine-sensing riboswitch (GRA). Since the few existing MD investigations of biomolecular energy flow have used quite different computational approaches, the applicability and performance of the various methods are compared first. In particular, a nonequilibrium correlation function C(ij)(tau) is introduced that describes the cumulative response of residue j at delay time tau to the energy source at residue i. Employing this analysis, the anisotropic energy flow and long-range correlations in GRA are studied, which can be monitored over distances up to approximately 4 nm. To test whether these long-range correlations are relevant for molecular function, the unbinding-induced conformational changes of GRA are calculated using the linear-response theory, assuming that the unbinding of the guanine ligand represents the first step responsible for the function of GRA. Interestingly, it is found that the same residues that are of functional importance are also prominently involved in the energy transfer. In particular, significant correlations between the guanine ligand and the distant "kissing" loops of GRA are found. This finding is in line with recent experiments which indicate that these long-range interactions may be important for the induced-fit binding of the ligand.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Comparison of the Green-Kubo and homogeneous non-equilibrium molecular dynamics methods for calculating thermal conductivity

    NASA Astrophysics Data System (ADS)

    Dongre, B.; Wang, T.; Madsen, G. K. H.

    2017-07-01

    Different molecular dynamics methods like the direct method, the Green-Kubo (GK) method and homogeneous non-equilibrium molecular dynamics (HNEMD) method have been widely used to calculate lattice thermal conductivity ({κ }{\\ell }). While the first two methods have been used and compared quite extensively, there is a lack of comparison of these methods with the HNEMD method. Focusing on the underlying computational parameters, we present a detailed comparison of the GK and HNEMD methods for both bulk and vacancy Si using the Stillinger-Weber potential. For the bulk calculations, we find both methods to perform well and yield {κ }{\\ell } within acceptable uncertainties. In case of the vacancy calculations, HNEMD method has a slight advantage over the GK method as it becomes computationally cheaper for lower {κ }{\\ell } values. This study could promote the application of HNEMD method in {κ }{\\ell } calculations involving other lattice defects like nanovoids, dislocations, interfaces.

  11. Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. Final report, September 15, 1987--March 14, 1997

    SciTech Connect

    Murad, S.

    1997-05-01

    Computer Simulation Studies were carried out using the method of equilibrium and nonequilibrium molecular dynamics (NEMD) to examine a wide range of transport processes in both fluids and fluid mixtures. This included testing a wide range of mixing rules for thermal conductivity and viscosity. In addition a method was developed to calculate the internal rotational contributions to thermal conductivity and the accuracy of current methods for predicting these contributions were examined. These comparisons were then used to suggest possible ways of improving these theories. The method of NEMD was also used to examine the critical enhancements of thermal conductivity. Finally, molecular simulations were carried out to study the various transport coefficients of fluids confined by membranes, as well as important transport processes such as osmosis, and reverse osmosis.

  12. Vibrational mean free paths and thermal conductivity of amorphous silicon from non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sääskilahti, K.; Oksanen, J.; Tulkki, J.; McGaughey, A. J. H.; Volz, S.

    2016-12-01

    The frequency-dependent mean free paths (MFPs) of vibrational heat carriers in amorphous silicon are predicted from the length dependence of the spectrally decomposed heat current (SDHC) obtained from non-equilibrium molecular dynamics simulations. The results suggest a (frequency)- 2 scaling of the room-temperature MFPs below 5 THz. The MFPs exhibit a local maximum at a frequency of 8 THz and fall below 1 nm at frequencies greater than 10 THz, indicating localized vibrations. The MFPs extracted from sub-10 nm system-size simulations are used to predict the length-dependence of thermal conductivity up to system sizes of 100 nm and good agreement is found with independent molecular dynamics simulations. Weighting the SDHC by the frequency-dependent quantum occupation function provides a simple and convenient method to account for quantum statistics and provides reasonable agreement with the experimentally-measured trend and magnitude.

  13. Elastic moduli and instability in molecular crystals

    NASA Astrophysics Data System (ADS)

    Shpakov, V. P.; Tse, J. S.; Belosludov, V. R.; Belosludov, R. V.

    1997-07-01

    The phenomenon of instability in pressurized molecular crystals is studied using the lattice-dynamics approach. General expressions for the elastic moduli are obtained taking into account both short-range and long-range (electrostatic) interactions within the framework of the quasi-harmonic approximation. The behaviour of a system under changing pressure and temperature conditions and the Born stability criteria are investigated. Two types of instabilities, dynamical and thermodynamical, associated with the elastic moduli are presented. The dynamical instability occurs when the instability of acoustic modes of the phonon Hamiltonian occurs in the q = 0 region. The nature of thermodynamical stability implies that the equilibrium state of the crystal becomes thermodynamically unstable with respect to a small homogeneous deformation of the crystal lattice when the Born stability criteria are violated for isothermal or adiabatic moduli. These types of instabilities are illustrated in a series of calculations for ice Ic using the SPC potential for water's interactions. The results show that one of the stability conditions for the isothermal (adiabatic) moduli 0953-8984/9/27/015/img7 is violated at 0953-8984/9/27/015/img8 kbar and, as a consequence, thermodynamical instability occurs. In contrast, the dynamical instability of the phonon spectrum occurs at a significantly higher pressure, about 20 kbar.

  14. 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.

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

    PubMed

    Zhang, Zhedong; Wang, Jin; 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

  16. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: A systematic study of several common force fields

    NASA Astrophysics Data System (ADS)

    Trinh, Thuat T.; Vlugt, Thijs J. H.; Kjelstrup, Signe

    2014-10-01

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  17. Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Solomentsev, Gleb Y.; O'Brien, Paul

    2009-07-01

    Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of both external static electric and low-frequency microwave (2.45 GHz) fields of varying intensity. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure relative to the zero-field state, depending on the field conditions, mutation, and orientation with respect to the applied field. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the dipolar alignment of water molecules in both the solvation layer and the bulk was also found to be influential. Substantial differences in behavior were found for proteins with and without overall net charges, particularly with respect to translational motion. Localized motion and perturbation of hydrogen bonds were also found to be evident for charged residues.

  18. Determination of the distance-dependent viscosity of mixtures in parallel slabs using non-equilibrium molecular dynamics.

    PubMed

    Pařez, Stanislav; Předota, Milan

    2012-03-14

    We generalize a technique for determination of the shear viscosity of mixtures in planar slabs using non-equilibrium computer simulations by applying an external force parallel to the surface generating Poiseuille flow. The distance-dependent viscosity of the mixture, given as a function of the distance from the surface, is determined by analysis of the resulting velocity profiles of all species. We present results for a highly non-ideal water + methanol mixture in the whole concentration range between rutile (TiO(2)) walls. The bulk results are compared to the existing equilibrium molecular dynamics and experimental data while the inhomogeneous viscosity profiles at the interface are interpreted using the structural data and information on hydrogen bonding.

  19. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: a systematic study of several common force fields.

    PubMed

    Trinh, Thuat T; Vlugt, Thijs J H; Kjelstrup, Signe

    2014-10-07

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  20. Thermodynamics, molecular mobility and crystallization kinetics of amorphous griseofulvin.

    PubMed

    Zhou, Deliang; Zhang, Geoff G Z; Law, Devalina; Grant, David J W; Schmitt, Eric A

    2008-01-01

    Griseofulvin is a small rigid molecule that shows relatively high molecular mobility and small configurational entropy in the amorphous phase and tends to readily crystallize from both rubbery and glassy states. This work examines the crystallization kinetics and mechanism of amorphous griseofulvin and the quantitative correlation between the rate of crystallization and molecular mobility above and below Tg. Amorphous griseofulvin was prepared by rapidly quenching the melt in liquid N2. The thermodynamics and dynamics of amorphous phase were then characterized using a combination of thermal analysis techniques. After characterization of the amorphous phase, crystallization kinetics above Tg were monitored by isothermal differential scanning calorimetry (DSC). Transformation curves for crystallization fit a second-order John-Mehl-Avrami (JMA) model. Crystallization kinetics below Tg were monitored by powder X-ray diffraction and fit to the second-order JMA model. Activation energies for crystallization were markedly different above and below Tg suggesting a change in mechanism. In both cases molecular mobility appeared to be partially involved in the rate-limiting step for crystallization, but the extent of correlation between the rate of crystallization and molecular mobility was different above and below Tg. A lower extent of correlation below Tg was observed which does not appear to be explained by the molecular mobility alone and the diminishing activation energy for crystallization suggests a change in the mechanism of crystallization.

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

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Garate, José-A.

    2016-08-01

    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.

  2. 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.

  3. 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.

  4. Control of vibrational distribution functions in nonequilibrium molecular plasmas and high-speed flows

    NASA Astrophysics Data System (ADS)

    Frederickson, Kraig; Hung, Yi-Chen; Lempert, Walter R.; Adamovich, Igor V.

    2017-01-01

    The control of the vibrational distribution of nitrogen by energy transfer to CO2 is studied in two closely related experiments. In the first experiment, the time-resolved N2(v  =  0-3) vibrational level populations and temperature in the afterglow of a diffuse filament nanosecond pulse discharge are measured using broadband coherent anti-Stokes Raman spectroscopy. The rotational-translational temperature in the afterglow is inferred from the partially rotationally resolved structure of the N2(v  =  0) band. The measurements are performed in nitrogen, dry air, and their mixtures with CO2. N2 vibrational excitation in the discharge occurs by electron impact, with subsequent vibration-vibration (V-V) energy transfer within the N2 vibrational manifold, vibration-translation (V-T) relaxation, and near-resonance V-V‧ energy transfer from the N2 to CO2 asymmetric stretch vibrational mode. The results show that rapid V-V‧ energy transfer to CO2, followed by collisional intramolecular energy redistribution to the symmetric stretch and bending modes of CO2 and their V-T relaxation, accelerate the net rate of energy thermalization and temperature increase in the afterglow. In the second experiment, injection of CO2 into a supersonic flow of vibrationally excited nitrogen demonstrates the effect of accelerated vibrational relaxation on a supersonic shear layer. The nitrogen flow is vibrationally excited in a repetitive nanosecond pulse/DC sustainer electric discharge in the plenum of a nonequilibrium flow supersonic wind tunnel. A transient pressure increase as well as an upward displacement of the shear layer between the supersonic N2 flow and the subsonic CO2 injection flow are detected when the source of N2 vibrational excitation is turned on. CO2 injection leads to the reduction of the N2 vibrational temperature in the shear layer, demonstrating that its displacement is caused by accelerated N2 vibrational relaxation by CO2, which produces a static

  5. Molecular-dynamics approach for studying the nonequilibrium behavior of x-ray-heated solid-density matter

    NASA Astrophysics Data System (ADS)

    Abdullah, Malik Muhammad; Anurag, Jurek, Zoltan; Son, Sang-Kil; Santra, Robin

    2017-08-01

    When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on subpicosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate nonequilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and three-dimensional spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above-mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven nonequilibrium dynamics in solids. To illustrate the potential of XMDYN for treating complex systems, we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.

  6. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  7. 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.

  8. Flow alignment phenomena in liquid crystals studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2009-10-01

    The flow alignment of a nematic liquid crystal has been studied as a function of temperature, beginning at high temperature in the nematic phase and down to the nematic-smectic A phase transition. The alignment angle is obtained by estimating the twist viscosities by nonequilibrium molecular dynamics (NEMD) methods. These estimates are cross-checked by evaluating the corresponding equilibrium fluctuation relations. As a further comparison, shear flow simulations are carried out by application of the SLLOD equations of motion (so named because of their close relationship to the Doll's equation of motion, which can be derived from the Doll's tensor Hamiltonian), whereby the alignment angle is obtained directly. All these methods give consistent results for the alignment angle. At low temperatures near the nematic-smectic A transition the system becomes flow unstable. In this region the alignment angle has been calculated as a function of time.

  9. A steady-state non-equilibrium molecular dynamics approach for the study of evaporation processes

    NASA Astrophysics Data System (ADS)

    Zhang, Jianguo; Müller-Plathe, Florian; Yahia-Ouahmed, Méziane; Leroy, Frédéric

    2013-10-01

    Two non-equilibrium methods (called bubble method and splitting method, respectively) have been developed and tested to study the steady state evaporation of a droplet surrounded by its vapor, where the evaporation continuously occurs at the vapor-liquid interface while the droplet size remains constant. In the bubble method, gas molecules are continuously reinserted into a free volume (represented by a bubble) located at the centre of mass of the droplet to keep the droplet size constant. In the splitting method, a molecule close to the centre of mass of the droplet is split into two: In this way, the droplet size is also maintained during the evaporation. By additional local thermostats confined to the area of insertion, the effect of frequent insertions on properties such as density and temperature can be limited to the immediate insertion area. Perturbations are not observed in other parts of the droplet. In the end, both the bubble method and the splitting method achieve steady-state droplet evaporation. Although these methods have been developed using an isolated droplet, we anticipate that they will find a wide range of applications in the study of the evaporation of isolated films and droplets or thin films on heated substrates or under confinement. They can in principle also be used to study the steady-state of other physical processes, such as the diffusion or permeation of gas molecules or ions in a pressure gradient or a concentration gradient.

  10. 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

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

    PubMed

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

    2015-03-10

    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.

  12. Non-equilibrium quantum transport of spin-polarized electrons and back action on molecular magnet tunnel-junction

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Yao, Hui; Nie, Yi-Hang; Liang, J.-Q.

    2016-11-01

    We investigate the non-equilibrium quantum transport through a single-molecule magnet embedded in a tunnel junction with ferromagnetic electrodes, which generate spin-polarized electrons. The lead magnetization direction is non-collinear with the uniaxial anisotropy easy-axis of molecule-magnet. Based on the Pauli rate-equation approach we demonstrate the magnetization reversion of molecule-magnet induced by the back action of spin-polarized current in the sequential tunnel regime. The asymptotic magnetization of molecular magnet and spin-polarization of transport current are obtained as functions of time by means of time-dependent solution of the rate equation. It is found that the antiparallel configuration of the ferromagnetic electrodes and molecular anisotropy easy-axis is an effective structure to reverse both the magnetization of molecule-magnet and spin-polarization of the transport current. Particularly the non-collinear angle dependence provides useful knowledge for the quantum manipulation of molecule-magnet and spin polarized electron-transport.

  13. 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.

  14. Control of liquid crystal molecular orientation using ultrasound vibration

    SciTech Connect

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

    2016-03-07

    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.

  15. Manifestations of two-dimensional electron gas in molecular crystals

    NASA Astrophysics Data System (ADS)

    Kuklja, Maija M.; Sharia, Onise; Tsyshevsky, Roman

    2017-03-01

    The existence of two-dimensional electron gas in molecular materials has not been reported or discussed. Intriguing properties of two-dimensional electron gas observed on interfaces of polar and nonpolar oxides spurred oxide electronics and advanced nanotechnology. Here we discover how an electrostatic instability occurs on polar surfaces of molecular crystals and explore its manifestations, chemical degradation of surfaces, charge separation, electrical conductivity, optical band-gap closure and surface metallization. A thin layer of polar surface of a dielectric molecular crystal becomes metallic due to interactions of polar molecules. Our findings are illustrated with two polymorphs of cyclotetramethylene-tetranitramine crystals, the polar δ-phase and nonpolar β-phase. Our theory offers an explanation to a relative stability of the β-phase versus the explosive reactivity of δ-phase and to the experimentally observed difference in conductivity of these crystals. We predict that the electrostatic instability takes place on all polar molecular materials.

  16. Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Futera, Zdenek; English, Niall J.

    2017-07-01

    The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

  17. 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.

  18. 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.

  19. Free energy of adsorption for a peptide at a liquid/solid interface via nonequilibrium molecular dynamics.

    PubMed

    Mijajlovic, Milan; Penna, Matthew J; Biggs, Mark J

    2013-03-05

    Protein adsorption is of wide interest including in many technological applications such as tissue engineering, nanotechnology, biosensors, drug delivery, and vaccine production among others. Understanding the fundamentals of such technologies and their design would be greatly aided by an ability to efficiently predict the conformation of an adsorbed protein and its free energy of adsorption. In the study reported here, we show that this is possible when data obtained from nonequilibrium thermodynamic integration (NETI) combined with steered molecular dynamics (SMD) is subject to bootstrapping. For the met-enkephalin pentapeptide at a water-graphite interface, we were able to obtain accurate predictions for the location of the adsorbed peptide and its free energy of adsorption from around 50 and 80 SMD simulations, respectively. It was also shown that adsorption in this system is both energetically and entropically driven. The free energy of adsorption was also decomposed into that associated with formation of the cavity in the water near the graphite surface sufficient to accommodate the adsorbed peptide and that associated with insertion of the peptide into this cavity. This decomposition reveals that the former is modestly energetically and entropically unfavorable, whereas the latter is the opposite in both regards to a much greater extent.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  1. 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.

  2. Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

    PubMed

    Neamţu, A; Suciu, Daniela

    2004-01-01

    Because of the great importance of physiological and pathophysiological processes in which ion channels are involved and because their operation is described by physicochemical laws, there have been many attempts to develop physical models able to describe the membrane permeability and also the structural and functional properties of the channel protein structures. In this study (in two parts) we present a series of simulations on a K+ channel model (KcsA) using Nonequilibrium Molecular Dynamics simulations (NEMD), in order to follow structure stability, permeation energetics and the possibility of obtaining quantitative information about the permeation process using the Linear Response Theory (LRT). On K+ ions were applied external forces to determine them to pass through the channel in a relatively small amount of time, accessible computationally. We ascertained a high resistance of the protein to deformation even in conditions when great forces were applied on ions (the system was far from equilibrium). The estimation of energy profiles in the course of ions passage through the channel demonstrates that these proteins create a conductivity pathway with no energetic barriers for ions movement across the channel (which could be present due to ions dehydration). The dynamic model used demonstrates (as proposed before in the literature after the examination of the static KcsA structure obtained by X-Ray crystallography) that this is due to the interaction of ions with the negatively charged carbonyl oxygens of the main polypeptide chain in the selectivity filter region.

  3. Evaluation of reptation-based modeling of entangled polymeric fluids including chain rotation via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Nafar Sefiddashti, Mohammad Hadi; Edwards, Brian J.; Khomami, Bamin

    2017-08-01

    Recent simulation results of a moderately entangled linear polyethylene C700H1402 liquid have confirmed prior simulation and experimental evidence that individual polymer molecules experience periodic rotation and retraction cycles under steady shear flow at high Weissenberg number. With this insight, theoreticians have begun to grapple with this additional complicating physical phenomenon that needs to be incorporated into rheological models to help explain the data under conditions of high shear. In this paper we examine these recent efforts by using nonequilibrium molecular dynamics simulations to provide insight into the requisite theoretical variables and their assigned evolution equations to evaluate the capability of these tube-based models to predict accurately the simulated data sets. This analysis reveals that the primary variables used in tube models to impart a conceptual basis to the theory, namely, the tube orientation tensor and the tube stretch, remain fundamental system properties even far away from equilibrium; however, the theory describing their evolution under flow is not well suited to quantitative prediction. Furthermore, it is demonstrated that key system properties, such as the entanglement number and disengagement time, should play a more significant role in model development since these quantities can change dramatically under flow, particularly at high Weissenberg number where the chain rotation and retraction cycles dominate the system physics.

  4. Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

    SciTech Connect

    Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi

    2016-07-15

    We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chain structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.

  5. Between Crystal and Glass: Thermal Transport in C60 Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Lu, Simon; Kumar, Sushant; McGaughey, Alan

    Molecular crystals of the fullerene C60 and its derivatives [e.g., phenyl-C61-butyric acid methyl ester (PCBM)] are candidate materials for use in photovoltaics and thermoelectrics. In thermoelectrics, their usefulness is due in part to their exceptionally low thermal conductivities (0.4 W/m-K for C60 and 0.05 W/m-K for PCBM) at room temperature. Little is known regarding the microscopic physics underlying these low thermal conductivities. An important question is whether thermal transport in the C60 molecular crystal is (i) crystal-like, where energy is transported as collective vibrations of the centers of mass of the molecules, or (ii) amorphous-like, where energy diffuses from molecule to molecule. We use molecular dynamics (MD) simulations and the Green-Kubo method to probe this question by predicting the relative contributions of crystal-like and amorphous-like transport to the thermal conductivity of the C60 molecular crystal. To isolate crystal-like transport, we perform simulations on C60 crystals where molecular rotations and intra-molecular vibrations are prohibited. To isolate amorphous-like transport, we fix the centers of mass of the molecules. We compare the MD results to predictions from a fully diffusive network resistance model. This work is supported by the National Science Foundation (Grant DMR-1507325).

  6. 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.

  7. Variable timestep algorithm for molecular dynamics simulation of non-equilibrium processes

    NASA Astrophysics Data System (ADS)

    Marks, Nigel A.; Robinson, Marc

    2015-06-01

    A simple, yet robust variable timestep algorithm is developed for use in molecular dynamics simulations of energetic processes. Single-particle Kepler orbits are studied to study the relationship between trajectory properties and the critical timestep for constant integration error. Over a wide variety of conditions the magnitude of the maximum force is found to correlate linearly with the inverse critical timestep. Other quantities used in the literature such as the time derivative of the force and the product of the velocity and force also show reasonable correlations, but not to the same extent. Application of the corresponding metric | |Fmax | | Δt in molecular dynamics simulation of radiation damage in graphite shows that the scheme is both straightforward to implement and effective. In tests on a 1 keV cascade the timestep varies by over two orders of magnitude with minimal loss of energy conservation.

  8. 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.

  9. 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.

  10. Nonequilibrium molecular dynamics simulations of nanoconfined fluids at solid-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Morciano, M.; Fasano, M.; Nold, A.; Braga, C.; Yatsyshin, P.; Sibley, D. N.; Goddard, B. D.; Chiavazzo, E.; Asinari, P.; Kalliadasis, S.

    2017-06-01

    We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory.

  11. Nonequilibrium molecular dynamics simulations of nanoconfined fluids at solid-liquid interfaces.

    PubMed

    Morciano, M; Fasano, M; Nold, A; Braga, C; Yatsyshin, P; Sibley, D N; Goddard, B D; Chiavazzo, E; Asinari, P; Kalliadasis, S

    2017-06-28

    We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory.

  12. Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks

    NASA Astrophysics Data System (ADS)

    Warrier, M.; Rawat, S.; Chaturvedi, S.

    2011-07-01

    Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.

  13. Investigation of PEG crystallization in frozen PEG-sucrose-water solutions. I. Characterization of the nonequilibrium behavior during freeze-thawing.

    PubMed

    Bhatnagar, Bakul S; Martin, Susan M; Teagarden, Dirk L; Shalaev, Evgenyi Y; Suryanarayanan, Raj

    2010-06-01

    Our objective was to characterize the nonequilibrium thermal behavior of frozen aqueous solutions containing PEG and sucrose. Aqueous solutions of (i) sucrose (10%, w/v) with different concentrations of PEG (1-20%, w/v), and (ii) PEG (10%, w/v) with different concentrations of sucrose (2-20%, w/v), were cooled to -70 degrees C at 5 degrees C/min and heated to 25 degrees C at 2 degrees C/min in a differential scanning calorimeter. Annealing was performed at temperatures ranging from -50 to -20 degrees C for 2 or 6 h. Similar experiments were also performed in the low-temperature stage of a powder X-ray diffractometer. A limited number of additional DSC experiments were performed wherein the samples were cooled to -100 degrees C. In unannealed systems with a fixed sucrose concentration (10%, w/v), the T'g decreased from -35 to -48 degrees C when PEG concentration was increased from 1% to 20% (w/v). On annealing at -25 degrees C, PEG crystallized. This was evident from the increase in T'g and the appearance of a secondary melting endotherm in the DSC. Low-temperature XRD provided direct evidence of PEG crystallization. Annealing at temperatures crystallization and a devitrification event was observed above the T'g. In unannealed systems with a fixed PEG concentration (10%, w/v), the T'g increased from -50 to -40 degrees C when sucrose concentration was increased from 5% to 50%, w/v. As the annealing time increased (at -25 degrees C), the T'g approached that of a sucrose-water system, reflecting progressive PEG crystallization. A second glass transition at approximately -65 degrees C was evident in unannealed systems [10%, w/v sucrose and 10 (or 20%), w/v PEG] cooled to -100 degrees C. Investigation of the nonequilibrium behavior of frozen PEG-sucrose-water ternary system revealed phase separation in the freeze-concentrate. Annealing facilitated PEG crystallization. (c) 2010 Wiley-Liss, Inc. and the American Pharmacists Association

  14. 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.

  15. 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

  16. Charge dynamics in molecular junctions: Nonequilibrium Green's function approach made fast

    NASA Astrophysics Data System (ADS)

    Latini, S.; Perfetto, E.; Uimonen, A.-M.; van Leeuwen, R.; Stefanucci, G.

    2014-02-01

    Real-time Green's function simulations of molecular junctions (open quantum systems) are typically performed by solving the Kadanoff-Baym equations (KBE). The KBE, however, impose a serious limitation on the maximum propagation time due to the large memory storage needed. In this work we propose a simplified Green's function approach based on the generalized Kadanoff-Baym ansatz (GKBA) to overcome the KBE limitation on time, significantly speed up the calculations, and yet stay close to the KBE results. This is achieved through a twofold advance: First, we show how to make the GKBA work in open systems and then construct a suitable quasiparticle propagator that includes correlation effects in a diagrammatic fashion. We also provide evidence that our GKBA scheme, although already in good agreement with the KBE approach, can be further improved without increasing the computational cost.

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

    PubMed Central

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

    2016-01-01

    Molecular recognition is often driven by transient processes beyond the reach of detection. Single-molecule fluorescence microscopy methods are uniquely suited for detecting such non-accumulating intermediates, yet achieving the time resolution and statistics to realize this potential has proven challenging. Here, we present a single-molecule fluorescence resonance energy transfer (smFRET) imaging and analysis platform leveraging advances in scientific complementary metal-oxide semiconductor (sCMOS) detectors that enable the imaging of more than 10,000 individual molecules simultaneously at millisecond rates. The utility of this advance is demonstrated through quantitative measurements of previously obscured processes relevant to the fidelity mechanism in protein synthesis. PMID:26878382

  18. The Crystal and Molecular Structure of Dianhydrogossypol

    USDA-ARS?s Scientific Manuscript database

    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...

  19. Molecular Photonics of Supra Nonlinear Liquid Crystals

    DTIC Science & Technology

    2003-05-11

    multifunctional optical devices have also been developed. Specifically, (i) the large optical nonlinearities of nematic liquid crystals in the optical ... communication wavelength regime (1 .55 microns) as well as the visible region have been quantitatively established. (ii) All-optical self-action processes such

  20. Nonequilibrium molecular dynamics simulation study on the orientation transition in the amphiphilic lamellar phase under shear flow.

    PubMed

    Guo, Hongxia

    2006-12-07

    By the extensive large-scale nonequilibrium molecular dynamics simulation on an effective generic model-A2B2 tetramer for amphiphiles, we investigate the shear-induced parallel to perpendicular orientation transition in the lamellar phase as a function of segregation degree and shear rate. Under low rate shear flow the evolution of parallel lamellar configurations at different segregation strengths shows a similar kinetic pathway independent of the segregation degree. While under high rate shear flow in which the lifetime of undulation instability exceeds the characteristic time of the applied shear flow, the kinetic pathway of the shear-induced parallel-to-perpendicular orientation transition in lamellar systems is the segregation degree dependent. Comparing the temporal mesoscopic domain morphology, the microscopic chain conformation, and macroscopic observable-viscosity changes with the experimentally proposed mechanisms, we find that the undulation instability, partial breakup of monodomain, grain rotation, and recombination combined with defect migration and annihilation are the kinetic pathway for the parallel-to-perpendicular orientation transition in the lamellar phase in or near the intermediate segregation limit, and that the undulation instability, domain dissolution, and reformation along the preferred direction combined with defect migration and annihilation are the kinetic pathway for the parallel-to-perpendicular orientation transition in the lamellar phase close to the order-to-disorder phase transition point. A detailed underlying microscopic picture of the alignment process illustrates that the orientation transition is driven by the alignment of molecules with shear flow. The orientation diagram that characterizes the steady-state orientations as a function of shear rate and attractive potential depth is built, in which the attractive potential depth takes the role of an inverse temperature, somewhat like the Flory-Huggins interaction parameter

  1. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.

    PubMed

    Chen, Alan A; García, Angel E

    2012-06-12

    An RNA kissing loop from the Moloney murine leukemia virus (MMLV) exhibits unusual mechanical stability despite having only two intermolecular base pairs. Mutations at this junction have been shown to destabilize genome dimerization, with concomitant reductions in viral packaging efficiency and infectivity. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an 11-bp RNA hairpin [Li PTX, Bustamante C, Tinoco I (2006) Proc Natl Acad Sci USA 103:15847-15852]. Using nonequilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV dimerization initiation site kissing loop. Two hundred and eight dissociation events were simulated (approximately 16 μs total simulation time) under conditions of constant applied external force, which we use to construct a Markov state model for kissing-loop dissociation. We find that the complex undergoes a conformational rearrangement, which allows for equal distribution of the applied force among all of the intermolecular hydrogen bonds, which is intrinsically more stable than the sequential unzipping of an ordinary hairpin. Stacking interactions with adjacent, unpaired loop adenines further stabilize the complex by increasing the repair rate of partially broken H-bonds. These stacking interactions are prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    The dynamic properties of liquid B2O3 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 B2O3 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).

  3. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations.

    PubMed

    Fischer, Sean A; Aprà, Edoardo; Govind, Niranjan; Hess, Wayne P; El-Khoury, Patrick Z

    2017-02-16

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  4. 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)

  5. Superconductivity in molecular crystals induced by charge injection.

    PubMed

    Schön, J H; Kloc, C; Batlogg, B

    2000-08-17

    Progress in the field of superconductivity is often linked to the discovery of new classes of materials, with the layered copper oxides being a particularly impressive example. The superconductors known today include a wide spectrum of materials, ranging in complexity from simple elemental metals, to alloys and binary compounds of metals, to multi-component compounds of metals and chalcogens or metalloids, doped fullerenes and organic charge-transfer salts. Here we present a new class of superconductors: insulating organic molecular crystals that are made metallic through charge injection. The first examples are pentacene, tetracene and anthracene, the last having the highest transition temperature, at 4 K. We anticipate that many other organic molecular crystals can also be made superconducting by this method, which will lead to surprising findings in the vast composition space of molecular crystals.

  6. Rotational defects and plastic deformation in molecular crystal RDX

    NASA Astrophysics Data System (ADS)

    Pal, Anirban; Picu, Catalin

    2013-03-01

    Defects in molecular crystals differ in many aspects from their atomic counterparts. Molecules in the crystal lattice can undergo conformational changes or twist and rotate into various configurations during deformation. These processes play an important role in the mechanics at a larger scale by controlling critical parameters like dislocation mobility. We present a computational study of such processes in cyclo-trimethylene-trinitramine (RDX), an energetic molecular crystal. Conformational changes, rotational defects and their role in the deformation mechanics of RDX is investigated using molecular dynamics simulations. Structure and mobility of dislocations are also presented and role of conformational and rotational defects in dislocation mobility is discussed. The authors acknowledge discussions with the Army Research Laboratory, and gratefully acknowledge the support from the Army Research Office

  7. Nucleation of Salt Crystals in Clay Minerals: Molecular Dynamics Simulation.

    PubMed

    Dashtian, Hassan; Wang, Haimeng; Sahimi, Muhammad

    2017-07-20

    Nucleation of salt crystals in confined media occurs in many processes of high importance, such as injection of CO2 in geological formations for its sequestration. In particular, salt precipitation in clays, a main component of sedimentary rock, is an important phenomenon. The crystals precipitate on the pores' surface, modify the pore space morphology, and reduce its flow and transport properties. Despite numerous efforts to understand the mechanisms of nucleation of salt crystals in confined media, the effect of the clay's chemistry on the growth, distribution, and properties of the crystals is not well understood. We report the results of extensive molecular dynamics simulation of nucleation and growth of NaCl crystals in a clay pore using molecular models of two types of clay minerals, Na-montmorillonite and kaolinite. Clear evidence is presented for the nucleation of the salt crystals that indicates that the molecular structure of clay minerals affects their spatial distribution, although the nucleation mechanism is the same in both types of clays.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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

  11. 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.

  12. Static and shock compressibility of TATB molecular crystal

    NASA Astrophysics Data System (ADS)

    Degtyarev, A. A.; Smirnov, E. B.; Kostitsin, O. V.; Stankevich, A. V.; Muzyrya, A. K.; Ten, K. A.; Pruuel, E. R.; Kashkarov, A. O.; Batretdinova, L. H.

    2016-11-01

    The paper presents analysis of experimental data on hydrostatic and shock-wave compression of TATB energy-saturated material. The semi-empirical Mie-Grüneisen equation of state was used to describe thermodynamic properties of metastable molecular crystals without considering phase transitions. The equation of state describes experimental data on isothermal compression of a molecular crystal, and this data are obtained using the powder diffraction method. The Hugoniot curve expression plausibly describes shock-compression data on the studied material having various initial porosities.

  13. Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude.

    PubMed

    Giovannelli, Edoardo; Cardini, Gianni; Chelli, Riccardo

    2016-03-08

    An important issue concerning computer simulations addressed to free energy estimates via nonequilibrium work theorems, such as the Jarzynski equality [Phys. Rev. Lett. 1997, 78, 2690], is the computational effort required to achieve results with acceptable accuracy. In this respect, the dynamical freezing approach [Phys. Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind of simulations, by blocking the dynamics of particles located outside an established mobility region. In this report, we show that dynamical freezing produces a systematic spurious decrease of the particle density inside the mobility region. As a consequence, the requirements to apply nonequilibrium work theorems are only approximately met. Starting from these considerations, we have developed a simulation scheme, called "elastic barrier dynamical freezing", according to which a stiff potential-energy barrier is enforced at the boundaries of the mobility region, preventing the particles from leaving this region of space during the nonequilibrium trajectories. The method, tested on the calculation of the distance-dependent free energy of a dimer immersed into a Lennard-Jones fluid, provides an accuracy comparable to the conventional steered molecular dynamics, with a computational speedup exceeding a few orders of magnitude.

  14. 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.

  15. Model for photoinduced bending of slender molecular crystals.

    PubMed

    Nath, Naba K; Pejov, Ljupčo; Nichols, Shane M; Hu, Chunhua; Saleh, Na'il; Kahr, Bart; Naumov, Panče

    2014-02-19

    The growing realization that photoinduced bending of slender photoreactive single crystals is surprisingly common has inspired researchers to control crystal motility for actuation. However, new mechanically responsive crystals are reported at a greater rate than their quantitative photophysical characterization; a quantitative identification of measurable parameters and molecular-scale factors that determine the mechanical response has yet to be established. Herein, a simple mathematical description of the quasi-static and time-dependent photoinduced bending of macroscopic single crystals is provided. This kinetic model goes beyond the approximate treatment of a bending crystal as a simple composite bilayer. It includes alternative pathways for excited-state decay and provides a more accurate description of the bending by accounting for the spatial gradient in the product/reactant ratio. A new crystal form (space group P21/n) of the photoresponsive azo-dye Disperse Red 1 (DR1) is analyzed within the constraints of the aforementioned model. The crystal bending kinetics depends on intrinsic factors (crystal size) and external factors (excitation time, direction, and intensity).

  16. Engineering molecular crystals with abnormally weak cohesion.

    PubMed

    Maly, Kenneth E; Gagnon, Eric; Wuest, James D

    2011-05-14

    Adding astutely placed methyl groups to hexaphenylbenzene increases molecular weight but simultaneously weakens key C-H···π interactions, thereby leading to decreased enthalpies of sublimation and showing that materials with abnormally weak cohesion can be made by identifying and then obstructing interactions that help control association.

  17. Head group effects on molecular packing in lamellar liquid crystals.

    PubMed

    Ishizuka, Chika; Arima, Satoshi; Aramaki, Kenji

    2011-09-01

    In this study, molecular packing in lamellar liquid crystals in poly(oxyethylene) dodecyl ether(C(12)EO(n)) pure systems and the two surfactant mixtures of C(12)EO(8)/1-dodecanol(C(12)EO(0)), C(12)EO(8)/lipophilic sucrose laurate (L-595), hydrophilic sucrose laurate (L-1695)/C(12)EO(2) is investigated in terms of mean molecular area and partial molecular area (PMA). Lamellar liquid crystals formed in the C(12)EO(8)/C(12)EO(0) mixed system show higher melting temperatures than those in the C(12)EO(n) pure systems, even though the average number of EO units in the mixed surfactant system is the same as in the pure system. We compared the mean molecular area at the interface between hydrophilic and lipophilic moieties in the lamellar liquid crystals in each system. In the mixed system, the molecules are packed more tightly than in the pure system. Among the C(12)EO(n) and sucrose laurate mixtures, the L-1695/C(12)EO(2) mixed system showed a smaller mean molecular area per lipophilic chain than the C(12)EO(8)/L-595 mixed system. We investigated the effect of mixing two surfactants with different head group geometry on molecular packing by comparing the PMA of each surfactant. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Nandi, Prithwish K.; Futera, Zdenek; English, Niall J.

    2016-11-01

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ˜220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

  19. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics.

    PubMed

    Nandi, Prithwish K; Futera, Zdenek; English, Niall J

    2016-11-28

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

  20. 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.

  1. Deformation distribution maps of β-HMX molecular crystals

    NASA Astrophysics Data System (ADS)

    Zamiri, Amir Reza; De, Suvranu

    2010-01-01

    β-HMX, extensively used as an energetic material, exists as monoclinic molecular crystals which exhibit highly nonlinear anisotropic mechanical behaviour. To explain the unique features of the deformation behaviour of β-HMX, we have developed the so-called 'deformation distribution maps' (DDMs) based on a single crystal plasticity model based on empirical data. These DDMs reveal that under uniaxial compression there are ten deformation fibres along which β-HMX exhibits maximum plastic deformation and six other deformation fibres along which the deformation response is mostly elastic. These DDMs are applicable to a wider class of molecular crystals for not only understanding their complex mechanical response, but also to serve as important design tools.

  2. Crystal and molecular structure of lancerodiol–p–hydroxybenzoate

    PubMed Central

    Abd El–Razek, Mohamed H.; Hegazy, Mohamed–Elamir F.; Mohamed, Abou El–Hamd H.

    2010-01-01

    Lancerodiol–p–hydroxybenzoate was isolated from the leaves of Ferula sinaica L. (Apiaceae) as light needle crystals. This work reports for the first time the molecular structure and relative configuration of compound 1, established by X-ray analysis. PMID:21808543

  3. 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.

  4. Molecular dynamics simulation of shock melting of aluminum single crystal

    NASA Astrophysics Data System (ADS)

    Ju, Yuanyuan; Zhang, Qingming; Gong, Zizheng; Ji, Guangfu; Zhou, Lin

    2013-09-01

    Molecular dynamics method in conjunction with multi-scale shock technique is employed to study the melting characteristics of aluminum single crystal under dynamic conditions. The simulated results show that a linear relationship exists between the shock wave velocity and particle velocity, in good agreement with the experimental data. Comparing the Lindemann melting curve with the two Hugoniot curves for the solid and liquid phases, the Hugoniot melting is found to begin at 93.6 GPa and end at 140 GPa, which is consistent with the theoretical calculations. The impact of crystal defects on the melting characteristics of aluminum single crystal is also studied, and the results indicate that the pressure and temperature increase slightly for the system experiencing the same dynamic loading due to the crystal defects.

  5. Molecular dynamics simulations of crystallization of Lennard-Jones nanoparticles

    NASA Astrophysics Data System (ADS)

    Thi Thuy Huong, Ta; Van Hoang, Vo; Khuong Cat, Phan Ngoc

    2014-07-01

    Crystallization of Lennard-Jones nanoparticles has been studied by molecular dynamics (MD) simulations. Spherical models with free surface are cooled from the melt to crystalline state. In the cooling process, thermodynamics, structural properties and atomic mechanism of the crystallization are investigated. We found that crystallization in nanoparticles follows the Ostwald's step rule like that found in the past. Due to free surface contribution, the solidification exhibits non-homogeneous behavior which proceeds in different manners between core and surface: homogeneous crystallization in the core and heterogeneous one in the surface layer of nanoparticles. It is due to the discrepancy between structures of two parts: highly ordered structure dominates in the core region while the surface exhibits defective one with a high fraction of undercoordinated sites. Also, our results are consistent with previous ones about the free surface-induced phenomena.

  6. Polymer Alignment Behavior with Molecular Switching of Ferroelectric Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Murashige, Takeshi; Fujikake, Hideo; Sato, Hiroto; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2007-01-01

    This paper describes the molecular alignment behavior of polymer networks with switching of a ferroelectric liquid crystal (FLC) in a molecularly aligned FLC/polymer composite film. The polymer alignment in the composite film, which was slowly formed by photopolymerization-induced phase separation of a heated nematic-phase solution of FLC and monomers, was observed by polarization Raman spectral microscopy. Raman peak intensities originating from the polymers were changed with those from the FLC, when the applied voltage polarity was changed. The trace patterns of the Raman peak intensity with in-plane rotation of the composite film indicated that the formed flexible polymers can follow FLC molecular switching.

  7. 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.

  8. Mixing of molecular excitation in a uniaxial liquid crystal

    SciTech Connect

    Aver`yanov, E.M.

    1995-07-01

    The influence of the mixing of molecular excitations due to local-field effects on the dielectric and spectral properties of uniaxial liquid crystals is investigated. The general properties of the spectrum of transverse optical excitations of the medium, viz, the sum rules for the oscillator strengths, frequencies, and damping constants of the dielectric function resonances, are established. The restricted applicability of the idea of a back ground polarizability (dielectric function) in the analysis of the mixing of molecular excitations is demonstrated. Mixing is taken into account in deriving new dispersion formulas for the imaginary and real parts of the dielectric tensor, which differ significantly from those used in the literature. A range of applicability has been established for the latter. Qualitative and quantitative interpretations of controversial experimental data for an extensive list of objects are given. The occurrence of mixing of dipole-active molecular vibrations, whose intensity has been found to be strongest for polyphilic objects that form nonchiral ferroelectric phases, has been demonstrated for molecular liquids and uniaxial liquid crystals from various chemical classes for the first time. The mixing of molecular excitations is considered as a possible mechanism for {open_quotes}polarization catastrophe{close_quotes} in liquid crystals having a soft mode in hthespectrum of transverse optical modes of vibration for the high-temperature phase. 53 refs., 1 fig.

  9. 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

  10. suPAR: The Molecular Crystal Ball

    PubMed Central

    Thunø, Maria; Macho, Betina; Eugen-Olsen, Jesper

    2009-01-01

    soluble urokinase Plasminogen Activator Receptor (suPAR) levels reflect inflammation and elevated suPAR levels are found in several infectious diseases and cancer. suPAR exists in three forms; suPARI-III, suPARII-III and suPARI which show different properties due to structural differences. Studies suggest that full-length suPAR is a regulator of uPAR/uPA by acting as uPA-scavenger, whereas the cleaved suPARII-III act as a chemotactic agent promoting the immune response via the SRSRY sequence in the linker-region. This review focus on the various suPAR fragments and their involvement in inflammation and pathogenic processes. We focus on the molecular mechanisms of the suPAR fragments and the link to the inflammatory process, as this could lead to medical applications in infectious and pathological conditions. PMID:19893210

  11. 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

  12. Design of ferroelectric organic molecular crystals with ultrahigh polarization.

    PubMed

    Chen, Shuang; Zeng, Xiao Cheng

    2014-04-30

    Inspired by recent successful synthesis of room-temperature ferroelectric supramolecular charge-transfer complexes, i.e., tetrathiafulvalene (TTF)- and pyromellitic diimide (PMDI)-based crystals (Tayi et al. Nature 2012, 488, 485-489), three new ferroelectric two-component organic molecular crystals are designed based on the TTF and PMDI motifs and an extensive polymorph search. To achieve energetically favorable packing structures for the crystals, a newly developed computational approach that combines polymorph predictor with density functional theory (DFT) geometry optimization is employed. Tens of thousands of packing structures for the TTF- and PMDI-based crystals are first generated based on the limited number of asymmetric units in a unit cell as well as limited common symmetry groups for organocarbon crystals. Subsequent filtering of these packing structures by comparing with the reference structures yields dozens of promising crystal structures. Further DFT optimizations allow us to identify several highly stable packing structures that possess the space group of P2₁ as well as high to ultrahigh spontaneous polarizations (23-127 μC/cm(2)) along the crystallographic b axis. These values are either comparable to or much higher than the computed value (25 μC/cm(2)) or measured value (55 μC/cm(2)) for the state-of-the-art organic supramolecular systems. The high polarization arises from the ionic displacement. We further construct surface models to derive the electric-field-switched low-symmetry structures of new TTF- and PMDI-based crystals. By comparing the high-symmetry and low-symmetry crystal structures, we find that the ferroelectric polarization of the crystals is very sensitive to atomic positions, and a small molecular displacement may result in relatively high polarizations along the a and c axes, polarity reversal, and/or electronic contribution to polarization. If these newly designed TTF- and PMDI-based crystals with high polarizations are

  13. 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. © 2015 The Protein Society.

  14. Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip.

    PubMed

    Castillo-Tejas, Jorge; Alvarado, Juan F J; González-Alatorre, Guillermo; Luna-Bárcenas, Gabriel; Sanchez, Isaac C; Macias-Salinas, Ricardo; Manero, Octavio

    2005-08-01

    Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation

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

    NASA Astrophysics Data System (ADS)

    Kuklja, Maija M.; Rashkeev, Sergey N.

    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. The authors suggest that shear plays a crucial role in the dissociation of molecules in organic energetic crystals and may be imperative in providing specific recommendations on ways for materials design.

  16. Theory of polaron bandwidth narrowing in organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Hannewald, K.; Stojanović, V. M.; Schellekens, J. M.; Bobbert, P. A.; Kresse, G.; Hafner, J.

    2004-02-01

    We present a theoretical description of polaron bandwidth narrowing in organic molecular crystals. Based on a solution of a Holstein-Peierls model for tightly bound electrons interacting with phonons, an explicit expression for the temperature dependence of the electronic bandwidths is found. This formula generalizes the result of Holstein polaron theory by treating local and nonlocal electron-phonon coupling on equal footing. The usefulness of the method is demonstrated by model studies for oligo-acene crystals from which microscopic insight into the relevance of the different coupling mechanisms is obtained.

  17. 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.

  18. Molecular simulations of solute transport in xylose isomerase crystals.

    PubMed

    Malek, Kourosh; Coppens, Marc-Olivier

    2008-02-07

    Cross-linked enzyme crystals (CLECs) enclose an extensive regular matrix of chiral solvent-filled nanopores, via which ions and solutes travel in and out. Several cross-linked enzyme crystals have recently been used for chiral separation and as biocatalysts. We studied the dynamics of solute transport in orthorhombic d-xylose isomerase (XI) crystals by means of Brownian dynamics (BD) and molecular dynamics (MD) simulations, which show how the protein residues influence the dynamics of solute molecules in confined regions inside the lattice. In the BD simulations, coarse-grained beads represent solutes of different sizes. The diffusion of S-phenylglycine molecules inside XI crystals is investigated by long-time MD simulations. The computed diffusion coefficients within a crystal are found to be orders of magnitude lower than in bulk water. The simulation results are compared to the recent experimental studies of diffusion and reaction inside XI crystals. The insights obtained from simulations allow us to understand the nature of solute-protein interactions and transport phenomena in CLECs, which is useful for the design of novel nanoporous biocatalysts and bioseparations based on CLECs.

  19. 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.

  20. 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.

  1. Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

    NASA Astrophysics Data System (ADS)

    Poloni, Laura N.

    The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L

  2. Determining the Molecular Growth Mechanisms of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

    Studies of the growth of tetragonal lysozyme crystals employing atomic force microscopy (AFM) have shown the advantages of this technique in investigating the growth mechanisms of protein crystals [1]. The resolution of these studies was in the micron range, which revealed surface features such as the occurrence of dislocations and 2D nucleation islands, similar to those found in inorganic systems. They clearly showed that the crystals grew by these surface growth mechanisms. However, the studies also revealed some surprising features, such as bimolecular growth step heights and pronounced growth anisotropies on the (110) face, which could not be explained. In previous studies we employed Periodic Bond Chain (PBC) theory to tetragonal lysozyme crystal growth and found that the crystals were constructed by strongly bonded molecular chains forming helices about the 43 axes [2,3]. The helices were connected to each other with weaker bonds. The growth process was shown to proceed by the formation of these 43 helices, resulting in bimolecular growth steps on the (110) face. It was also shown to explain many other observations on tetragonal lysozyme crystal growth. Although PBC analysis is not a new technique [4], it has not been widely used as the mechanisms predicted from it could not be experimentally verified. In this study the growth process of these crystals was investigated, particularly for the (110) face, employing some newly developed high resolution AFM techniques. These techniques allowed individual lysozyme molecules on the crystal faces to be resolved and predictions from PBC analyses to be tested. The analyses had shown that of the two possible packing arrangements on (110) faces, only one would actually occur. Employing the first of the newly developed techniques, these faces were scanned by high resolution AFM. The resulting images were then compared with the theoretically constructed images for the two possible packing arrangements on the (110) face

  3. Nonequilibrium molecular dynamics simulations of the thermal conductivity of water: a systematic investigation of the SPC/E and TIP4P/2005 models.

    PubMed

    Römer, Frank; Lervik, Anders; Bresme, Fernando

    2012-08-21

    We report an extensive nonequilibrium molecular dynamics investigation of the thermal conductivity of water using two of the most accurate rigid nonpolarizable empirical models available, SPC/E and TIP4P/2005. Our study covers liquid and supercritical states. Both models predict the anomalous increase of the thermal conductivity with temperature and the thermal conductivity maximum, hence confirming their ability to reproduce the complex anomalous behaviour of water. The performance of the models strongly depends on the thermodynamic state investigated, and best agreement with experiment is obtained for states close to the liquid coexistence line and at high densities and temperatures. Considering the simplicity of these two models the overall agreement with experiments is remarkable. Our results show that explicit polarizability and molecular flexibility are not needed to reproduce the anomalous heat conduction of water.

  4. Anisotropy of the thermal conductivity in a crystalline polymer: Reverse nonequilibrium molecular dynamics simulation of the δ phase of syndiotactic polystyrene

    NASA Astrophysics Data System (ADS)

    Rossinsky, Eddie; Müller-Plathe, Florian

    2009-04-01

    The thermal conductivity of the crystalline δ phase of syndiotactic polystyrene has been investigated by reverse nonequilibrium molecular dynamics simulations. The results are in the expected range. An anisotropy is found for the thermal conductivity, with the component in chain direction being 2.5-3 larger than perpendicular to it. Any increase in the density causes an increase also in the thermal conductivity, particularly in the perpendicular directions. As side results, the simulations confirm an earlier finding on the force field dependence of the thermal conductivity: The thermal conductivity has a tendency to decrease when the number of active degrees of freedom in the system is reduced by the introduction of constraints. This dependence is, however, weaker and more erratic than previously found for molecular liquids and amorphous polymers.

  5. 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

  6. 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

  7. Solute transport in orthorhombic lysozyme crystals: a molecular simulation study.

    PubMed

    Malek, Kourosh

    2007-12-01

    Long-time equilibrium molecular dynamics simulations were performed to study the passage of a substrate, L: -arabinose, through nanopores of orthorhombic hen egg white lysozyme crystals. Cross-linked protein crystals (CLPC), as novel biological nanoporous media, consist of an extensive regular matrix of chiral solvent-filled nanopores via which ions and solutes, e.g. sugars and amino acids, travel in and out. We studied the diffusive motion of arabinose inside protein channels. The computed diffusion coefficients within the crystal were orders of magnitudes lower relative to the diffusion coefficient of the solute in water. This study is valuable for understanding the nature of solute-protein interactions and transport phenomena in CLPCs and provides an understanding of biocatalytic and bioseparation processes using CLPC.

  8. Calculating Hugoniots for molecular crystals from first principles.

    SciTech Connect

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

    2010-03-01

    Density Functional Theory (DFT) has over the last few years emerged as an indispensable tool for understanding the behavior of matter under extreme conditions. DFT based molecular dynamics simulations (MD) have for example confirmed experimental findings for shocked deuterium, enabled the first experimental evidence for a triple point in carbon above 850 GPa, and amended experimental data for constructing a global equation of state (EOS) for water, carrying implications for planetary physics. The ability to perform high-fidelity calculations is even more important for cases where experiments are impossible to perform, dangerous, and/or prohibitively expensive. For solid explosives, and other molecular crystals, similar success has been severely hampered by an inability of describing the materials at equilibrium. The binding mechanism of molecular crystals (van der Waals forces) is not well described within traditional DFT. Among widely used exchange-correlation functionals, neither LDA nor PBE balances the strong intra-molecular chemical bonding and the weak inter-molecular attraction, resulting in incorrect equilibrium density, negatively affecting the construction of EOS for undetonated high explosives. We are exploring a way of bypassing this problem by using the new Armiento-Mattsson 2005 (AM05) exchange-correlation functional. The AM05 functional is highly accurate for a wide range of solids, in particular in compression. In addition, AM05 does not include any van der Waals attraction, which can be advantageous compared to other functionals: Correcting for a fictitious van der Waals like attraction with unknown origin can be harder than correcting for a complete absence of all types of van der Waals attraction. We will show examples from other materials systems where van der Waals attraction plays a key role, where this scheme has worked well, and discuss preliminary results for molecular crystals and explosives.

  9. On calculating the equilibrium structure of molecular crystals

    NASA Astrophysics Data System (ADS)

    Mattsson, Ann E.; Wixom, Ryan R.; Mattsson, Thomas R.

    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. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  10. Continuous diffraction of molecules and disordered molecular crystals

    PubMed Central

    Yefanov, Oleksandr M.; Ayyer, Kartik; White, Thomas A.; Barty, Anton; Morgan, Andrew; Mariani, Valerio; Oberthuer, Dominik; Pande, Kanupriya

    2017-01-01

    The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities. This situation arises in the continuous diffraction of laser-aligned molecules or translationally disordered molecular crystals. This paper develops the analysis of the intensity statistics of such continuous diffraction to obtain parameters such as scaling, beam coherence and the number of contributing independent object orientations. When measured, continuous molecular diffraction is generally weak and accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities or their mean value to guide the subtraction of the background, it is shown how all measured values can be utilized to estimate the background, noise and signal, by employing a modified ‘noisy Wilson’ distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously published continuous diffraction data measured from crystals of photosystem II [Ayyer et al. (2016 ▸), Nature, 530, 202–206]. PMID:28808434

  11. Simulation and understanding of atomic and molecular quantum crystals

    NASA Astrophysics Data System (ADS)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

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

  12. 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

  13. 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

  14. 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.

  15. The photoluminescence response to structural changes of Yb implanted ZnO crystals subjected to non-equilibrium processing

    NASA Astrophysics Data System (ADS)

    Ratajczak, R.; Prucnal, S.; Guziewicz, E.; Mieszczynski, C.; Snigurenko, D.; Stachowicz, M.; Skorupa, W.; Turos, A.

    2017-02-01

    In this paper, we present the detailed study of optical and structural properties of Yb implanted single ZnO crystals. Hydrothermally grown wurtzite (0001) ZnO crystals were implanted with 150 keV Yb ions to fluencies of 5 × 1014 and 1 × 1015 at/cm2. After ion implantation, two different types of annealing were performed: rapid thermal annealing (RTA) and millisecond range flash lamp annealing (FLA). Crystalline quality, damage recovery, and Yb lattice site location were evaluated by the Channeling Rutherford Backscattering Spectrometry (RBS/c). It is shown that independent of the used annealing technique, defects formed in ZnO during ion implantation can be removed. Upon RTA performed at the temperature higher than 800 °C, strong out-diffusion of implanted Yb atoms and precipitation on the surface takes place. Consequently, the degradation of the photoluminescence (PL) efficiency is observed. The diffusion of implanted Yb during millisecond range FLA does not occur for such experimental conditions. Moreover, FLA treatment for 20 ms leads to the formation of single crystalline ZnO layer with Yb incorporated in the substitutional lattice sites. According to RBS/c and PL data, Yb atoms substituted in the Zn sublattice are predominantly in the 2+ oxidation state. The most intensive PL has been observed after annealing at 800 °C for 20 min which is accompanied with the reduction of Yb substitutional fraction and formation of octahedron Yb-oxygen clusters within ZnO.

  16. Contribution of molecular flexibility to the elastic-plastic properties of molecular crystal α-RDX

    NASA Astrophysics Data System (ADS)

    Pal, Anirban; Picu, Catalin R.

    2017-01-01

    We show in this work that the mechanical properties of molecular crystals are strongly affected by the flexibility of the constituent molecules. To this end, we explore several kinematically restrained models of the molecular crystal cyclotrimethylene trinitramine in the α phase. We evaluate the effect of gradually removing the flexibility of the molecule on various crystal-scale parameters such as the elastic constants, the lattice parameters, the thermal expansion coefficients, the stacking fault energy and the critical stress for the motion of a dislocation (the Peierls-Nabarro stress). The values of these parameters evaluated with the fully refined, fully flexible atomistic model of the crystal are taken as reference. It is observed that the elastic constants, the lattice parameters and their dependence on pressure, and the thermal expansion coefficient can be accurately predicted with models that consider the NO2 and CH2 groups rigid, and the N-N bonds and the bonds of the triazine ring inextensible. Eliminating the dihedral flexibility of the ring leads to larger errors. The model in which the entire molecule is considered rigid or is mapped to a blob leads to even larger errors. Only the fully flexible, reference model provides accurate values for the stacking fault energy and the Peierls-Nabarro critical stress. Removing any component of the molecular flexibility leads to large errors in these parameters. These results also provide guidance for the development of coarse grained models of molecular crystals.

  17. Comment on ``Modified nonequilibrium molecular dynamics for fluid flows with energy conservation'' [J. Chem. Phys. 106, 5615 (1997)

    NASA Astrophysics Data System (ADS)

    Evans, Denis J.; Searles, Debra J.; Hoover, Wm. G.; Hoover, C. G.; Holian, Brad Lee; Posch, Harald A.; Morriss, Gary P.

    1998-03-01

    In their recent paper and the associated Response to this Comment, Tuckerman et al. dispute the form of the Liouville equation, as proposed by Liouville in 1838. They go on to introduce a definition of the entropy which is at variance with Boltzmann's H-function and with Gibbs' definition of entropy. They argue that their "entropy" is a constant of the motion, equal to its initial equilibrium value regardless of the imposition of external fields. We argue that the analysis of Tuckerman et al. is incorrect and that issues raised by Tuckerman et al. are not at all new but have already been correctly incorporated into nonequilibrium statistical mechanics.

  18. 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.

  19. New opportunities in crystal engineering--the role of atomic force microscopy in studies of molecular crystals.

    PubMed

    Chow, Ernest H H; Bučar, Dejan-Krešimir; Jones, William

    2012-09-25

    Here, we highlight recent research involving atomic force microscopy investigations of molecular crystals, and focus particularly on the latest relevant advances in our knowledge of crystal-growth mechanisms and structure-property relationships in organic crystals. This brief survey features the importance of incorporating AFM into solid-state research as an essential tool for the informed design and construction of crystalline materials.

  20. 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.

  1. 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.

  2. Tampering with molecular cohesion in crystals of hexaphenylbenzenes.

    PubMed

    Gagnon, Eric; Halperin, Shira D; Métivaud, Valérie; Maly, Kenneth E; Wuest, James D

    2010-01-15

    Hexaphenylbenzene (HPB) and analogous compounds have properties of broad utility in science and technology, including conformationally well-defined molecular structures, high thermal stability, high HOMO-LUMO gaps, little self-association, inefficient packing, and high solubilities. Previous structural studies of HPB and its analogues have revealed persistent involvement of the central aromatic ring in strong C-H...pi interactions. These interactions can be blocked by adding simple ortho alkyl substituents to the peripheral phenyl groups. Comparison of the structures of HPB and a series of ortho-substituted derivatives has shown systematic changes in molecular cohesion and packing, as measured by packing indices, densities, solubilities, temperatures of sublimation, melting points, and ratios of H...H, C...H, and C...C contacts. These results illustrate how crystal engineering can guide the search for improved materials by identifying small but telling molecular alterations that thwart established patterns of association.

  3. Molecular dynamics simulations of Li transport between cathode crystals

    NASA Astrophysics Data System (ADS)

    Garofalini, S. H.

    The molecular dynamics (MD) computer simulation technique has been used to study the effect of an amorphous intergranular film (IGF) present in a polycrystalline cathode on Li transport. The solid electrolyte is a model lithium silicate glass while the cathode is a nanocrystalline vanadia with an amorphous V 2O 5 IGF separating the crystals. Thin (˜1 to a few nanometer thick) IGFs are known to be present in most polycrystalline oxide materials. However, the role of such a film on Li transport in oxide cathodes has not been addressed. Current scanning probe microscopy (SPM) studies have shown that the orientation of the layered nanocrystalline vanadia crystals near the cathode/solid electrolyte interface is not optimized for Li ion transport. While the precise structure of the material between the crystals has not been identified, initially it can be initially considered as likely to be a thin non-crystalline (amorphous) film. This is based on the ubiquitous presence of such a structure in other polycrystalline oxides. Also, and with more relevance to the materials used in thin film batteries, an amorphous film can be expected to form between nanocrystals that crystallized from an amorphous matrix, as would be the case in a deposited thin film cathode. Consistent with simulations of Li transport in amorphous vanadia, the current simulations show that Li ions diffuse more rapidly into the amorphous intergranular thin film than into the layered vanadia with the (0 0 1) planes parallel to the cathode/electrolyte interface.

  4. Absorbate-induced piezochromism in a porous molecular crystal

    SciTech Connect

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

    2015-02-23

    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. Lastly, 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.

  5. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  6. Absorbate-induced piezochromism in a porous molecular crystal

    DOE PAGES

    Hendon, Christopher H.; Wittering, Kate E.; Chen, Teng -Hao; ...

    2015-02-23

    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 toluenemore » is also found to crystallize within the pore. Lastly, 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.« less

  7. 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.

  8. Non-equilibrium proteins.

    PubMed

    Klonowski, W

    2001-07-01

    There exist no methodical studies concerning non-equilibrium systems in cellular biology. This paper is an attempt to partially fill this shortcoming. We have undertaken an extensive data-mining operation in the existing scientific literature to find scattered information about non-equilibrium subcellular systems, in particular concerning fast proteins, i.e. those with short turnover half-time. We have advanced the hypothesis that functionality in fast proteins emerges as a consequence of their intrinsic physical instability that arises due to conformational strains resulting from co-translational folding (the interdependence between chain elongation and chain folding during biosynthesis on ribosomes). Such intrinsic physical instability, a kind of conformon (Klonowski-Klonowska conformon, according to Ji, (Molecular Theories of Cell Life and Death, Rutgers University Press, New Brunswick, 1991)) is probably the most important feature determining functionality and timing in these proteins. If our hypothesis is true, the turnover half-time of fast proteins should be positively correlated with their molecular weight, and some experimental results (Ames et al., J. Neurochem. 35 (1980) 131) indeed demonstrated such a correlation. Once the native structure (and function) of a fast protein macromolecule is lost, it may not be recovered--denaturation of such proteins will always be irreversible; therefore, we searched for information on irreversible denaturation. Only simulation and modeling of protein co-translational folding may answer the questions concerning fast proteins (Ruggiero and Sacile, Med. Biol. Eng. Comp. 37 (Suppl. 1) (1999) 363). Non-equilibrium structures may also be built up of protein subunits, even if each one taken by itself is in thermodynamic equilibrium (oligomeric proteins; sub-cellular sol-gel dissipative network structures).

  9. Nanoindentation hardness anisotropy of alumina crystal: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nishimura, Kenji; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2008-04-01

    Atomistic mechanisms of the initial stage of plasticity during nanoindentation are studied by molecular dynamics simulations for three surface orientations of alumina crystal. The simulations predict significant anisotropy and indentation depth dependence of the hardness value at the nanometer scale. The nanohardness anisotropy is found to arise from orientation-dependent dislocation activities. In the (0001) basal plane indentation, prism dislocations are emitted, followed by basal and pyramidal dislocations, to form massive subsurface defects; prism and pyramidal dislocations are emitted on (011¯0) and (21¯1¯0) prism plane indentations, respectively, to cause modest deformations. Stacking faults are also observed because these dislocations are extended to Shockley partial dislocations.

  10. 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..

  11. 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.

  12. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  13. Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

    PubMed

    Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

    2010-05-07

    Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

  14. Photophysics of Molecular Materials: From Single Molecules to Single Crystals

    NASA Astrophysics Data System (ADS)

    Lanzani, Guglielmo

    2005-12-01

    Carbon based pi-conjugated materials offer a broad range of applications, going from molecular electronics and single molecule devices to nanotechnology, plastic electronics and optoelectronics. The proper physical description of such materials is in between that of molecular solids and that of low-dimensional covalent semiconductors. This book is a comprehensive review of their elementary excitations processes and dynamics, which merges the two viewpoints, sometimes very different if not contrasting. In each chapter, a broad tutorial introduction provides a solid physical background to the topic, which is further discussed based on recent experimental results obtained via state-of-the-art techniques. Both the molecular, intra-chain character and the solid state, inter-molecular physics is addressed. Reports on single molecule and single polymer chain spectroscopy introduce the on-site phenomena. Several chapters are dedicated to nano-probes, steady state and transient spectroscopies. The highly ordered state, occurring in single crystals, is also discussed thoroughly. Finally, less conventional tools such as THz spectroscopy are discussed in detail. The book provides a useful introduction to the field for newcomers, and a valid reference for experienced researchers in the field.

  15. Photophysics of Molecular Materials: From Single Molecules to Single Crystals

    NASA Astrophysics Data System (ADS)

    Lanzani, Guglielmo

    2003-09-01

    Carbon based pi-conjugated materials offer a broad range of applications, going from molecular electronics and single molecule devices to nanotechnology, plastic electronics and optoelectronics. The proper physical description of such materials is in between that of molecular solids and that of low-dimensional covalent semiconductors. This book is a comprehensive review of their elementary excitations processes and dynamics, which merges the two viewpoints, sometimes very different if not contrasting. In each chapter, a broad tutorial introduction provides a solid physical background to the topic, which is further discussed based on recent experimental results obtained via state-of-the-art techniques. Both the molecular, intra-chain character and the solid state, inter-molecular physics is addressed. Reports on single molecule and single polymer chain spectroscopy introduce the on-site phenomena. Several chapters are dedicated to nano-probes, steady state and transient spectroscopies. The highly ordered state, occurring in single crystals, is also discussed thoroughly. Finally, less conventional tools such as THz spectroscopy are discussed in detail. The book provides a useful introduction to the field for newcomers, and a valid reference for experienced researchers in the field.

  16. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

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

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

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

  18. Infrared Space Observatory Observations of Molecular Hydrogen in HH 54: Measurement of a Nonequilibrium Ratio of Ortho- to Para-H2

    NASA Technical Reports Server (NTRS)

    Neufeld, David A.; Melnick, Gary J.; Harwit, Martin

    1998-01-01

    We have detected the S(1), S(2), S(3), S(4), and S(5) pure rotational lines of molecular hydrogen toward the outflow source HH 54 using the Short Wavelength Spectrometer on board the Infrared Space Observatory. The observed H2 line ratios indicate the presence of warm molecular gas with an H2 density of at least 10(sup 5) /cc and a temperature approximately 650 K in which the ratio of ortho- to para-H2 is only 1.2 -+ 0.4, significantly smaller than the equilibrium ratio of 3 expected in gas at that temperature. These observations imply that the measured ratio of ortho- to para-H2 is the legacy of an earlier stage in the thermal history of the gas when the gas had reached equilibrium at a temperature approximately 90 K. Based upon the expected timescale for equilibration, we argue that the nonequilibrium ratio of ortho- to para-H2 observed in HH 54 serves as a chronometer that places a conservative upper limit of approximately 5000 yr on the period for which the emitting gas has been warm. The S(2)/,S(l) and S(3)/S(1) H2 line ratios measured toward HH 54 are consistent with recent theoretical models of Timmermann for the conversion of para- to ortho-H2 behind slow, C-type shocks, but only if the preshock ratio of ortho- to para-H2 was approximately < 0.2.

  19. Infrared Space Observatory Observations of Molecular Hydrogen in HH 54: Measurement of a Nonequilibrium Ratio of Ortho- to Para-H2

    NASA Technical Reports Server (NTRS)

    Neufeld, David A.; Melnick, Gary J.; Harwit, Martin

    1998-01-01

    We have detected the S(1), S(2), S(3), S(4), and S(5) pure rotational lines of molecular hydrogen toward the outflow source HH 54 using the Short Wavelength Spectrometer on board the Infrared Space Observatory. The observed H2 line ratios indicate the presence of warm molecular gas with an H2 density of at least 10(sup 5) /cc and a temperature approximately 650 K in which the ratio of ortho- to para-H2 is only 1.2 -+ 0.4, significantly smaller than the equilibrium ratio of 3 expected in gas at that temperature. These observations imply that the measured ratio of ortho- to para-H2 is the legacy of an earlier stage in the thermal history of the gas when the gas had reached equilibrium at a temperature approximately 90 K. Based upon the expected timescale for equilibration, we argue that the nonequilibrium ratio of ortho- to para-H2 observed in HH 54 serves as a chronometer that places a conservative upper limit of approximately 5000 yr on the period for which the emitting gas has been warm. The S(2)/,S(l) and S(3)/S(1) H2 line ratios measured toward HH 54 are consistent with recent theoretical models of Timmermann for the conversion of para- to ortho-H2 behind slow, C-type shocks, but only if the preshock ratio of ortho- to para-H2 was approximately < 0.2.

  20. Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors

    PubMed Central

    Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

    2017-01-01

    Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology. PMID:28245588

  1. 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.

  2. Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors.

    PubMed

    Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

    2017-02-24

    Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology.

  3. Hydrogen-bonding directed crystal engineering of some molecular solids

    NASA Astrophysics Data System (ADS)

    Xue, Feng

    2000-10-01

    and shown to include various solvent molecules with different size, shape and symmetry in ( 26) ˜ (36). The rational strategy employed to assemble the hexahost involves the halogen-halogen interaction (X···X) and the molecular symmetry (C3). The designed matching of trigonal symmetry at molecular (triazine) and supramolecular (X 3 synthon) nodes steers crystallization in a predictable manner, and leads to the idea that molecular and supramolecular synthons may be interchanged to facilitate the retrosynthesis of target networks.

  4. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  5. 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.

  6. Progress in organic molecular single crystal FET electronics

    NASA Astrophysics Data System (ADS)

    Butko, Vladimir; Chi, Xiaoliu; Ramirez, Arthur

    2004-03-01

    Semiconducting organic materials have received increased attention because they promise bulk processing of flexible, large-area electronic devices. Field Effect Transistors (FETs) provide a powerful method of investigating two-dimensional properties of these materials. We report on fabrication and characterization of FETs on organic molecular single-crystals of pentacene and tetracene [1,2]. The FETs exhibit hole conductivity with room temperature record effective mobility, up to 2 -3 cm^2/Vs and on/off ratios up to 2*10^7. We were able to suppress an activation energy of pentacene down to ˜ 30 mK by applying gate voltage of 45 V. 1. V.Y. Butko, X. Chi, D. V. Lang and A. P. Ramirez, Applied Physics Letters, v.83, #23, pp. 4773-4775, December 8, 2003 2. V.Y. Butko, X. Chi, A. P. Ramirez , Solid State Communications, v. 128/11, pp. 431, 2003

  7. InPBi single crystals grown by molecular beam epitaxy.

    PubMed

    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

    2014-06-26

    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.

  8. Solvothermal Molecular Precursor Routes to Semiconductor Film and Crystal Growth

    NASA Astrophysics Data System (ADS)

    Gillan, Edward G.

    2002-08-01

    This research project explored the utility of molecular precursor decomposition in superheated non-aqueous solvents directed towards semiconductor crystal growth. Reactions were run in toluene, THF, and under solvent free conditions. An in situ precursor synthesis and decomposition resulted in GaN nanoparticles from simple starting materials (GaCl(3) and NaN(3)). Particle sizes range from about 10 to hundreds of nanometers. Upon annealing to 1000 degrees C, the poorly crystalline products ordered into crystalline hexagonal GaN and luminescence. The conversion of synthesized organometallic dimeric gallium amino precursors to GaN was less successful; however they showed some utility in vapor phase film growth. Silver and silver sulfide nanoparticles were also produced in a solvothermal system via silver azide decomposition producing particles in the 100 mn to micron size regime.

  9. Collective and molecular relaxation in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Wrobel, S.; Marzec, M.; Godlewska, Malgorzata; Gestblom, B.; Hiller, Steffen; Haase, Wolfgang

    1995-08-01

    Ferroelectric liquid crystals are molecular ferroelectrics showing up in the tilted liquid crystalline systems (SmC*, SmI*, SmF*) composed of chiral molecules. In this work, we present the dielectric, electro-optic, and calorimetric studies of a single component system: 3-octyloxy-6[2-fluor-4-(2-fluoroctyloxy)phenyl]-pyridine showing interesting ferroelectric properties. The compound exhibits a first order N*- SmC* phase transition which leads to a qualitatively new behavior, for instance the relaxation frequency of the soft mode below TC seems to be temperature independent. The high frequency relaxation process, connected with the reorientation around the long axis, is practically undisturbed at the N*-SmC* transition. Yet, it was found that in the SmC* phase, the best fit was obatined with two Cole-Cole functions yielding two relaxation times to describe a biased reorientation of molecules in the SmC* phase.

  10. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  11. Detection of organophosphorus compounds using a molecularly imprinted photonic crystal.

    PubMed

    Liu, Feng; Huang, Shuyue; Xue, Fei; Wang, Yifei; Meng, Zihui; Xue, Min

    2012-02-15

    A label free molecularly imprinted photonic crystal (MIPC) was developed to detect the degradation product of nerve agents. Mono-dispersed poly-methyl methacrylate colloidal particles with the diameter of 280 nm were used to fabricate a closely packed colloidal crystal array (CCA), and a methyl phosphonic acid (MPA) imprinted hydrogel was prepared within the CCA using 2-hydroxyethyl-methacrylate and N-isopropylacrylamide as monomers, ethyleneglycol dimethacrylate and N, N'-methylenebisacrylamide as cross-linkers, a mixture of n-octanol and acetonitrile as porogen. The diffraction intensity of the MIPC decreased significantly upon the MPA adsorption with a limit of detection (LOD) of 10(-6) molL(-1). Furthermore, the diffraction intensity decreased and blue shifted with the increase of temperature, decreased and red shifted with the increase of ionic strength. At higher pH, the diffraction intensity increased without obvious diffraction shift. The MIPC provides an indirect path to detect nerve agents (Sarin, Soman, VX and R-VX) by monitoring the MPA released from the hydrolysis of nerve agents, with LODs of 3.5 × 10(-6) molL(-1), 2.5 × 10(-5) molL(-1), 7.5 × 10(-5) molL(-1) and 7.5 × 10(-5) molL(-1) for Sarin, Soman, VX and R-VX, respectively.

  12. Crystallization force--a density functional theory concept for revealing intermolecular interactions and molecular packing in organic crystals.

    PubMed

    Li, Tonglei; Ayers, Paul W; Liu, Shubin; Swadley, Matthew J; Aubrey-Medendorp, Clare

    2009-01-01

    Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short-range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal-growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self-assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, so-called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.

  13. Molecular Dynamics Modeling of PPTA Crystals in Aramid Fibers

    SciTech Connect

    Mercer, Brian Scott

    2016-05-19

    In this work, molecular dynamics modeling is used to study the mechanical properties of PPTA crystallites, which are the fundamental microstructural building blocks of polymer aramid bers such as Kevlar. Particular focus is given to constant strain rate axial loading simulations of PPTA crystallites, which is motivated by the rate-dependent mechanical properties observed in some experiments with aramid bers. In order to accommodate the covalent bond rupture that occurs in loading a crystallite to failure, the reactive bond order force eld ReaxFF is employed to conduct the simulations. Two major topics are addressed: The rst is the general behavior of PPTA crystallites under strain rate loading. Constant strain rate loading simulations of crystalline PPTA reveal that the crystal failure strain increases with increasing strain rate, while the modulus is not a ected by the strain rate. Increasing temperature lowers both the modulus and the failure strain. The simulations also identify the C N bond connecting the aromatic rings as weakest primary bond along the backbone of the PPTA chain. The e ect of chain-end defects on PPTA micromechanics is explored, and it is found that the presence of a chain-end defect transfers load to the adjacent chains in the hydrogen-bonded sheet in which the defect resides, but does not in uence the behavior of any other chains in the crystal. Chain-end defects are found to lower the strength of the crystal when clustered together, inducing bond failure via stress concentrations arising from the load transfer to bonds in adjacent chains near the defect site. The second topic addressed is the nature of primary and secondary bond failure in crystalline PPTA. Failure of both types of bonds is found to be stochastic in nature and driven by thermal uctuations of the bonds within the crystal. A model is proposed which uses reliability theory to model bonds under constant strain rate loading as components with time-dependent failure rate

  14. Petascale Molecular Dynamics Simulations of Polymers and Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Nguyen, Trung Dac; Carrillo, Jan-Michael; Brown, W. Michael

    2014-03-01

    The availability of faster and larger supercomputers and more efficient parallel algorithms now enable us to perform unprecedented simulations approaching experimental scales. Here we present two examples of our latest large-scale molecular dynamics simulations using the Titan supercomputer in the Oak Ridge Leadership Computing Facility (OLCF). In the first study, we address the rupture origin of liquid crystal thin films wetting a solid substrate. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation. Importantly, we found evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. In the second study, we used coarse-grained molecular dynamics to simulate the thermal annealing of poly(3-hexylthiophene) (P3HT) and Phenyl-C61-butyric acid methyl ester (PCBM) blends in the presence of a silicon substrate found in organic solar cells. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. Furthermore, the ternary blend of short and long P3HT chains with PCBM affects the vertical phase segregation of PCBM decreasing its concentration in the vicinity of the substrate. U.S. DOE Contract No. DE-AC05-00OR22725.

  15. 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.

  16. 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.

  17. Nonequilibrium chemo-electronic conversion of water on the nanosized YSZ: experiment and Molecular Dynamics modelling problem formulation

    NASA Astrophysics Data System (ADS)

    Doroshkevich, A. S.; Lyubchyk, A. I.; Islamov, A. K.; Turchenko, V. A.; Glazunova, V. A.; Zelenyak, T. Yu; Burkhovetskiy, V. V.; Shylo, A. V.; Balasoiu, M.; Saprykina, A. V.; Ohmura, S.; Lygina, O. S.; Lyubchyk, S. I.; Konstantinova, T. E.; Lakusta, M. V.; Bodnarchuk, V. I.; Lyubchyk, S. B.; Bacherikov, Yu Yu; Aliyeva, Ye; Kholmurodov, Kh T.

    2017-05-01

    The exothermic heterogeneous electrochemical energy conversion to the electric energy through interaction of the ZrO2 based nanopowder system with atmospheric moisture have been explored within this work. Electrical properties of the experimental samples were investigated during humidification at the conditions of molecular flux density gradient. The morphological features of the surface cross-section and aggregates of 3 mol% Y2O3 doped ZrO2 nanopowder systems were investigated. Initial conditions for molecular dynamics modelling of the adsorption processes were obtained. A novel approach for developing of chemo-electronic converters based on nanoscale processes and materials with dielectric conductivity type proposed.

  18. Non-equilibrium molecular dynamics simulations of the transient Ludwig-Soret effect in a binary Lennard-Jones/spline mixture.

    PubMed

    Hafskjold, Bjørn

    2017-01-01

    A binary isotope mixture of Lennard-Jones/spline particles at equilibrium was perturbed by a sudden change in the system's boundary temperatures. The system's response was determined by non-equilibrium molecular dynamics (NEMD). Three transient processes were studied: 1) The propagation of a pressure (shock) wave, 2) heat diffusivity and conduction, and 3) thermal diffusion (the Ludwig-Soret effect). These three processes occur at different time scales, which makes it possible to separate them in one single NEMD run. The system was studied in liquid, supercritical, and dense gas states with various forms and strengths of the thermal perturbation. The results show that heat was initially transported by two separate mechanisms: 1) heat diffusion as described by the transient heat equation and 2) as a consequence of a pressure wave. The pressure wave travelled faster than the speed of sound, generating a shock wave in the system. Local equilibrium was found in the transient phase, even with very strong perturbations and in the shock front. Although the mass separation due to the Ludwig-Soret effect developed much slower than the pressure and temperature fields in the system at large, it was found that the Soret coefficient could be accurately determined from the initial phase of the transient and close to the heat source. This opens the possibility of a new way to analyse results from transient experiments and thereby minimize effects of gravity and convection due to buoyancy.

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

    NASA Astrophysics Data System (ADS)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

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

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

    PubMed

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

    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. (12)C and (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 (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 (12)C-(14)C mixtures, we computed the thermal conductivity of systems where the (14)C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

  1. 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.

  2. Infrared Space Observatory Observations of Molecular Hydrogen in HH 54: Measurement of a Nonequilibrium Ratio of Ortho- to Para-H2

    NASA Technical Reports Server (NTRS)

    Neufeld, David A.; Melnick, Gary J.; Harwit, Martin

    1998-01-01

    We have detected the S(1), S(2), S(3), S(4), and S(5) pure rotational lines of molecular hydrogen toward the outflow source HH 54 using the Short Wavelength Spectrometer on board the Infrared Space Observatory. The observed H2 line ratios indicate the presence of warm molecular gas with an H2 density of at least 10(exp 5) cm(exp -3) and a temperature approximately 650 K in which the ratio of ortho- to para-H2 is only 1.2 +/- 0.4, significantly smaller than the equilibrium ratio of 3 expected in gas at that temperature. These observations imply that the measured ratio of ortho- to para-H2 is the legacy of an earlier stage in the thermal history of the gas when the gas had reached equilibrium at a temperature approximately less than 90 K. Based upon the expected timescale for equilibration, we argue that the nonequilibrium ratio of ortho- to para-H2 observed in HH 54 serves as a chronometer that places a conservative upper limit of approximately 5000 yr on the period for which the emitting gas has been warm. The S(2)/S(1) and S(3)/S(1) H2 line ratios measured toward HH 54 are consistent with recent theoretical models of Timmermann for the conversion of para- to ortho-H2 behind slow, C-type shocks, but only if the preshock ratio of ortho- to para-H2 was approximately less than 0.2.

  3. Infrared Space Observatory Observations of Molecular Hydrogen in HH 54: Measurement of a Nonequilibrium Ratio of Ortho- to Para-H2

    NASA Technical Reports Server (NTRS)

    Neufeld, David A.; Melnick, Gary J.; Harwit, Martin

    1998-01-01

    We have detected the S(1), S(2), S(3), S(4), and S(5) pure rotational lines of molecular hydrogen toward the outflow source HH 54 using the Short Wavelength Spectrometer on board the Infrared Space Observatory. The observed H2 line ratios indicate the presence of warm molecular gas with an H2 density of at least 10(exp 5) cm(exp -3) and a temperature approximately 650 K in which the ratio of ortho- to para-H2 is only 1.2 +/- 0.4, significantly smaller than the equilibrium ratio of 3 expected in gas at that temperature. These observations imply that the measured ratio of ortho- to para-H2 is the legacy of an earlier stage in the thermal history of the gas when the gas had reached equilibrium at a temperature approximately less than 90 K. Based upon the expected timescale for equilibration, we argue that the nonequilibrium ratio of ortho- to para-H2 observed in HH 54 serves as a chronometer that places a conservative upper limit of approximately 5000 yr on the period for which the emitting gas has been warm. The S(2)/S(1) and S(3)/S(1) H2 line ratios measured toward HH 54 are consistent with recent theoretical models of Timmermann for the conversion of para- to ortho-H2 behind slow, C-type shocks, but only if the preshock ratio of ortho- to para-H2 was approximately less than 0.2.

  4. 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

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

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    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

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

    PubMed

    Fang, Tao; Jia, Junteng; Li, Shuhua

    2016-05-05

    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.

  7. CO/sub 2/ laser absorption and saturation studies of molecular impurities in alkali halide crystals

    SciTech Connect

    Sievers, A.J.

    1980-12-01

    The objective of this research program has been to explore the equilibrium and non-equilibrium dynamical properties of ReO/sub 4//sup -/ molecules embedded in alkali halide lattices using electromagnetic radiation. Both incoherent sources and CO/sub 2/ laser radiation have been used to explore the full dynamic range of the molecular vibrational modes. To achieve this objective stable molecular dopant - alkali halide combinations have been fabricated which have vibrational modes near the CO/sub 2/ laser frequencies. In order to uncouple the molecular modes from the lattice modes, to simplify the analysis as much as possible, low temperature spectroscopic measurements were required. In general, it was found that the molecular vibrational modes in the low temperature quiescent lattice had extremely narrow linewidths (less than 0.1 cm/sup -1/) so that most of the coincidences with the CO/sub 2/ laser lines were eliminated.

  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. Molecular dynamics simulations of polymer crystallization via self-seeding

    NASA Astrophysics Data System (ADS)

    Luo, Chuanfu; Sommer, Jens-Uwe

    2010-03-01

    We use large scale molecular dynamics (MD) to simulate the processes of polymer crystallization with a coarse-grained model. In total we are able to simulate 1000 polymer chains made of 1000 monomers each, a system large enough to compare to experimental relevant, entangled melts. It is found that some micro crystalline domains (MCDs) can survive slightly above the apparent melting temperature after a consistent cooling and reheating cycle. We chose the stablest MCD as a baby seed and let it grow at a constant quenched temperature. A single lamella can be formed via this self-seeding process. We observe the growth pathway and analyze the chain dynamics especially at the growth front.[4pt] [1] C. Luo and J. Sommer, Comp Phys. Comm. 180, 1382 (2009)[0pt] [2] C. Luo and J. Sommer, Phys. Rev. Lett. 102, 147801 (2009)[0pt] [3] J-J. Xu, Y. Ma, W.B. Hu, M. Rehahn and G. Reiter, Nature Materials 8, 348 (2009)

  10. 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.

  11. Full quantification of frequency-dependent interfacial thermal conductance contributed by two- and three-phonon scattering processes from nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Hu, Ming

    2017-03-01

    Understanding phonon transport across interfaces serves as a major tool to advance a diverse spectrum of fundamental and applied research. Unlike bulk materials, where the three-phonon scattering process is relatively straightforward to investigate, little research has been dedicated to the detailed analysis of the three-phonon scattering process at interfaces due to the complexity of interfaces and the mismatch of phonon dispersions of the two connecting parts. Based on the nonequilibrium molecular dynamics simulation, which is one of the most popular approaches to investigate the thermal conductance, we develop an explicit theoretical framework by considering the full third-order force constants field to quantify the two- and three-phonon scattering at interfaces. Bulk Ar is used as a benchmark to validate the computational scheme by comparing the results with those using the all-order phonon scattering method [frequency-dependent directly decomposed method; Y. Zhou and M. Hu, Phys. Rev. B 92, 195205 (2015), 10.1103/PhysRevB.92.195205]. Then, Ar-heavy Ar and Si-Ge interfaces are studied and the respective role of two- and three-phonon scattering processes is quantitatively characterized at different temperatures. Moreover, all four different types of the three-phonon scattering process are explicitly evaluated. The method developed herein for splitting the two- and three-phonon scattering processes in the interfacial heat transport is expected to advance our understanding of the phonon process at interfaces, and will facilitate designing high-performance interfacial structures in terms of efficient thermal management.

  12. Laser synthesis of a copper-single-walled carbon nanotube nanocomposite via molecular-level mixing and non-equilibrium solidification

    NASA Astrophysics Data System (ADS)

    Tu, Jay F.; Rajule, Nilesh; Molian, Pal; Liu, Yi

    2016-12-01

    A copper-single-walled carbon nanotube (Cu-SWCNT) metal nanocomposite could be an ideal material if it can substantially improve the strength of copper while preserving the metal’s excellent thermal and electrical properties. However, synthesis of such a nanocomposite is highly challenging, because copper and SWCNTs do not form intermetallic compounds and are insoluble; as a result, there are serious issues regarding wettability and fine dispersion of SWCNTs within the copper matrix. In this paper we present a novel wet process, called the laser surface implantation process (LSI), to synthesize Cu-SWCNT nanocomposites by mixing SWCNTs into molten copper. The LSI process includes drilling several microholes on a copper substrate, filling the microholes with SWCNTs suspended in solution, and melting the copper substrate to create a micro-well of molten copper. The molten copper advances radially outward to engulf the microholes with pre-deposited SWCNTs to form the Cu-SWCNT implant upon solidification. Rapid and non-equilibrium solidification is achieved due to copper’s excellent heat conductivity, so that SWCNTs are locked in position within the copper matrix without agglomerating into large clusters. This wet process is very different from the typical dry processes used in powder metallurgy. Very high hardness improvement, up to 527% over pure copper, was achieved, confirmed by micro-indentation tests, with only a 0.23% SWCNT volume fraction. The nanostructure of the nanocomposite was characterized by TEM imaging, energy-dispersive x-ray spectroscopy mapping and spectroscopy measurements. The SWCNTs were found to be finely dispersed within the copper matrix with cluster sizes in the range of nanometers, achieving the goal of molecular-level mixing.

  13. Molecular simulation study of the effect of various additives on salbutamol sulfate crystal habit.

    PubMed

    Yani, Yin; Chow, Pui Shan; Tan, Reginald B H

    2011-10-03

    The effects of polyvinylpyrrolidone (PVP), hydroxypropyl methyl cellulose (HPMC), and lecithin additives on salbutamol sulfate (SS) crystal growth are studied using molecular dynamics (MD) simulation, to provide an insight into the interaction between the additives and SS crystal faces at the atomistic level. The interaction energy between additives and crystal faces is presented. The intermolecular contacts between the additives and the crystal faces are analyzed by calculating the average number of contacts between O atoms of the additives and the H atoms of the first layer of the SS crystal. The mobility of each additive on SS crystal faces is also reported by determining the mean square displacement. Our results suggest that PVP is the most effective among the three additives for the inhibition of SS crystal growth. The methodology used in this study could be a powerful tool for selection of habit-modifying additives in other crystallization systems.

  14. Molecular dynamics study of non-equilibrium energy transport from a cylindrical track: Part II. Spike models for sputtering yield

    NASA Astrophysics Data System (ADS)

    Bringa, E. M.; Johnson, R. E.; Dutkiewicz, Ł .

    1999-05-01

    Thermal spike models have been used to calculate the yields for electronic sputtering of condensed-gas solids by fast ions. In this paper molecular dynamics (MD) calculations are carried out to describe the evolution of solid Ar and O 2 following the excitation of a cylindrical track in order to test spike models. The calculated sputtering yields were found to depend linearly on the energy deposition per unit path length, d E/d x, at the highest d E/d x. This is in contrast to the spike models and the measured yields for a number of condensed-gas solids which depend quadratically on d E/d x at high d E/d x. In paper I [E.M. Bringa, R.E. Johnson, Nucl. Instr. and Meth. B 143 (1998) 513] we showed that the evolution of energy from the cylindrical track was, typically, not diffusive, as assumed in the spike models. Here we show that it is the description of the radial transport and the absence of energy transport to the surface, rather than the treatment of the ejection process, that accounts for the difference between the analytic spike models and the MD calculations. Therefore, the quadratic dependence on d E/d x of the measured sputtering yield reflects the nature of the energizing process rather than the energy transport. In this paper we describe the details of the sputtering process and compare the results here for crystalline samples to the earlier results for amorphous solids.

  15. Nonequilibrium is different

    NASA Astrophysics Data System (ADS)

    Kirkpatrick, T. R.; Dorfman, J. R.

    2015-08-01

    Nonequilibrium and equilibrium fluid systems differ due to the existence of long-range correlations in nonequilibrium that are not present in equilibrium, except at critical points. Here we examine fluctuations of the temperature, of the pressure tensor, and of the heat current in a fluid maintained in a nonequilibrium stationary state (NESS) with a fixed temperature gradient, a system in which the nonequilibrium correlations are especially long-ranged. For this particular NESS, our results show that (i) the mean-squared fluctuations in nonequilibrium differ markedly in their system-size scaling compared to their equilibrium counterparts, and (ii) there are large, nonlocal correlations of the normal stress in this NESS. These terms provide important corrections to the fluctuating normal stress in linearized Landau-Lifshitz fluctuating hydrodynamics.

  16. Molecular dynamics simulation of thermomechanical properties of montmorillonite crystal. 3. montmorillonite crystals with PEO oligomer intercalates.

    PubMed

    Mazo, Mikhail A; Manevitch, Leonid I; Gusarova, Elena B; Shamaev, Mikhail Yu; Berlin, Alexander A; Balabaev, Nikolay K; Rutledge, Gregory C

    2008-03-27

    We present the results of molecular dynamics (MD) simulation of the structure and thermomechanical behavior of Wyoming-type Na+-montmorillonite (MMT) with poly(ethylene oxide) (PEO) oligomer intercalates. Periodic boundary conditions in all three directions and simulation cells containing two MMT lamellae [Si248Al8][Al112Mg16]O640[OH]128 oriented parallel to the XY-plane were used. The interlamellar space, or gallery, between neighboring MMT lamellae was populated by 24 Na+ counterions and PEO macromolecules of different lengths, ranging from 2 up to 240 repeat units. We considered three different loadings of PEO within the gallery: 80, 160, and 240 repeat units, corresponding to 13, 23, and 31 wt % PEO based on total mass of the nanocomposite, respectively. In the cases of 13 and 23 wt %, the polymer chains formed one or two well-defined amorphous layers with interlayer distances of 1.35 and 1.8 nm, respectively. We have observed also formation of a wider monolayer gallery with interlayer distances of 1.6 nm. Three-layer PEO films formed in the case of 31 wt % loading. The thermal properties were analyzed over the range 300-400 K, and the isothermal linear compressibility, transversal moduli, and shear moduli were calculated at 300 K. These properties are compared with the results of our simulation of thermal and mechanical properties of MMT crystal with galleries filled by one or two water layers as well as with those of an isolated clay nanoplate.

  17. Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex.

    PubMed

    Yao, Zi-Shuo; Mito, Masaki; Kamachi, Takashi; Shiota, Yoshihito; Yoshizawa, Kazunari; Azuma, Nobuaki; Miyazaki, Yuji; Takahashi, Kazuyuki; Zhang, Kuirun; Nakanishi, Takumi; Kang, Soonchul; Kanegawa, Shinji; Sato, Osamu

    2014-12-01

    Many molecular machines with controllable molecular-scale motors have been developed. However, transmitting molecular movement to the macroscopic scale remains a formidable challenge. Here we report a single crystal of a Ni complex whose shape changes abruptly and reversibly in response to thermal changes at around room temperature. Variable-temperature single-crystal X-ray diffraction studies show that the crystalline shape change is induced by an unusual 90° rotation of uniaxially aligned oxalate molecules. The oxalate dianions behave as molecular-scale rotors, with their movement propagated through the entire crystalline material via intermolecular hydrogen bonding. Consequently, the subnanometre-scale changes in the oxalate molecules are instantly amplified to a micrometre-scale contraction or expansion of the crystal, accompanied by a thermal hysteresis loop. The shape change in the crystal was clearly detected under an optical microscope. The large directional deformation and prompt response suggest a role for this material in microscale or nanoscale thermal actuators.

  18. Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex

    NASA Astrophysics Data System (ADS)

    Yao, Zi-Shuo; Mito, Masaki; Kamachi, Takashi; Shiota, Yoshihito; Yoshizawa, Kazunari; Azuma, Nobuaki; Miyazaki, Yuji; Takahashi, Kazuyuki; Zhang, Kuirun; Nakanishi, Takumi; Kang, Soonchul; Kanegawa, Shinji; Sato, Osamu

    2014-12-01

    Many molecular machines with controllable molecular-scale motors have been developed. However, transmitting molecular movement to the macroscopic scale remains a formidable challenge. Here we report a single crystal of a Ni complex whose shape changes abruptly and reversibly in response to thermal changes at around room temperature. Variable-temperature single-crystal X-ray diffraction studies show that the crystalline shape change is induced by an unusual 90° rotation of uniaxially aligned oxalate molecules. The oxalate dianions behave as molecular-scale rotors, with their movement propagated through the entire crystalline material via intermolecular hydrogen bonding. Consequently, the subnanometre-scale changes in the oxalate molecules are instantly amplified to a micrometre-scale contraction or expansion of the crystal, accompanied by a thermal hysteresis loop. The shape change in the crystal was clearly detected under an optical microscope. The large directional deformation and prompt response suggest a role for this material in microscale or nanoscale thermal actuators.

  19. Real-time molecular scale observation of crystal formation

    NASA Astrophysics Data System (ADS)

    Schreiber, Roy E.; Houben, Lothar; Wolf, Sharon G.; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J.; Poblet, Josep M.; Neumann, Ronny

    2017-04-01

    How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

  20. Real-time molecular scale observation of crystal formation.

    PubMed

    Schreiber, Roy E; Houben, Lothar; Wolf, Sharon G; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J; Poblet, Josep M; Neumann, Ronny

    2017-04-01

    How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

  1. 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.

  2. 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.

  3. Slow molecular dynamics close to crystal surfaces during crystallization of a protein lysozyme studied by fluorescence correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Tanaka, S.

    2010-09-01

    Fluorescence correlation spectroscopy (FCS) was applied to the crystallization processes of egg-white lysozyme. Utilizing FCS's high spatial resolution of about the laser wavelength used, the molecular dynamics close to crystal surfaces was investigated for both tetragonal single crystals and needlelike spherulites. When the FCS measurement was done at the point closer than 1 μm to the surface of a tetragonal single crystal, the relaxation time became several times longer than that in bulk solution, but the fluorescence intensity (thus concentration) was similar to that observed in bulk solution. On the other hand, the peculiar slow dynamics (a few orders of magnitude slower than that in bulk solution) of concentrated liquid states of the lysozyme molecules was observed in needlelike spherulites. We suggested that these observations could be explained by the formation of softly connected aggregates accumulating around the needlelike crystals, which could cause the instability of the crystal growth and thus the formation of spherulites. These aggregates gradually disappeared as the crystallization further proceeded. After the disappearance of the aggregates, the spherulites started to mature.

  4. Polymer crystallization under nano-confinement of droplets studied by molecular simulations.

    PubMed

    Hu, Wenbing; Cai, Tao; Ma, Yu; Hobbs, Jamie K; Farrance, O; Reiter, Günter

    2009-01-01

    Fabrication of polymer nano-crystals proceeds usually through hierarchical ordering of the different-scale structures. Nano-scale patterns are produced first, which serve as a spatial template for subsequent polymer crystallization under nano-confinement. We begin with a survey of the effects of nano-confinement on polymer crystallization, mainly on the basis of the knowledge obtained from molecular simulations. After that, we report dynamic Monte Carlo simulations of polymer crystallization confined in nano-droplets. We observed that the shape of droplets on a solid substrate appears as a pancake, and both initiation and development of crystallization are depressed with the decrease of droplet size. Surface-induced crystal nucleation guides the dominant edge-on crystal orientation at high temperatures; however, its contribution to nucleation rates is not much greater than crystal nucleation in the volume of the droplet. At low temperatures, edge-on crystals are frequent at both substrate/polymer and polymer/air interfaces. In conclusion, molecular simulations can shed light on the microscopic mechanisms of polymer crystallization under nano-confinement.

  5. Nonequilibrium fluctuations during diffusion in liquid layers

    NASA Astrophysics Data System (ADS)

    Brogioli, Doriano; Vailati, Alberto

    2017-07-01

    Theoretical analysis and experiments have provided compelling evidence of the presence of long-range nonequilibrium concentration fluctuations during diffusion processes in fluids. In this paper, we investigate the dependence of the features of the fluctuations from the dimensionality of the system. In three-dimensional fluids the amplitude of nonequilibrium fluctuations can become several orders of magnitude larger than that of equilibrium fluctuations. Notwithstanding that, the amplitude of nonequilibrium fluctuations remains small with respect to the concentration difference driving the diffusion process. By extending the theory to two-dimensional systems, such as liquid monolayers and bilayers, we show that the amplitude of the fluctuations becomes much stronger than in three-dimensional systems. We investigate the properties of the fronts of diffusion and show that they have a self-affine structure characterized by a Hurst exponent H =1 . We discuss the implications of these results for diffusion in liquid crystals and in cellular membranes of living organisms.

  6. Molecular alignment enhancement phenomenon of polymer formed from a liquid crystal monomer in a liquid crystal solvent

    NASA Astrophysics Data System (ADS)

    Fujikake, Hideo; Murashige, Takeshi; Sato, Hiroto; Kawakita, Masahiro; Kikuchi, Hiroshi

    2003-03-01

    We report an abnormal alignment enhancement phenomenon of polymer molecules. The alignment order of a rigid-skeleton polymer made from a liquid crystalline monomer in a low-molecular-weight liquid crystal solvent was drastically enhanced with increasing temperature, even though the alignment order of the solution of the liquid crystal and monomer decreased. From polymer molecular alignment observations using polarizing Raman scattering microscopy, it was found that the polymer alignment order was three times greater than that of the original aligned monomer and polymer. This super alignment technique of polymer using a molecular-scaled self-assembly mechanism is applicable to the formation of electrically and/or optically functional nanopolymer wires.

  7. Raman study of uniaxial deformation of single-crystal mats of ultrahigh molecular weight linear polyethylene

    NASA Astrophysics Data System (ADS)

    Zavgorodnev, Yu V.; Chvalun, S. N.; Nikolaeva, G. Yu; Sagitova, E. A.; Pashinin, P. P.; Gordeyev, S. A.; Prokhorov, K. A.

    2015-03-01

    We present for the first time a Raman spectroscopic study of the deformation process of solution-crystallized single-crystal mats of ultrahigh molecular weight linear polyethylene (UHMW PE). We study the deformed regions of the films, drawn only until the formation of the neck, and the films of much higher draw ratios, just before rupture starts. For comparison, we have also carried out Raman investigations of films produced by compression of UHMW PE powder. We have found that the uniaxial molecular orientation in the neck region of the single-crystal mat films develops more slowly as compared to the films, prepared by compression of the UHMW PE powder.

  8. Dielectric spectroscopy and simulation of cryptophane and metal-organic framework crystals containing internal molecular rotors

    NASA Astrophysics Data System (ADS)

    Winston, Erick B.

    With recent advances in chemistry and crystal engineering, it is now possible to flexibly synthesize stable crystals with internal molecular electric dipole rotors. This represents a nanoscale design approach to the creation of new materials. Potential applications of such systems include electro-optic materials, new ferroelectrics and dielectrics, and perhaps even information storage. In this thesis, the rotational dynamics of molecular rotors in single crystals is investigated by dielectric spectroscopy. Using X-ray crystallography in combination with molecular mechanics or ab initio calculations, the influence of the local crystal environment on the observed dynamics is ascertained. Additionally, the atomic coordinates from the X-ray structure, and molecular dipole moments determined from ab initio calculations, are used to create an approximate model for a Monte Carlo study of the significance of the dipole-dipole interactions among the rotors. The systems studied here represent two different families of synthetic approaches to creating molecular rotors in crystals. One approach consists of synthesizing inclusion compounds in which molecular crystals have internal cavities capable of hosting small molecular guests. Specifically, we look at the globular cryptophane complexes and find that iodomethane rotates in cryptophane-A with remarkably low barriers near 2 kcal·mol-1 (1000 K), in agreement with the molecular mechanics calculations. The other approach consists of synthesizing covalent crystals where the rotor elements are themselves part of the covalently bonded network. We study metal-organic open frameworks (MOFs), in particular IRMOF-2, and find rotation with a single barrier near 7 kcal·mol-1 (3500 K). The barrier is in approximate agreement with ab initio calculations. Statistical analysis of an MC simulation of IRMOF-2 suggests a dipolar phase change at lower temperatures. The residual dielectric effects of the dipole-dipole interaction above the

  9. Study of spectroscopic and thermal characteristics of nonlinear optical molecular crystals based on 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Pavlovetc, I. M.; Fokina, M. I.

    2016-08-01

    The paper presents the results of study of spectroscopic and thermal characteristics of molecular co-crystals: 2-aminopyridine-4-nitrophenol-4-mtrophenolate (2AP4N) and 2,6- diaminopyridine-4-nitrophenol-4nitrophenolate (26DAP4N). Crystals were successfully grown by slow evaporation technique. Optical transparency in the region of 190-1100 was found to be suitable for applications with cut off wavelengths 420 and 430 nm respectively. Thermogravimetric and differential thermal analysis show good quality and thermal stability for studied crystals. Kurtz and Perry powder technique proves that the crystals are acentric and have significant nonlinear optical response.

  10. 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.

  11. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Molecular insights into the heterogeneous crystal growth of si methane hydrate.

    PubMed

    Vatamanu, Jenel; Kusalik, Peter G

    2006-08-17

    In this paper we report a successful molecular simulation study exploring the heterogeneous crystal growth of sI methane hydrate along its [001] crystallographic face. The molecular modeling of the crystal growth of methane hydrate has proven in the past to be very challenging, and a reasonable framework to overcome the difficulties related to the simulation of such systems is presented. Both the microscopic mechanisms of heterogeneous crystal growth as well as interfacial properties of methane hydrate are probed. In the presence of the appropriate crystal template, a strong tendency for water molecules to organize into cages around methane at the growing interface is observed; the interface also demonstrates a strong affinity for methane molecules. The maximum growth rate measured for a hydrate crystal is about 4 times higher than the value previously determined for ice I in a similar framework (Gulam Razul, M. S.; Hendry, J. G.; Kusalik, P. G. J. Chem. Phys. 2005, 123, 204722).

  13. The use of photolithography on molecular orientation of the liquid crystals

    NASA Astrophysics Data System (ADS)

    Yilmaz, Suleyman

    2017-02-01

    The photolithography was used on molecular orientation of liquid crystals as an alternative to other conventional methods. Either planar or homeotropic orientation were provided with surface anchoring energy for the molecular alignment. The photolithography were applied to provide micro-grooving on the film surface, which is including polyimide coatings, UV exposure, chemical etching and thermal curing process, respectively. Three type liquid crystal cells were made by provided rubbing and photolithography for planar alignment and also homeotropic alignment. Electro-optical properties of the liquid crystals were examined under the electric field at phase transition region for three type liquid crystal cells. It was observed that the photolithographic method was the more effective and acceptable results than the other conventional methods on the molecular orientations.

  14. Assembling of three-dimensional crystals by optical depletion force induced by a single focused laser beam.

    PubMed

    Deng, Hai-Dong; Li, Guang-Can; Liu, Hai-Ying; Dai, Qiao-Feng; Wu, Li-Jun; Lan, Sheng; Gopal, Achanta Venu; Trofimov, Vyacheslav A; Lysak, Tatiana M

    2012-04-23

    We proposed a method to assemble microspheres into a three-dimensional crystal by utilizing the giant nonequilibrium depletion force produced by nanoparticles. Such assembling was demonstrated in a colloid formed by suitably mixing silica microspheres and magnetic nanoparticles. The giant nonequilibrium depletion force was generated by quickly driving magnetic nanoparticles out of the focusing region of a laser light through both optical force and thermophoresis. The thermophoretic binding of silica beads is so tight that a colloidal photonic crystal can be achieved after complete evaporation of solvent. This technique could be employed for fabrication of colloidal photonic crystals and molecular sieves.

  15. 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.

  16. Anomalous doping of a molecular crystal monitored with confocal fluorescence microscopy: Terrylene in a p-terphenyl crystal.

    PubMed

    Białkowska, Magda; Deperasińska, Irena; Makarewicz, Artur; Kozankiewicz, Bolesław

    2017-09-21

    Highly terrylene doped single crystals of p-terphenyl, obtained by co-sublimation of both components, showed bright spots in the confocal fluorescence images. Polarization of the fluorescence excitation spectra, blinking and bleaching, and saturation behavior allowed us to attribute them to single molecules of terrylene anomalously embedded between two neighbor layers of the host crystal, in the (a,b) plane. Such an orientation of terrylene molecules results in much more efficient absorption and collection of the fluorescence photons than in the case of previously investigated molecules embedded in the substitution sites. The above conclusion was supported by quantum chemistry calculations. We postulate that the kind of doping considered in this work should be possible in other molecular crystals where the host molecules are organized in a herringbone pattern.

  17. Anomalous doping of a molecular crystal monitored with confocal fluorescence microscopy: Terrylene in a p-terphenyl crystal

    NASA Astrophysics Data System (ADS)

    Białkowska, Magda; Deperasińska, Irena; Makarewicz, Artur; Kozankiewicz, Bolesław

    2017-09-01

    Highly terrylene doped single crystals of p-terphenyl, obtained by co-sublimation of both components, showed bright spots in the confocal fluorescence images. Polarization of the fluorescence excitation spectra, blinking and bleaching, and saturation behavior allowed us to attribute them to single molecules of terrylene anomalously embedded between two neighbor layers of the host crystal, in the (a,b) plane. Such an orientation of terrylene molecules results in much more efficient absorption and collection of the fluorescence photons than in the case of previously investigated molecules embedded in the substitution sites. The above conclusion was supported by quantum chemistry calculations. We postulate that the kind of doping considered in this work should be possible in other molecular crystals where the host molecules are organized in a herringbone pattern.

  18. 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.

  19. Molecular environment and temperature dependence of hyperfine interactions in sugar crystal radicals from first principles.

    PubMed

    Declerck, R; Pauwels, E; Speybroeck, V Van; Waroquier, M

    2008-02-07

    The effect of the molecular environment and the temperature dependence of hyperfine parameters in first principles calculations in alpha-d-glucose and beta-d-fructose crystal radicals have been investigated. More specifically, we show how static (0 K) cluster in vacuo hyperfine calculations, commonly used today, deviate from more advanced molecular dynamics calculations at the experimental temperature using periodic boundary conditions. From the latter approach, more useful information can be extracted, allowing us to ascertain the validity of proposed molecular models.

  20. Molecular motion, dielectric response, and phase transition of charge-transfer crystals: acquired dynamic and dielectric properties of polar molecules in crystals.

    PubMed

    Harada, Jun; Ohtani, Masaki; Takahashi, Yukihiro; Inabe, Tamotsu

    2015-04-08

    Molecules in crystals often suffer from severe limitations on their dynamic processes, especially on those involving large structural changes. Crystalline compounds, therefore, usually fail to realize their potential as dielectric materials even when they have large dipole moments. To enable polar molecules to undergo dynamic processes and to provide their crystals with dielectric properties, weakly bound charge-transfer (CT) complex crystals have been exploited as a molecular architecture where the constituent polar molecules have some freedom of dynamic processes, which contribute to the dielectric properties of the crystals. Several CT crystals of polar tetrabromophthalic anhydride (TBPA) molecules were prepared using TBPA as an electron acceptor and aromatic hydrocarbons, such as coronene and perylene, as electron donors. The crystal structures and dielectric properties of the CT crystals as well as the single-component crystal of TBPA were investigated at various temperatures. Molecular reorientation of TBPA molecules did not occur in the single-component crystal, and the crystal did not show a dielectric response due to orientational polarization. We have found that the CT crystal formation provides a simple and versatile method to develop molecular dielectrics, revealing that the molecular dynamics of the TBPA molecules and the dielectric property of their crystals were greatly changed in CT crystals. The TBPA molecules underwent rapid in-plane reorientations in their CT crystals, which exhibited marked dielectric responses arising from the molecular motion. An order-disorder phase transition was observed for one of the CT crystals, which resulted in an abrupt change in the dielectric constant at the transition temperature.

  1. Dual-functional molecular crystals from [Fe(C2O4)Cl2-]n

    NASA Astrophysics Data System (ADS)

    Zhang, Bin

    2008-10-01

    Depending on cation templet, three types of one-dimensional antiferromagnetic [Fe(C2O4)Cl2-]n chains have been found in molecular crystal: zigzag chain, boat-shape chain, and chiral chain. They are good building block in conductive molecular magnet: weak-ferromagnetic conductor, semiconductor and insulator as well as in molecular magnet. Molecular magnet and magnetic molecular conductor with porosity, and homogenous magnetic conducting polymer of [Fe(C2O4)Cl2-]n were obtained and studied.

  2. Molecular tectonics: tubular crystals with controllable channel size and orientation.

    PubMed

    Lin, Mei-Jin; Jouaiti, Abdelaziz; Pocic, David; Kyritsakas, Nathalie; Planeix, Jean-Marc; Hosseini, Mir Wais

    2010-01-07

    The combination of flexible neutral organic tectons based on two pyridines interconnected by a thioether or thioester type spacer with an inorganic ZnSiF(6) pillar leads to the formation of 2-D coordination networks and the packing of the latter generates crystals offering controllable tubular channels with imposed orientation along the pillar axis.

  3. A Computer Simulation of Detonation within an Energetic Molecular Crystal.

    DTIC Science & Technology

    1986-07-11

    desired condition or time. A nonhomogeneous crystal of diatomic molecules was monitored to discover the atomic interactions during detonation. A Lennard ... Jones potential equation was used to represent the exothermic reaction between diatomic hydrogen and chlorine molecules. This is the first project to

  4. Thermal and Mechanical Non-Equilibrium Effects on Turbulent Flows: Fundamental Studies of Energy Exchanges Through Direct Numerical Simulations, Molecular Simulations and Experiments

    DTIC Science & Technology

    2016-02-26

    fidelity and the functional forms of the energy exchange mechanisms (i.e., the coupling terms) between the energy pools. Descriptions of the underlying...AFRL-AFOSR-VA-TR-2016-0104 Thermal and mechanical non-equilibrium effects on turbulent flows:fundamental studies of energy exchanges through direct...information. Send comments regarding this burden estimate or    any other aspect of this collection of information, including suggestions for reducing

  5. 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.

  6. 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.

  7. 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.

  8. Adsorption behavior of acetone solvent at the HMX crystal faces: A molecular dynamics study.

    PubMed

    Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Ma, Yiding; Kang, Ying; Ge, Zhongxue

    2017-03-10

    Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011). The adsorption sites for solvent incorporation at the crystal surface were found and visualized with the aid of occupancy analysis. A uniform arrangement of adsorption sites is observed at the rough (020) surface as a result of ordered adsorption motif.

  9. Sublimation rate of molecular crystals - role of internal degrees of freedom

    SciTech Connect

    Maiti, A; Zepeda-Ruiz, L A; Gee, R H; Burnham, A

    2007-01-19

    It is a common practice to estimate site desorption rate from crystal surfaces with an Arrhenius expression of the form v{sub eff} exp(-{Delta}E/k{sub B}T), where {Delta}E is an activation barrier to desorb and v{sub eff} is an effective vibrational frequency {approx} 10{sup 12} sec{sup -1}. However, such a formula can lead to several to many orders of magnitude underestimation of sublimation rates in molecular crystals due to internal degrees of freedom. We carry out a quantitative comparison of two energetic molecular crystals with crystals of smaller entities like ice and Argon (solid) and uncover the errors involved as a function of molecule size. In the process, we also develop a formal definition of v{sub eff} and an accurate working expression for equilibrium vapor pressure.

  10. Solid state amorphization of organic molecular crystals using a vibrating mill

    NASA Astrophysics Data System (ADS)

    Tsukushi, Itaru; Yamamuro, Osamu; Matsuo, Takasuke

    1995-06-01

    The solid-state amorphization of organic molecular crystals was studied by differential scanning calorimetry (DSC) and X-ray powder diffraction. Two clathrate compounds of tri- O-methyl-β-cyclodextrin (TMCD) containing p-nitrobenzoic acid (NBA) and p-hydroxybenzoic acid (HBA), and seven other organic compounds, sucrose (SUC), salicin (SAL), phenolphthalein (PP), 1,3,5-tri-α-naphthylbenzene (TNB), p-quaterphenyl ( p-QP), p-terphenyl ( p-TP) and 1,3,5-triphenylbenzene (TPB) were ground for 2-16 h with a vibrating mill at room temperature. A halo diffraction pattern and exothermic effect due to the crystallization were observed in TMCD-NBA, TMCD-HBA, SUC, SAL, PP and TNB, indicating amorphization of these crystals. The ability of solid-state amorphization in organic molecular crystals was discussed from a thermodynamic point of view.

  11. Crystal Properties and Radiation Effects in Solid Molecular Hydrogens

    SciTech Connect

    Kozioiziemski, B

    2000-09-01

    The crystal lattice structure, growth shapes and helium generated by beta-decay of solid deuterium-tritium (D-T) mixtures have been studied. Understanding of these D-T properties is important for predicting and optimizing the target design of the National Ignition Facility (NIF). Raman spectroscopy showed the D-T crystal structure is hexagonal close packed, common to the non-tritiated isotopes. The isotopic mixtures of both tritiated and non-tritiated species broadens the rotational transitions, especially of the lighter species in the mixture. The vibrational frequencies of each isotope is shifted to higher energy in the mixture than the pure components. The J = 1-0 population decreases exponentially with a 1/e time constant which rapidly increases above 10.5 K for both D{sub 2} and T{sub 2} in D-T. The conversion rate is nearly constant from 5 K to 10 K for both D{sub 2} and T{sub 2} at 7.1 hours and 2.1 hours, respectively. The smoothing of D-T layers by beta decay heating is limited by the crystal surface energy. Deuterium and hydrogen-deuteride crystals were grown at a number of temperatures below the triple point to determine the surface energy and roughening transition. Several distinct crystal shapes were observed on a number of different substrates. The a facet roughens between 0.9 T{sub TP} and T{sub TP}, while the c facet persists up to the melting temperature. This is very different from the behavior of the other rare gas crystals which grow completely rounded above 0.8 T{sub TP}. Helium bubbles formed as a product of the beta decay were observed using optical microscopy and the diffusion of smaller bubbles measured with dynamic light scattering. Bubble diffusion coefficients as high as 2.0 x 10{sup -16} m{sup 2}/s were measured for 10-50 nm bubbles. The bubbles move in response to a thermal gradient, with speeds between 1 {micro}m/hour and 100 {micro}m/hour for thermal gradients and temperatures appropriate to NIF targets.

  12. 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.

  13. Molecular dynamics analysis of the crystallization of an overcooled aluminum melt

    NASA Astrophysics Data System (ADS)

    Norman, G. E.; Pisarev, V. V.

    2012-09-01

    The homogeneous nucleation of a crystal in an overcooled aluminum melt was modeled by the molecular dynamics (MD) method. The MD simulation used the embedded-atom potential. The crystallization delay times were determined from MD simulation data. In a set of systems at the same temperature and pressure, the lifetimes were distributed exponentially. Nucleation frequencies at different temperatures and pressures were determined. The resulting nucleation frequencies were compared with the ones predicted by classical nucleation theory.

  14. 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.

  15. Protein crystallization screens developed at the MRC Laboratory of Molecular Biology.

    PubMed

    Gorrec, Fabrice

    2016-05-01

    In order to solve increasingly challenging protein structures with crystallography, crystallization reagents and screen formulations are regularly investigated. Here, we briefly describe 96-condition screens developed at the MRC Laboratory of Molecular Biology: the LMB sparse matrix screen, Pi incomplete factorial screens, the MORPHEUS grid screens and the ANGSTROM optimization screen. In this short review, we also discuss the difficulties and advantages associated with the development of protein crystallization screens.

  16. Nonequilibrium diagrammatic technique for Hubbard Green functions

    NASA Astrophysics Data System (ADS)

    Chen, Feng; Ochoa, Maicol A.; Galperin, Michael

    2017-03-01

    We introduce diagrammatic technique for Hubbard nonequilibrium Green functions. The formulation is an extension of equilibrium considerations for strongly correlated lattice models to description of current carrying molecular junctions. Within the technique intra-system interactions are taken into account exactly, while molecular coupling to contacts is used as a small parameter in perturbative expansion. We demonstrate the viability of the approach with numerical simulations for a generic junction model of quantum dot coupled to two electron reservoirs.

  17. Molecular dynamics of ethylene glycol dimethacrylate glass former: influence of different crystallization pathways.

    PubMed

    Viciosa, María T; Correia, Natália T; Salmerón Sánchez, Manuel; Gómez Ribelles, José L; Dionísio, Madalena

    2009-10-29

    The crystallization induced by different thermal treatments of a low molecular weight glass former, ethylene glycol dimethacrylate (EGDMA), was investigated by dielectric relaxation spectroscopy (DRS) and differential scanning calorimetry (DSC). The fully amorphous material, dielectrically characterized for the first time, exhibits three relaxation processes: the alpha-relaxation related to dynamic glass transition whose relaxation rate obeys a Vogel-Fulcher-Tamman-Hesse (VFTH) law and two secondary processes (beta and gamma) with Arrhenius temperature dependence. Therefore, the evaluation of distinct crystallization pathways driven by different thermal histories was accomplished by monitoring the mobility changes in the multiple dielectric relaxation processes. Besides isothermal cold-crystallization, nonisothermal crystallizations coming from both the melt and the glassy states were induced. While an amorphous fraction, characterized by a glass transition, remains subsequent to crystallization from the melt, no alpha-relaxation is detected after the material undergoes nonisothermal cold-crystallization. In the latter, the secondary relaxations persist with a new process that evolves at low frequencies, designated as alpha' that was also detected at advanced crystallization states under isothermal cold-crystallization. Under the depletion of the alpha-relaxation, the beta-process when detected becomes better resolved keeping the same location prior to crystallization leading to a decoupled temperature dependence relative to the alpha-process.

  18. Molecular Recognition Directed Self-Assembly of Supramolecular Liquid Crystals

    DTIC Science & Technology

    1994-06-30

    supramolecular (generated via H-bonding, ionic and electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal...electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal (0h), nematic and re-entrant isotropic phases by...trihydroxybenzoate with either bromoalkanes or with alkoxybenzyloxybenzyl chloride. Variants of these taper shaped side groups were attached to polymer

  19. Solid solution hardening of molecular crystals: tautomeric polymorphs of omeprazole.

    PubMed

    Mishra, Manish Kumar; Ramamurty, Upadrasta; Desiraju, Gautam R

    2015-02-11

    In the context of processing of molecular solids, especially pharmaceuticals, hardness is an important property that often determines the manufacturing steps employed. Through nanoindentation studies on a series of omeprazole polymorphs, in which the proportions of the 5- and 6-methoxy tautomers vary systematically, we demonstrate that solid-solution strengthening can be effectively employed to engineer the hardness of organic solids. High hardness can be attained by increasing lattice resistance to shear sliding of molecular layers during plastic deformation.

  20. Gas permeation in a molecular crystal and space expansion.

    PubMed

    Takasaki, Yuichi; Takamizawa, Satoshi

    2014-05-14

    A novel single-crystal membrane [Cu(II)2(4-F-bza)4(2-mpyz)]n (4-F-bza = 4-fluorobenzoate; 2-mpyz = 2-methylpyrazine) was synthesized and its identical permeability in any crystal direction in the correction for tortuosity proved that gas diffuses inside the channels without detour. H2 permeated by 1.18 × 10(-12) mol m m(-2) s(-1) Pa(-1) with a high selectivity (Fα: 23.5 for H2/CO and 48.0 for H2/CH4) through its 2D-channels having a minimum diameter of 2.6 Å, which is narrower than the Lennard-Jones diameter of H2 (2.827 Å), CO (3.690 Å), and CH4 (3.758 Å). The high rate of permeation was well explained by a modified Knudsen diffusion model based on the space expansion effect, which agrees with the observed permselectivity enhanced for smaller gases in considering the expansion of a channel resulting from the collision of gas molecules or atoms onto the channel wall. An analysis of single-crystal X-ray data showed the expansion order to be H2 > Ar > CH4, which was expected from the permeation analysis. The permselectivity of a porous solid depends on the elasticity of the pores as well as on the diameter of the vacant channel and the size of the target gas.

  1. 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.

  2. 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

    2014-12-09

    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.

  3. Symmetry-adapted-cluster/symmetry-adapted-cluster configuration interaction methodology extended to giant molecular systems: Ring molecular crystals

    NASA Astrophysics Data System (ADS)

    Nakatsuji, Hiroshi; Miyahara, Tomoo; Fukuda, Ryoichi

    2007-02-01

    The symmetry adapted cluster (SAC)/symmetry adapted cluster configuration interaction (SAC-CI) methodology for the ground, excited, ionized, and electron-attached states of molecules was extended to giant molecular systems. The size extensivity of energy and the size intensivity of excitation energy are very important for doing quantitative chemical studies of giant molecular systems and are designed to be satisfied in the present giant SAC/SAC-CI method. The first extension was made to giant molecular crystals composed of the same molecular species. The reference wave function was defined by introducing monomer-localized canonical molecular orbitals (ml-CMO's), which were obtained from the Hartree-Fock orbitals of a tetramer or a larger oligomer within the electrostatic field of the other part of the crystal. In the SAC/SAC-CI calculations, all the necessary integrals were obtained after the integral transformation with the ml-CMO's of the neighboring dimer. Only singles and doubles excitations within each neighboring dimer were considered as linked operators, and perturbation selection was done to choose only important operators. Almost all the important unlinked terms generated from the selected linked operators were included: the unlinked terms are important for keeping size extensivity and size intensivity. Some test calculations were carried out for the ring crystals of up to 10 000-mer, confirming the size extensivity and size intensivity of the calculated results and the efficiency of the giant method in comparison with the standard method available in GAUSSIAN 03. Then, the method was applied to the ring crystals of ethylene and water 50-mers, and formaldehyde 50-, 100-, and 500-mers. The potential energy curves of the ground state and the polarization and electron-transfer-type excited states were calculated for the intermonomer distances of 2.8-100Å. Several interesting behaviors were reported, showing the potentiality of the present giant SAC

  4. 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

  5. Towards first-principles molecular design of liquid crystal-based chemoresponsive systems

    NASA Astrophysics Data System (ADS)

    Roling, Luke T.; Scaranto, Jessica; Herron, Jeffrey A.; Yu, Huaizhe; Choi, Sangwook; Abbott, Nicholas L.; Mavrikakis, Manos

    2016-11-01

    Nematic liquid crystals make promising chemoresponsive systems, but their development is currently limited by extensive experimental screening. Here we report a computational model to understand and predict orientational changes of surface-anchored nematic liquid crystals in response to chemical stimuli. In particular, we use first-principles calculations to evaluate the binding energies of benzonitrile, a model for 4'-pentyl-4-biphenylcarbonitrile, and dimethyl methylphosphonate to metal cation models representing the substrate chemical sensing surface. We find a correlation between these quantities and the experimental response time useful for predicting the response time of cation-liquid crystal combinations. Consideration of charge donation from chemical species in the surface environment is critical for obtaining agreement between theory and experiment. Our model may be extended to the design of improved chemoresponsive liquid crystals for selectively detecting other chemicals of practical interest by choosing appropriate combinations of metal cations with liquid crystals of suitable molecular structure.

  6. 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.

  7. The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis.

    PubMed

    Devedjiev, Yancho D

    2015-02-01

    Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.

  8. 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.

  9. 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.

  10. A molecular dynamics simulation of solvent effects on the crystal morphology of HMX.

    PubMed

    Duan, Xiaohui; Wei, Chunxue; Liu, Yonggang; Pei, Chonghua

    2010-02-15

    The solvent has a large effect on the crystal morphology of the organic explosive compound octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, C(4)H(8)N(8)O(8)). The attachment energy calculations predict a growth morphology in vacuum dominated by (020), (011), (102 ), (111 ) and (100) crystal forms. Molecular dynamics simulations are performed for these crystal faces of HMX in contact with acetone solvent. A corrected attachment energy model, accounting for the surface chemistry and the associated topography (step structure) of the habit crystal plane, is applied to predict the morphological importance of a crystal surface in solvent. From the solvent-effected attachment energy calculations it follows that the (100) face becomes morphologically more important compared with that in vacuum, while the (020) and (102 ) are not visible at all. This agrees well with the observed experimental HMX morphology grown from the acetone solution.

  11. The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis

    PubMed Central

    Devedjiev, Yancho D.

    2015-01-01

    Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed. PMID:25664789

  12. Towards first-principles molecular design of liquid crystal-based chemoresponsive systems

    PubMed Central

    Roling, Luke T.; Scaranto, Jessica; Herron, Jeffrey A.; Yu, Huaizhe; Choi, Sangwook; Abbott, Nicholas L.; Mavrikakis, Manos

    2016-01-01

    Nematic liquid crystals make promising chemoresponsive systems, but their development is currently limited by extensive experimental screening. Here we report a computational model to understand and predict orientational changes of surface-anchored nematic liquid crystals in response to chemical stimuli. In particular, we use first-principles calculations to evaluate the binding energies of benzonitrile, a model for 4′-pentyl-4-biphenylcarbonitrile, and dimethyl methylphosphonate to metal cation models representing the substrate chemical sensing surface. We find a correlation between these quantities and the experimental response time useful for predicting the response time of cation–liquid crystal combinations. Consideration of charge donation from chemical species in the surface environment is critical for obtaining agreement between theory and experiment. Our model may be extended to the design of improved chemoresponsive liquid crystals for selectively detecting other chemicals of practical interest by choosing appropriate combinations of metal cations with liquid crystals of suitable molecular structure. PMID:27804955

  13. A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon tetrachloride mixtures III: nonequilibrium hydrogen-bond dynamics and infrared pump-probe spectra.

    PubMed

    Kwac, Kijeong; Geva, Eitan

    2013-06-27

    We present a mixed quantum-classical molecular dynamics study of the nonequilibrium hydrogen-bond dynamics following vibrational energy relaxation of the hydroxyl stretch in a 10 mol % methanol/carbon tetrachloride mixture and pure methanol. The ground and first-excited energy levels and wave functions are identified with the eigenvalues and eigenfunctions of the hydroxyl's adiabatic Hamiltonian and as such depend parametrically on the configuration of the remaining, classically treated, degrees of freedom. The dynamics of the classical degrees of freedom are in turn governed by forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields and nonlinear mapping relations between the hydroxyl transition frequencies and dipole moments and the electric field along the hydroxyl bond are used, which were previously shown to quantitatively reproduce the experimental infrared steady-state absorption spectra and excited state lifetime [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184; 2012, 116, 2856]. The relaxation from the first-excited state to the ground state is treated as a nonadiabatic transition. Within the mixed quantum-classical treatment, relaxation from the excited state to the ground state is accompanied by a momentum-jump in the classical degrees of freedom, which is in turn dictated by the nonadiabatic coupling vector. We find that the momentum jump leads to breaking of hydrogen bonds involving the relaxing hydroxyl, thereby blue-shifting the transition frequency by more than the Stokes shift between the steady-state emission and absorption spectra. The subsequent nonequilibrium relaxation toward equilibrium on the ground state potential energy surface is thereby accompanied by red shifting of the transition frequency. The signature of this nonequilibrium relaxation process on the pump-probe spectrum is analyzed in detail. The calculated pump-probe spectrum is found

  14. Molecular interactions in bis(2-aminopyridinium) malonate: A crystal isostructural to bis(2-aminopyridinium) maleate crystal

    NASA Astrophysics Data System (ADS)

    Chitra, R.; Choudhury, R. R.; Thiruvenkatam, Vijay; Hosur, M. V.; Guru Row, T. N.

    2012-02-01

    Crystals of a new salt in 2:1 ratio of 2-aminopyridine and malonic acid are grown by slow evaporation. These crystals of bis(2-aminopyridinium) malonate are orthorhombic and belong to the non-centrosymmetric space group, Fdd2 with parameters a = 22.0786(6), b = 23.0218(6), c = 5.5595(1) Å and Z = 8 at 300 K. The crystals are isostructural to those of bis(2-aminopyridinium) maleate, which is a NLO material. The isostructurality index between bis(2-aminopyridinium) maleate and bis(2-aminopyridinium) malonate was also calculated. The hyperpolarizability calculated using semi empirical method MOPAC2009 showed that bis(2-aminopyridinium) malonate has slightly higher β value compared to that of bis(2-aminopyridinium) maleate.

  15. X-Ray Diffraction From Shocked Crystals: Experiments and Predications of Molecular Dynamics Simulations

    SciTech Connect

    Rosolankova, K; Kalantar, D H; Belak, J F; Bringa, E M; Caturla, M J; Hawreliak, J; Holian, B L; Kadau, K; Lomdahl, P S; Germann, T C; Ravelo, R; Sheppard, J; Wark, J S

    2003-09-24

    When a crystal is subjected to shock compression beyond its Hugoniot Elastic Limit (HEL), the deformation it undergoes is composed of elastic and plastic strain components. In situ time-dependent X-ray diffraction, which allows direct measurement of lattice spacings, can be used to investigate such phenomena. This paper presents recent experimental results of X-ray diffraction from shocked fcc crystals. Comparison is made between experimental data and simulated X-ray diffraction using a post-processor to Molecular Dynamics (MD) simulations of shocked fcc crystals.

  16. Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.

    PubMed

    Uto, Takuya; Mawatari, Sho; Yui, Toshifumi

    2014-08-07

    The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.

  17. Molecular design, crystal packing and TFT performance of novel polythiophenes

    NASA Astrophysics Data System (ADS)

    Pan, Hualong

    This thesis presents the design, synthesis and thin-film-transistor performance of a novel series of polythiophenes. The work can be divided into two parts: (1) study of crystal packing of the alkyl side chains in single crystals of model oligothiophene compounds for soluble polythiophenes; (2) exploration of a new series of polythiophenes to achieve favorable crystal packing and hense high mobility for use in organic thin-film-transistors. The first part is based on the crystal packing of a series of compounds derived from the monomer of a high-performance semiconductor, poly(3,3"didodecylquarter-thiophene), PQT-12. A unique conformational polymorphism arising from side chains was observed when the conjugation of backbone of PQT-monomer was extended with phenyl, methyl-phenyl, trifluoromethyl-phenyl. The alkyl side chains preferred tilting towards the middle and then being parallel with the backbones when crystallized from a poor solvent, whereas, the side chains extended out vertically to the backbones when crystallized from a good solvent. The conformational polymorphism of the side chains in the dip-coated film was also studied. The following chapters focus on the design, characterization and TFT performance test of novel polymer semiconductors. A novel and symmetrical poly(4,8-didodecylbenzo[1,2-b:4,5-b']dithiophene) with alkyl side chains tethered to the middle of the large fused backbone was synthesized from 2,6-dibromo-4,8-didodecylbenzo[1,2-b:4,5-b']dithiophene by a dehalogenative coupling polymerization. The thin-film transistors made from this polymer as a semiconductor produced a field-effect mobility of 0.012 cm2V-1s-1 and current on/off ratio ˜2.5x105 after thermal annealing at 140°C. The performance was greatly enhanced (field-effect mobility ˜0.15 cm 2V-1s-1 and current on/off ratio x10 6) when two 3-methyl-thienylenes were incorporated into the backbone, poly(4,8-dodecyl-2,6-bis-(3-methylthiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene). Such good

  18. 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).

  19. A mixed quantum-classical molecular dynamics study of anti-tetrol and syn-tetrol dissolved in liquid chloroform II: infrared emission spectra, vibrational excited-state lifetimes, and nonequilibrium hydrogen-bond dynamics.

    PubMed

    Kwac, Kijeong; Geva, Eitan

    2013-11-21

    The effect of vibrational excitation and relaxation of the hydroxyl stretch on the hydrogen-bond structure and dynamics of stereoselectively synthesized syn-tetrol and anti-tetrol dissolved in deuterated chloroform are investigated via a mixed quantum-classical molecular dynamics simulation. Emphasis is placed on the changes in hydrogen-bond structure upon photoexcitation and the nonequilibrium hydrogen-bond dynamics that follows the subsequent relaxation from the excited to the ground vibrational state. The propensity to form hydrogen bonds is shown to increase upon photoexcitation of the hydroxyl stretch, thereby leading to a sizable red-shift of the infrared emission spectra relative to the corresponding absorption spectra. The vibrational excited state lifetimes are calculated within the framework of Fermi's golden rule and the harmonic-Schofield quantum correction factor, and found to be sensitive reporters of the underlying hydrogen-bond structure. The energy released during the relaxation from the excited to the ground state is shown to break hydrogen bonds involving the relaxing hydroxyl. The spectral signature of this nonequilibrium relaxation process is analyzed in detail.

  20. 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

    SciTech Connect

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

    2016-05-28

    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 (C{sub 20}H{sub 42}, C{sub 24}H{sub 50}, C{sub 26}H{sub 54}, and C{sub 30}H{sub 62}) 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

  1. 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

  2. The mechanical properties of as-grown noncubic organic molecular crystals assessed by nanoindentation

    DOE PAGES

    Taw, Matthew R.; Yeager, John D.; Hooks, Daniel E.; ...

    2017-06-19

    Organic molecular crystals are often noncubic and contain significant steric hindrance within their structure to resist dislocation motion. Plastic deformation in these systems can be imparted during processing (tableting and comminution of powders), and the defect density impacts subsequent properties and performance. This paper measured the elastic and plastic properties of representative monoclinic, orthorhombic, and triclinic molecular crystalline structures using nanoindentation of as-grown sub-mm single crystals. The variation in modulus due to in-plane rotational orientation, relative to a Berkovich tip, was approximately equal to the variation of a given crystal at a fixed orientation. The onset of plasticity occurs consistentlymore » at shear stresses between 1 and 5% of the elastic modulus in all three crystal systems, and the hardness to modulus ratio suggests conventional Berkovich tips do not generate fully self-similar plastic zones in these materials. Finally, this provides guidance for mechanical models of tableting, machining, and property assessment of molecular crystals.« less

  3. Molecular-dynamics simulation of polymer ordering. I. Crystallization from vapor phase

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takashi

    1998-09-01

    We investigate the molecular mechanism of secondary nucleation on a growth surface of the polymer crystal. We adopt a simplified model of polyethylene molecule made of 500 beads connected by springs, and consider the crystallization from a vapor phase neglecting surrounding molecules. A strongly collapsed chain in a vacuum is placed near the infinitely wide lateral surface of the polymer crystal, and the molecular processes of adsorption and ordering are investigated by molecular-dynamics simulation. It is found that the polymer chain is quickly adsorbed, in a stepwise manner, to form a layer structure: A multilayered at lower temperature and a monolayered at higher temperature. The chain segments adsorbed to the surface align parallel with each other and gradually, within several ns, grow into a neat chain folded lamella with predominantly adjacent-reentry folds. The thickness of the lamella sensibly depends on the crystallization temperature and shows a rapid increase around the melting point. It is found that the polymer ordering on the surface is not a sequential process from the chain-end but a rather cooperative process of many segments. Furthermore, we investigate the effect of finite thickness of the substrate crystal, and find that the limited thickness of the substrate gives rise to the frequent generation of chain loops at and the segregation of chain entanglements toward the lamella surfaces.

  4. Molecular engineering of chiral colloidal liquid crystals using DNA origami

    NASA Astrophysics Data System (ADS)

    Siavashpouri, Mahsa; Wachauf, Christian H.; Zakhary, Mark J.; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

    2017-08-01

    Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials.

  5. Crystal and molecular structure of sodium paratungstate 26 hydrate

    SciTech Connect

    Cruywagen, J.J.; Nassibemi, L.R.; Niven, M.L.; Vander Merwe, I.F.

    1986-08-01

    On standing, an acid solution of tungstate yields single crystals of the paratungstate salt Na/sub 10/(H/sub 2/W/sub 12/O/sub 42/ /SUB sd/ /SUP ./ 26H/sub 2/O. The space group is P1, (No. 2), a 11.811(2), b = 12.486(2), c = 12.206(2) A, ..cap alpha.. = 82.29(1), ..beta.. = 115.12(1), ..gamma.. = 113.76(1) /sup 0/, V = 1485.6 A/sup 3/, Z = 1. The structure was solved by direct methods and refined to R = 0.0397, R /SUB w/ = 0.0403 (w = (sigma/sup 2/F)/sup -1/). The 12 WO/sub 6/ octahedra (shared edges and vertices) are distorted from regular geometry; one of the sodium ions exhibits disorder and there is extensive hydrogen bonding between the water molecules and the oxygens of the paratungstate anion.

  6. Molecular field theory for biaxial smectic A liquid crystals

    NASA Astrophysics Data System (ADS)

    To, T. B. T.; Sluckin, T. J.; Luckhurst, G. R.

    2013-10-01

    Thermotropic biaxial nematic phases seem to be rare, but biaxial smectic A phases less so. Here we use molecular field theory to study a simple two-parameter model, with one parameter promoting a biaxial phase and the second promoting smecticity. The theory combines the biaxial Maier-Saupe and McMillan models. We use alternatively the Sonnet-Virga-Durand (SVD) and geometric mean approximations (GMA) to characterize molecular biaxiality by a single parameter. For non-zero smecticity and biaxiality, the model always predicts a ground state biaxial smectic A phase. For a low degree of smectic order, the phase diagram is very rich, predicting uniaxial and biaxial nematic and smectic phases, with the addition of a variety of tricritical and tetracritical points. For higher degrees of smecticity, the region of stability of the biaxial nematic phase is restricted and eventually disappears, yielding to the biaxial smectic phase. Phase diagrams from the two alternative approximations for molecular biaxiality are similar, except inasmuch that SVD allows for a first-order isotropic-biaxial nematic transition, whereas GMA predicts a Landau point separating isotropic and biaxial nematic phases. We speculate that the rarity of thermotropic biaxial nematic phases is partly a consequence of the presence of stabler analogous smectic phases.

  7. Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

    PubMed Central

    Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

    2017-01-01

    Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

  8. 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.

  9. Molecular Optics Nonlinear Optical Processes in Organic and Polymeric Crystals and Films

    DTIC Science & Technology

    1988-04-01

    LAr 9B L Appr 1~ forjIbi1893 2 8 I I IE2 Molecular Optics: Nonlinear Optical Processes in Organic and Polymeric Crystals and Films i Professor A. F...frequency dependent local field factors. While there are various prevalent models (Lorentz- Lorenz, Onsager ) all of them give the field factors in terms of

  10. 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.

  11. Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates

    PubMed Central

    Liu, Chao-Fei; Fan, Heng; Gou, Shih-Chuan; Liu, Wu-Ming

    2014-01-01

    Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction. PMID:24573303

  12. Controlling crystal phases in GaAs nanowires grown by Au-assisted molecular beam epitaxy.

    PubMed

    Dheeraj, D L; Munshi, A M; Scheffler, M; van Helvoort, A T J; Weman, H; Fimland, B O

    2013-01-11

    Control of the crystal phases of GaAs nanowires (NWs) is essential to eliminate the formation of stacking faults which deteriorate the optical and electronic properties of the NWs. In addition, the ability to control the crystal phase of NWs provides an opportunity to engineer the band gap without changing the crystal material. We show that the crystal phase of GaAs NWs grown on GaAs(111)B substrates by molecular beam epitaxy using the Au-assisted vapor-liquid-solid growth mechanism can be tuned between wurtzite (WZ) and zinc blende (ZB) by changing the V/III flux ratio. As an example we demonstrate the realization of WZ GaAs NWs with a ZB GaAs insert that has been grown without changing the substrate temperature.

  13. Cystine growth inhibition through molecular mimicry: a new paradigm for the prevention of crystal diseases.

    PubMed

    Lee, Michael H; Sahota, Amrik; Ward, Michael D; Goldfarb, David S

    2015-05-01

    Cystinuria is a genetic disease marked by recurrent kidney stone formation, usually at a young age. It frequently leads to chronic kidney disease. Treatment options for cystinuria have been limited despite comprehensive understanding of its genetic pathophysiology. Currently available therapies suffer from either poor clinical adherence to the regimen or potentially serious adverse effects. Recently, we employed atomic force miscopy (AFM) to identify L-cystine dimethylester (CDME) as an effective molecular imposter of L-cystine, capable of inhibiting crystal growth in vitro. More recently, we demonstrated CDME's efficacy in inhibiting L-cystine crystal growth in vivo utilizing a murine model of cystinuria. The application of AFM to discover inhibitors of crystal growth through structural mimicry suggests a novel approach to preventing and treating crystal diseases.

  14. Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

    SciTech Connect

    Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

    2016-08-08

    Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

  15. Shape-Memory and Self-Healing Effects in Mechanosalient Molecular Crystals.

    PubMed

    Karothu, Durga Prasad; Weston, James; Desta, Israel Tilahun; Naumov, Panče

    2016-10-12

    The thermosalient crystals of terephthalic acid are extraordinarily mechanically compliant and reversibly shape-shift between two forms with different crystal habits. While the transition of form II to form I is spontaneous, the transition of form I to form II is latent and can be triggered by applying local mechanical stress, whereby crystals leap several centimeters in air. This mechanosalient effect (mechanically stimulated motility) is due to sudden release of strain that has accrued in the crystal of form I, which is a metastable structure at ambient conditions. High-speed optical analysis and serial scanning electron microscopy reveal that the mechanical effect is due to rapid reshaping of crystal domains on a millisecond time scale triggered by mechanical stimulation. Mechanically pre-deformed crystals taken over the thermal phase transition exhibit memory effects and partially regain their shape, while cracked, sliced, or otherwise damaged crystals tend to recover their macroscopic integrity by restorative action of intermolecular π-π interactions in a manner which resembles the behavior of shape-memory and self-healing polymers. These observations provide additional evidence that the thermo-/photo-/mechanosalient effects are macroscopic manifestations of martensitic-type transitions in molecular solids.

  16. Uncovering molecular details of urea crystal growth in the presence of additives.

    PubMed

    Salvalaglio, Matteo; Vetter, Thomas; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

    2012-10-17

    Controlling the shape of crystals is of great practical relevance in fields like pharmacology and fine chemistry. Here we examine the paradigmatic case of urea which is known to crystallize from water with a needle-like morphology. To prevent this undesired effect, inhibitors that selectively favor or discourage the growth of specific crystal faces can be used. In urea the most relevant faces are the {001} and the {110} which are known to grow fast and slow, respectively. The relevant growth speed difference between these two crystal faces is responsible for the needle-like structure of crystals grown in water solution. To prevent this effect, additives are used to slow down the growth of one face relative to another, thus controlling the shape of the crystal. We study the growth of fast {001} and slow {110} faces in water solution and the effect of shape controlling inhibitors like biuret. Extensive sampling through molecular dynamics simulations provides a microscopic picture of the growth mechanism and of the role of the additives. We find a continuous growth mechanism on the {001} face, while the slow growing {110} face evolves through a birth and spread process, in which the rate-determining step is the formation on the surface of a two-dimensional crystalline nucleus. On the {001} face, growth inhibitors like biuret compete with urea for the adsorption on surface lattice sites; on the {110} face instead additives cannot interact specifically with surface sites and play a marginal sterical hindrance of the crystal growth. The free energies of adsorption of additives and urea are evaluated with advanced simulation methods (well-tempered metadynamics) allowing a microscopic understanding of the selective effect of additives. Based on this case study, general principles for the understanding of the anisotropic growth of molecular crystals from solutions are laid out. Our work is a step toward a rational development of novel shape-affecting additives.

  17. Molecular-field-theory approach to the Landau theory of liquid crystals: uniaxial and biaxial nematics.

    PubMed

    Luckhurst, Geoffrey R; Naemura, Shohei; Sluckin, Timothy J; Thomas, Kenneth S; Turzi, Stefano S

    2012-03-01

    Nematic liquid crystal phase diagrams in temperature-biaxiality space are usually complex. We construct a Landau theory based on the analogous molecular-field theory for orthorhombic biaxial nematic fluids. A formal procedure yields coefficients (some of which, unusually, can be tensorial) in this Landau expansion, correctly predicts the complete set of invariants formed from the ordering tensors, and avoids ad hoc parametrization of the molecular biaxiality. By regularizing the Landau expansion to avoid unwanted order parameter divergences at low temperatures, we predict phase behavior over the whole range of biaxiality. The resulting phase diagrams have the same topology as those of molecular-field theory.

  18. 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

  19. Molecular and crystal structure of anhydrous zirconium perchlorate

    SciTech Connect

    Genkina, E.A.; Babaeva, V.P.; Rosolovskii, V.Ya.

    1985-08-01

    An x-ray diffraction investigation (diffractometer, Mo K..cap alpha.., graphite monochromator, omega scan technique, Theta less than or equal to 30/sup 0/, 1060 reflections, least-squares method in the anisotropic approximation to R = 0.058) of anhydrous zirconium perchlorate has been carried out. The crystals of Zr(Cl0/sub 4/)/sub 4/ are monoclinic: ..cap alpha.. = 12.899(3), b = 13.188(7), c = 7.937(3) A, ..gamma.. = 107.91/sup 0/, Z = 4, space group Bb. The structure has an island character and is built up from isolated Zr(ClO/sub 4/)/sub 4/ molecules. The Zr atom is surrounded by eight O atoms in four bidentate perchlorato groups. The Zr-O distances lie in the range from 2.13 to 2.23 A, averaging 2.19 A. The eight-vertex polyhedron around Zr is the mmmm steroisomer of a dodecahedron. The centers of the perchlorato groups are located at the vertices of flattened tetrahedron. The ClO/sub 4/ groups have a distorted tetrahedral structure, and the mean length of the Cl-O/sub b/ bonds (1.50 A) is 0.11 A greater than the mean length of the Cl-O/sub t/ bonds, pointing out the essentially covalent character of the bonds of the perchlorato groups with the central Zr atom.

  20. Direct evidence of the molecular interaction propagation in the phase transition of liquid crystals

    NASA Astrophysics Data System (ADS)

    Katayama, Kenji; Sato, Takahiro; Kuwahara, Shota

    2016-09-01

    The molecular interaction sometimes propagates in a collective manner, reaching for a long distance on the order of millimeters. Such interactions have been well known in the field of strongly-correlated electron systems in a beautiful crystal interleaved by donor and acceptor layers, induced by photo-stimulus. The other examples can be found in liquid crystals (LCs), which could be found in many places in nature such as bio-membrane. Different from crystals, LCs features "softness", which enables it to be a curved structure such as a cell. In LCs, even a small molecular change would trigger the overall structural change by the propagation of the molecular interaction. Here we will show, for the first time, how long and how fast the molecular interaction propagates in LCs. The patterned phase transition was induced in a LC, causing the phase transition propagation in a controlled way and the propagation was measured with an time-resolved optical technique, called the transient grating. A LC sample doped with azobenzene was put into a thermally controlled LC cell. A grating pattern of a pulse light with 355 nm was impinged to the LC cell, and the light was absorbed by the dyes, releasing heat or photomechanical motion. We could observe the fringe spacing dependence on the phase transition response, which indicates that phase transition was delayed as the fringe spacing due to the delay by the phase transition propagation. This is the first direct evidence of the molecular interaction propagation of the LC molecules.

  1. 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

  2. Molecular imprinted photonic crystal hydrogels for the rapid and label-free detection of imidacloprid.

    PubMed

    Wang, Xuan; Mu, Zhongde; Liu, Ran; Pu, Yuepu; Yin, Lihong

    2013-12-15

    A novel sensor for the rapid and label-free detection of imidacloprid was developed based on the combination of a colloidal crystal templating method and a molecular imprinting technique. The molecular imprinted photonic hydrogel film was prepared with methacrylic acid as monomers, ethylene glycol dimethylacrylate as cross-linkers and imidacloprid as imprinting template molecules. When the colloidal crystal template and the molecularly imprinted template was removed, the resulted MIPH film possessed a highly ordered three-dimensional macroporous structure with nanocavities. The response of the MIPH film to imidacloprid in aqueous solution can be detected through a readable Bragg diffraction red shift. When the concentration of imidacloprid increased from 10(-13) to 10(-7) g/mL, the Bragg diffraction peak shifted from 551 to 589 nm, while there were no obvious peak shifts for thiamethoxam and acetamiprid. This sensor which comprises of no label techniques and expensive instruments has potential application for the detection of trace imidacloprid.

  3. Effect of annealing on the nonequilibrium carrier lifetime in GaAs grown at low temperatures

    SciTech Connect

    Pastor, A. A.; Prokhorova, U. V.; Serdobintsev, P. Yu.; Chaldyshev, V. V. Yagovkina, M. A.

    2013-08-15

    GaAs samples grown by molecular-beam epitaxy at low (230 Degree-Sign C) temperatures are investigated. One of the samples is subjected to aftergrowth annealing at 600 Degree-Sign C. Using an unconventional pump-probe scheme for measuring the dynamic variation in the light refractive index, the nonequilibrium charge-carrier lifetime (275 {+-} 30 fs before annealing) is determined. Such a short carrier lifetime in the unannealed material is due to the high concentration of point defects, mainly As{sub Ga} antisite defects. According to X-ray diffraction and steady-state optical absorption data, the As{sub Ga} concentration in the samples is 3 Multiplication-Sign 10{sup 19} cm{sup -3}, which corresponds to an arsenic excess of 0.26 at %. Upon annealing at 600 Degree-Sign C, the superstoichiometric As defects self-organize and form As nanoinclusions in the GaAs crystal matrix. It is shown that in this case the nonequilibrium charge-carrier lifetime increases to 452 {+-} 5 fs. This lifetime is apparently ensured by the capture of non-equilibrium charge carriers at metal As nanoinclusions.

  4. Interplay between Long-Range Crystal Order and Short-Range Molecular Interactions Tunes Carrier Mobility in Liquid Crystal Dyes

    PubMed Central

    2017-01-01

    We investigated the influence of molecular packing on the optical and electrical properties of the liquid crystalline dye 4,7-bis[5-(2-fluoro-4-pentyl-phenyl)-2-thienyl]-2,1,3-benzothiadiazole (FPPTB). FPPTB is crystalline at room temperature, exhibits a nematic phase at temperatures above 149 °C and is in an isotropic melt at temperatures above 230 °C. Solution processed FPPTB films were subject to thermal annealing through these phase transition temperatures and characterized with X-ray diffraction and polarized optical microscopy. Cooling FPPTB films from the nematic and isotropic phases increased crystal domain size, but also induced local structural variations in the molecular packing of crystalline FPPTB. The decrease in long-range order was correlated with an increase in short-range π–π interactions, leading to changes in molecular aggregation which persisted even when the FPPTB films were cooled to room temperature. Annealing-induced changes in molecular aggregation were confirmed with optical spectroscopy. The carrier mobility in FPPTB films increased over 2 orders of magnitude from (2.2 ± 0.4) × 10–5 cm2 V–1 s–1 in as-spun films to μ = (5.0 ± 0.8) × 10–3 cm2 V–1 s–1 in films cooled from the isotropic melt. We discuss the relationship between thermal stability and high carrier mobility values in terms of the interplay between long-range molecular order and increased π–π interactions between molecular pairs in the FPPTB film. PMID:28139915

  5. 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.

  6. 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%.

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

    PubMed Central

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

    2016-01-01

    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

  8. 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.

  9. The nature of singlet excitons in oligoacene molecular crystals

    SciTech Connect

    Yamagata, H.; Norton, J.; Hontz, E.; Olivier, Y.; Beljonne, D.; Bredas, J. L.; Silbey, R. J.; Spano, F. C.

    2011-01-01

    A theory for polarized absorption in crystalline oligoacenes is presented, which includes Frenkel exciton coupling, the coupling between Frenkel and charge-transfer (CT) excitons, and the coupling of all neutral and ionic excited states to the dominant ring-breathing vibrational mode. For tetracene, spectra calculated using all Frenkel couplings among the five lowest energy molecular singlet states predict a Davydov splitting (DS) of the lowest energy (0–0) vibronic band of only -32 cm-1, far smaller than the measured value of 631 cm-1 and of the wrong sign--a negative sign indicating that the polarizations of the lower and upper Davydov components are reversed from experiment. Inclusion of Frenkel-CT coupling dramatically improves the agreement with experiment, yielding a 0–0 DS of 601 cm-1 and a nearly quantitative reproduction of the relative spectral intensities of the 0–n vibronic components. Our analysis also shows that CT mixing increases with the size of the oligoacenes. We discuss the implications of these results on exciton dissociation and transport.

  10. Tracking and Motion Analysis of Crack Propagations in Crystals for Molecular Dynamics

    SciTech Connect

    Tsap, L V; Duchaineau, M; Goldgof, D B

    2001-05-14

    This paper presents a quantitative analysis for a discovery in molecular dynamics. Recent simulations have shown that velocities of crack propagations in crystals under certain conditions can become supersonic, which is contrary to classical physics. In this research, they present a framework for tracking and motion analysis of crack propagations in crystals. It includes line segment extraction based on Canny edge maps, feature selection based on physical properties, and subsequent tracking of primary and secondary wavefronts. This tracking is completely automated; it runs in real time on three 834-image sequences using forty 250 MHZ processors. Results supporting physical observations are presented in terms of both feature tracking and velocity analysis.

  11. Four- and five-component molecular solids: crystal engineering strategies based on structural inequivalence.

    PubMed

    Mir, Niyaz A; Dubey, Ritesh; Desiraju, Gautam R

    2016-03-01

    A synthetic strategy is described for the co-crystallization of four- and five-component molecular crystals, based on the fact that if any particular chemical constituent of a lower cocrystal is found in two different structural environments, these differences may be exploited to increase the number of components in the solid. 2-Methylresorcinol and tetramethylpyrazine are basic template molecules that allow for further supramolecular homologation. Ten stoichiometric quaternary cocrystals and one quintinary cocrystal with some solid solution character are reported. Cocrystals that do not lend themselves to such homologation are termed synthetic dead ends.

  12. Molecular and crystal structure of liquid crystalline p-octyloxyphenyl p Prime -pentyloxybenzoate

    SciTech Connect

    Konstantinov, I. I.; Lermontova, E. Kh.; Kuz'mina, L. G.

    2011-01-15

    The crystal and molecular structure of p-octyloxyphenyl p Prime -pentyloxybenzoate C{sub 5}H{sub 11}-O-C{sub 6}H{sub 4}-C(O)-O-C{sub 6}H{sub 4}-O-C{sub 8}H{sub 17}, which forms a nematic mesophase upon melting, was determined by X-ray diffraction. There is one system of weak directional intermolecular C-H Horizontal-Ellipsis {pi} interactions responsible for the formation of the nematic phase in these crystals.

  13. A molecular dynamics study of ferroelectric nanoparticles immersed in a nematic liquid crystal.

    PubMed

    Pereira, M S S; Canabarro, A A; de Oliveira, I N; Lyra, M L; Mirantsev, L V

    2010-01-01

    A large number of interesting phenomena related to the insertion of colloidal particles in liquid crystals (LC) have recently been reported. Here, we investigate effects caused by the addition of spherically shaped ferroelectric nanoparticles to a nematic liquid crystal. Using molecular dynamics (MD) simulations, the density of LC molecules, the orientational order parameter, and the polar and azimuthal angle profiles are calculated as functions of the distance to the center of the immersed nanoparticle for different temperatures of the system. We observe that the assembly of ferroelectric nanoparticles enhances the nematic order in the LC medium changing many properties of its host above the nematic-isotropic transition temperature T (*) (NI) .

  14. Hedgehog-Like Upconversion Crystals: Controlled Growth and Molecular Sensing at Single-Particle Level.

    PubMed

    Liu, Xiaowang; Li, Xiyan; Qin, Xian; Xie, Xiaoji; Huang, Ling; Liu, Xiaogang

    2017-10-01

    Topological control of nanostructures plays a crucial role in understanding the crystal growth process at the nanometer length scale. Here, the scalable synthesis of upconversion materials with distinct hedgehog-like morphologies by a seed-mediated synthetic procedure is reported. It is demonstrated that a close match in the crystal lattice between the core and shell components is essential for synthesizing such hierarchical nanostructures. These optical nanomaterials also enable the development of a single-particle-based platform for high-sensitivity molecular sensing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Crystal and molecular structure of 1α-hydroxylated analogs of vitamins D

    NASA Astrophysics Data System (ADS)

    Kolodziejski, Waclaw; Woźniak, Krzysztof; Herold, Joanna; Dominiak, Paulina M.; Kutner, Andrzej

    2005-01-01

    Structures of two 1α-hydroxylated analogs of vitamins D, 1α-hydroxycholecalciferol and 1α-hydroxyergocalciferol, were solved and refined using single crystal X-ray diffraction. Crystallographic results are verified by 13C CP/MAS NMR. This method provided also information on molecular mobility of analogs. In the crystal state, both molecules adopt exclusively a chair β-conformation of the 6-member ring A. It has been suggested that this conformation is preferred, when vitamin D molecules participate in hydrogen bonding. This is consistent with the earlier hypothesis that the β-conformers are involved in the interaction of vitamins D with their receptors.

  16. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    SciTech Connect

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  17. Molecular Dynamics in a Liquid Crystal with Reentrant Mesophases

    NASA Astrophysics Data System (ADS)

    Sebastião, P. J.; Ribeiro, A. C.; Nguyen, H. T.; Noack, F.

    1995-11-01

    It is well known that liquid crystalline compounds with a cyano terminal group can present peculiar polymorphisms in particular different types of smectic A mesophases and a reentrant behaviour for both nematic and smectic A mesophases. In this work we study by proton NMR relaxation the influence of these features on the molecular dynamics of the compound 4-cyanobenzoate-4'-octylbenzoyloxyphenyl (DB8CN Sym) in its nematic (N), partial bilayer smectic A (SAd), reentrant nematic (Nre) and reentrant smectic A (SA1) mesophases. Standard and fast field-cycling techniques were used for our spin-lattice relaxation's study over a broad frequency range of 6 decades (200 Hz up to 300 MHz). It was found that the molecular dynamics in the nematic mesophases is rather different from the molecular dynamics in the smectic A mesophases. However, the reentrant aspect present in both nematic and smectic A states is not associated to a major difference on the molecular dynamics of the nematic and reentrant nematic or smectic and reentrant smectic A mesophases. Order director fluctuations and rotations/reorientations are the most important relaxation mechanisms in the nematic mesophases in the lower and higher frequency limits, respectively, while self-diffusion has a very small contribution to the overall relaxation. As for the smectic A mesophases, self-diffusion and rotations/reorientations are the predominant relaxation mechanisms for frequencies above 20 kHz. The collective motions, which for these mesophases have to be associated with layer undulations with the frequency law T_1sim ν, are only important to the spin-lattice relaxation on the low part of the frequency spectrum (ν<10 kHz). The inclusion in the relaxation study of a contribution from the cross-relaxation between protons and nitrogen nuclei improves the quality of the 1/T_1 data fits in both kinds of mesophases. The combined study of the molecular dynamics in the N, SAd, Nre and SA1 mesophases of DB8CN Sym reveals

  18. In situ observation of mono-molecular growth steps on aqueous solution grown crystals and the transport of molecules to the crystals

    NASA Technical Reports Server (NTRS)

    Tsukamoto, Katsuo

    1987-01-01

    Direct in situ observation of mono-molecular growth steps on a crystal growing in an aqueous solution became possible. The combination of this method with high resolution Schlieren methods or interferometry, permits the growth mechanism of crystals to be investigated directly. Since the observation of growth steps on crystals is the most direct and sensitive way for investigating a crystal growth mechanism, it would contribute to revealing fundamental differences between the growth in space and on Earth. The method was recently extended to in situ observation of the growth processes at high temperatures (1800K).

  19. Phenomenological model of spin crossover in molecular crystals as derived from atom-atom potentials.

    PubMed

    Sinitskiy, Anton V; Tchougréeff, Andrei L; Dronskowski, Richard

    2011-08-07

    The method of atom-atom potentials, previously applied to the analysis of pure molecular crystals formed by either low-spin (LS) or high-spin (HS) forms (spin isomers) of Fe(II) coordination compounds (Sinitskiy et al., Phys. Chem. Chem. Phys., 2009, 11, 10983), is used to estimate the lattice enthalpies of mixed crystals containing different fractions of the spin isomers. The crystals under study were formed by LS and HS isomers of Fe(phen)(2)(NCS)(2) (phen = 1,10-phenanthroline), Fe(btz)(2)(NCS)(2) (btz = 5,5',6,6'-tetrahydro-4H,4'H-2,2'-bi-1,3-thiazine), and Fe(bpz)(2)(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2'-bipyridine). For the first time the phenomenological parameters Γ pertinent to the Slichter-Drickamer model (SDM) of several materials were independently derived from the microscopic model of the crystals with use of atom-atom potentials of intermolecular interaction. The accuracy of the SDM was checked against the numerical data on the enthalpies of mixed crystals. Fair semiquantitative agreement with the experimental dependence of the HS fraction on temperature was achieved with use of these values. Prediction of trends in Γ values as a function of chemical composition and geometry of the crystals is possible with the proposed approach, which opens a way to rational design of spin crossover materials with desired properties.

  20. A study of the solvent effect on the morphology of RDX crystal by molecular modeling method.

    PubMed

    Chen, Gang; Xia, Mingzhu; Lei, Wu; Wang, Fengyun; Gong, Xuedong

    2013-12-01

    Molecular dynamics simulations have been performed to investigate the effect of acetone solvent on the crystal morphology of RDX. The results show that the growth morphology of RDX crystal in vacuum is dominated by the (111), (020), (200), (002), and (210) faces using the BFDH laws, and (111) face is morphologically the most important. The analysis of surface structures of RDX crystal indicates that (020) face is non-polar, while (210), (111), (002), and (200) faces are polar among which (210) face has the strongest polarity. The interaction between acetone solvent and each RDX crystal face is different, and the order of binding energy on these surfaces is (210) > (111) > (002) > (200) > (020). The analysis of interactions among RDX and acetone molecules reveal that the system nonbond interactions are primary strong van der Waals and electrostatic interactions containing π-hole interactions, the weak hydrogen bond interactions are also existent. The effect of acetone on the growth of RDX crystal can be evaluated by comparing the binding energies of RDX crystalline faces. It can be predicted that compared to that in vacuum, in the process of RDX crystallization from acetone, the morphological importance of (210) face is increased more and (111) face is not the most important among RDX polar surfaces, while the non-polar (020) face probably disappears. The experimentally obtained RDX morphology grown from acetone is in agreement with the theoretical prediction.

  1. Evaluating the effects of loading parameters on single-crystal slip in tantalum using molecular mechanics

    NASA Astrophysics Data System (ADS)

    Alleman, Coleman; Ghosh, Somnath; Luscher, D. J.; Bronkhorst, Curt A.

    2014-01-01

    This study is aimed at developing a physics-based crystal plasticity finite element model for body-centred cubic (BCC) metals, through the introduction of atomic-level deformation information from molecular dynamics (MD) investigations of dislocation motion at the onset of plastic flow. In this study, three critical variables governing crystal plasticity mediated by dislocation motion are considered. MD simulations are first performed across a range of finite temperatures up to 600K to quantify the temperature dependence of critical stress required for slip initiation. An important feature of slip in BCC metals is that it is not solely dependent on the Schmid law measure of resolved shear stress, commonly employed in crystal plasticity models. The configuration of a screw dislocation and its subsequent motion is studied under different load orientations to quantify these non-Schmid effects. Finally, the influence of strain rates on thermal activation is studied by inducing higher stresses during activation at higher applied strain rates. Functional dependence of the critical resolved shear stress on temperature, loading orientation and strain rate is determined from the MD simulation results. The functional forms are derived from the thermal activation mechanisms that govern the plastic behaviour and quantification of relevant deformation variables. The resulting physics-based rate-dependent crystal plasticity model is implemented in a crystal plasticity finite element code. Uniaxial simulations reveal orientation-dependent tension-compression asymmetry of yield that more accurately represents single-crystal experimental results than standard models.

  2. Layered and molecular-structural control in polyoxomolybdate hybrid crystals by surfactant chain length

    NASA Astrophysics Data System (ADS)

    Ito, Takeru; Nakagawa, Masashi; Kobayashi, Jun; Matsumoto, Takashi; Otobe, Saki; Naruke, Haruo

    2016-02-01

    Polyoxomolybdate-surfactant hybrid layered crystals were synthesized by using single-tailed alkyltrimethylammonium ([CnH2n+1N(CH3)3]+ (Cn), n = 8, 10, 12, 14, 16, and 18) cations. The crystal structures consisted of alternate stacking of octamolybdate ([Mo8O26]4-, Mo8) anionic layers and surfactant cationic layers. The layered distance of the hybrid crystals became longer from 18.5 Å to 26.5 Å with an increase in alkyl chain length. Interestingly, the molecular structures of Mo8, which has several isomers, depended on the alkyl chain length of the employed surfactants. Shorter surfactant (C8 and C10) formed hybrid crystals containing β-type Mo8 isomer, while surfactant with longer alkyl chain (C12, C14, C16, and C18) gave crystals containing δ-type Mo8 isomer. This structural controllability will lead to the precise functional control in the polyoxomolybdate-surfactant hybrid layered crystals.

  3. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  4. Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

    PubMed

    Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

    2016-11-15

    Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic

  5. A quartz crystal microbalance sensor based on mussel-inspired molecularly imprinted polymer.

    PubMed

    Zhou, Wen-Hui; Tang, Shui-Fen; Yao, Qiu-Hong; Chen, Fa-Rong; Yang, Huang-Hao; Wang, Xiao-Ru

    2010-10-15

    In this work, we describe a simple, inexpensive and fast method for the generation of molecularly imprinted polymer (MIP) film on quartz crystal microbalance (QCM) crystals using mussel-inspired polymer. Commonly known as a neurotransmitter, dopamine is also a small-molecule mimic of the adhesive proteins of mussels. Polymerization of dopamine in the presence of template molecule (1,3,5-pentanetricarboxylic acid, an analogue of domoic acid, in this case) could produce an adherent molecularly imprinted polydopamine film coating on QCM crystals. Advantages, such as high hydrophilicity, high biocompatibility and controllable thickness, make this molecularly imprinted polydopamine film an attractive recognition element for sensors. Selective rebinding of domoic acid on mussel-inspired molecularly imprinted polymer (m-MIP) coated crystal was observed as a frequency shift quantified by piezoelectric microgravimetry with the QCM system. The decreasing frequency shows a good linear relationship with the concentration of domoic acid. The quantitation limit of domoic acid was 5 ppb with the linear range of 0-100 ppb. The QCM sensor has high selectivity and was able to distinguish domoic acid from its analogous p-phthalic acid and o-phthalic acid owing to the molecular imprinting effect. In addition, the practical analytical performance of the sensor was examined by evaluating the detection of domoic acid in mussel extracts with satisfactory results. It is envisaged that m-MIP could be suitable as recognition element for sensors and the proposed m-MIP QCM sensor could be employed to detect analyte of interest in complex matrices. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Understanding molecular crystals with dispersion-inclusive density functional theory: pairwise corrections and beyond.

    PubMed

    Kronik, Leeor; Tkatchenko, Alexandre

    2014-11-18

    CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids.

  7. Non-equilibrium dynamics from RPMD and CMD

    NASA Astrophysics Data System (ADS)

    Welsch, Ralph; Song, Kai; Shi, Qiang; Althorpe, Stuart C.; Miller, Thomas F.

    2016-11-01

    We investigate the calculation of approximate non-equilibrium quantum time correlation functions (TCFs) using two popular path-integral-based molecular dynamics methods, ring-polymer molecular dynamics (RPMD) and centroid molecular dynamics (CMD). It is shown that for the cases of a sudden vertical excitation and an initial momentum impulse, both RPMD and CMD yield non-equilibrium TCFs for linear operators that are exact for high temperatures, in the t = 0 limit, and for harmonic potentials; the subset of these conditions that are preserved for non-equilibrium TCFs of non-linear operators is also discussed. Furthermore, it is shown that for these non-equilibrium initial conditions, both methods retain the connection to Matsubara dynamics that has previously been established for equilibrium initial conditions. Comparison of non-equilibrium TCFs from RPMD and CMD to Matsubara dynamics at short times reveals the orders in time to which the methods agree. Specifically, for the position-autocorrelation function associated with sudden vertical excitation, RPMD and CMD agree with Matsubara dynamics up to O (t4) and O (t1) , respectively; for the position-autocorrelation function associated with an initial momentum impulse, RPMD and CMD agree with Matsubara dynamics up to O (t5) and O (t2) , respectively. Numerical tests using model potentials for a wide range of non-equilibrium initial conditions show that RPMD and CMD yield non-equilibrium TCFs with an accuracy that is comparable to that for equilibrium TCFs. RPMD is also used to investigate excited-state proton transfer in a system-bath model, and it is compared to numerically exact calculations performed using a recently developed version of the Liouville space hierarchical equation of motion approach; again, similar accuracy is observed for non-equilibrium and equilibrium initial conditions.

  8. Non-equilibrium dynamics from RPMD and CMD.

    PubMed

    Welsch, Ralph; Song, Kai; Shi, Qiang; Althorpe, Stuart C; Miller, Thomas F

    2016-11-28

    We investigate the calculation of approximate non-equilibrium quantum time correlation functions (TCFs) using two popular path-integral-based molecular dynamics methods, ring-polymer molecular dynamics (RPMD) and centroid molecular dynamics (CMD). It is shown that for the cases of a sudden vertical excitation and an initial momentum impulse, both RPMD and CMD yield non-equilibrium TCFs for linear operators that are exact for high temperatures, in the t = 0 limit, and for harmonic potentials; the subset of these conditions that are preserved for non-equilibrium TCFs of non-linear operators is also discussed. Furthermore, it is shown that for these non-equilibrium initial conditions, both methods retain the connection to Matsubara dynamics that has previously been established for equilibrium initial conditions. Comparison of non-equilibrium TCFs from RPMD and CMD to Matsubara dynamics at short times reveals the orders in time to which the methods agree. Specifically, for the position-autocorrelation function associated with sudden vertical excitation, RPMD and CMD agree with Matsubara dynamics up to O(t(4)) and O(t(1)), respectively; for the position-autocorrelation function associated with an initial momentum impulse, RPMD and CMD agree with Matsubara dynamics up to O(t(5)) and O(t(2)), respectively. Numerical tests using model potentials for a wide range of non-equilibrium initial conditions show that RPMD and CMD yield non-equilibrium TCFs with an accuracy that is comparable to that for equilibrium TCFs. RPMD is also used to investigate excited-state proton transfer in a system-bath model, and it is compared to numerically exact calculations performed using a recently developed version of the Liouville space hierarchical equation of motion approach; again, similar accuracy is observed for non-equilibrium and equilibrium initial conditions.

  9. The Role of Anharmonicity and Nuclear Quantum Effects in the Pyridine Molecular Crystal: An ab initio Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto

    Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

  10. Investigation of the linear and second-order nonlinear optical properties of molecular crystals within the local field theory.

    PubMed

    Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

    2013-09-21

    In this paper it is shown that modest calculations combining first principles evaluations of the molecular properties with electrostatic interaction schemes to account for the crystal environment effects are reliable for predicting and interpreting the experimentally measured electric linear and second-order nonlinear optical susceptibilities of molecular crystals within the experimental error bars. This is illustrated by considering two molecular crystals, namely: 2-methyl-4-nitroaniline and 4-(N,N-dimethylamino)-3-acetamidonitrobenzene. Three types of surrounding effects should be accounted for (i) the polarization due to the surrounding molecules, described here by static electric fields originating from their electric dipoles or charge distributions, (ii) the intermolecular interactions, which affect the geometry and particularly the molecular conformation, and (iii) the screening of the external electric field by the constitutive molecules. This study further highlights the role of electron correlation on the linear and nonlinear responses of molecular crystals and the challenge of describing frequency dispersion.

  11. Schiff bases or glycosylamines: crystal and molecular structures of four derivatives of D-mannose.

    PubMed

    Ojala, W H; Ostman, J M; Ojala, C R

    2000-06-02

    Crystal and molecular structures of four derivatives of D-mannose are described. Each could exist as either an open-chain Schiff base or as a glycosylamine in the solid state. The derivative formed upon reaction of D-mannose with hydroxylamine is an open-chain oxime, but those formed upon reaction with semicarbazide, aniline, and p-chloroaniline are glycosylamines. The oxime, which crystallizes as the syn-(E) isomer, has a fully extended carbon chain. The glycosylamines are all beta-pyranoses. The packing arrangement of the oxime involves 'head-to-tail' hydrogen bonding. The semicarbazide derivative, which crystallizes as a dihydrate, features a hydrogen-bonded intramolecular bridge formed by the two water molecules and linking O-6 to the carbonyl oxygen atom. The packing arrangements of the aniline and p-chloroaniline derivatives differ from each other but are nevertheless closely related by similar hydrogen-bonding interactions.

  12. Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Zhou, Li-Li; Liu, Rang-Su; Tian, Ze-An; Liu, Hai-Rong; Hou, Zhao-Yang; Peng, Ping

    2016-08-01

    The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90-150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule.

  13. Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

    NASA Astrophysics Data System (ADS)

    Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

    2015-04-01

    The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

  14. Reflection of light by anisotropic molecular crystals including exciton-polaritons and spatial dispersion.

    PubMed

    Meskers, Stefan C J; Lakhwani, Girish

    2016-11-21

    A theory for the reflection of light by molecular crystals is described, which reproduces the minimum within the reflection band that is observed experimentally. The minimum in reflection is related to the excitation of polaritons in the crystal. The theory involves reformulation of the boundary conditions for electromagnetic waves at the interface between vacuum and material. The material is modeled by a cubic lattice of oriented Lorentz oscillators. By requiring uniformity of gauge of the electromagnetic potential across the interface between vacuum and the dipole lattice, the need for additional boundary conditions is obviated. The frequency separation between the maxima in reflectance on both sides of the minimum allows for the extraction of a plasma frequency. The plasma frequencies extracted from reflection spectra are compared to the plasma frequencies calculated directly from structural data on the crystals and the oscillator strengths of the constituent molecules. A good agreement between extracted and calculated plasma frequency is obtained for a set of 11 dye molecules.

  15. Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study

    PubMed Central

    Zhou, Li-li; Liu, Rang-su; Tian, Ze-an; Liu, Hai-rong; Hou, Zhao-yang; Peng, Ping

    2016-01-01

    The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90–150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule. PMID:27526660

  16. The Crystal and Molecular Structure of Acetatochlorobis(4-methylpyridine)oxovanadium (IV)

    NASA Technical Reports Server (NTRS)

    Schupp, John D.; Hepp, Aloysius F.; Duraj, Stan A.; Richman, Robert M.; Fanwick, Phillip E.; Hakimzadeh, Roshanak (Technical Monitor)

    2001-01-01

    The crystal and molecular structure of the title compound, VOCl(O2CCH3)(4-CH3C5H4N)2, has been determined by single-crystal x-ray diffraction. The material crystallizes in the space group P 1(bar) (#2) with a = 7.822(2), b = 8.023(l), c = 14.841(2) Angstroms, alpha = 99.73(l), beta = 91.41(l), and gamma = 117.13(l). The coordination geometry around the vanadium is a highly distorted octahedron. The molecule is remarkable for being a monomeric oxovanadium (IV) carboxylate. A generalized synthetic strategy is proposed for the preparation of oxovanadium (IV) monomers.

  17. Molecular rotation-vibration dynamics of low-symmetric hydrate crystal in the terahertz region.

    PubMed

    Fu, Xiaojian; Wu, Hongya; Xi, Xiaoqing; Zhou, Ji

    2014-01-16

    The rotational and vibrational dynamics of molecules in copper sulfate pentahydrate crystal are investigated with terahertz dielectric spectra. It is shown that the relaxation-like dielectric dispersion in the low frequency region is related to the reorientation of water molecules under the driving of terahertz electric field, whereas the resonant dispersion can be ascribed to lattice vibration. It is also found that, due to the hydrogen-bond effect, the vibrational mode at about 1.83 THz along [-111] direction softens with decreasing temperature, that is, the crystal expands in this direction when cooled. On the contrary, the mode hardens in the direction perpendicular to [-111] during the cooling process. This contributes to the further understanding of the molecular structure and bonding features of hydrate crystals.

  18. Molecular dynamics simulations of crystal growth from melted silicon: Defect formation processes

    SciTech Connect

    Ishimaru, Manabu; Motooka, Teruaki

    1999-07-01

    Molecular dynamics calculations have been performed to simulate crystal growth from melted silicon (Si) and defect formation processes based on the ordinary Langevin equation employing the Tersoff interatomic potential. The findings of this investigation are as follows: (1) The [110] bonds at the solid-liquid interface induce the eclipsed configurations or hexagonal Si structures which stabilize microfacets composed of the {l{underscore}brace}111{r{underscore}brace} planes. (2) Defect formation during crystal growth processes is due to misorientations at the {l{underscore}brace}111{r{underscore}brace} interfaces which result in an elementary grown-in defect structure including five- and seven-member rings. (3) The elementary grown-in defect migrates in c-Si by bond-switching motions during further crystal pulling or annealing.

  19. Molecular dynamics modeling of polymer crystallization; from simple polymers to helical ones.

    PubMed

    Yamamoto, Takashi; Orimi, Naohiko; Urakami, Naohiko; Sawada, Kaoru

    2005-01-01

    Crystallization of helical polymers is a very big challenge for molecular simulation. It involves many significant issues, such as folding in biomolecules and molecular recognition during crystal growth. Though direct molecular simulations of the process still involve very difficult problems, we here report our recent efforts toward better understanding of the crystallization in helical polymers. We begin with a brief review of our former studies on simple polyethylene-like polymers, and then we introduce several helical polymer models which are systematically made more complicated. We have already reported that a simple polyethylene-like polymer crystallizes very fast into chain folded lamellae from the melt. A slight modification of this simple polymer model by introducing proper bond angle and dihedral angle potentials gives one of the present models of the helical polymer. This helical polymer model is devised to be relatively rigid but mobile, to show easy helix-reversals, and to have a definite preference for gauche bonds. We find that this highly mobile helical polymer shows quick chain folded crystallization and forms approximate 4/1 helical structure. The intra- and the intermolecular order grow quite simultaneously suggesting highly cooperative nature of the phenomena. Further elaboration of the helical model, giving pendant side groups and higher energy barrier to the helix reversals, leads us to a realistic united atom model of iPP. The conventional and the multi-canonical Monte Carlo simulations are applied to find probable modes of chain folding and the ground state conformations. Though a very short chain readily forms a regular 3/1 helix of alternating trans and gauche bonds, much longer chains of 30- and 50-propylene units are not found to have energetic ground states in the regularly folded conformations.

  20. Non-equilibrium control of complex solids by nonlinear phononics.

    PubMed

    Mankowsky, Roman; Först, Michael; Cavalleri, Andrea

    2016-06-01

    We review some recent advances in the use of optical fields at terahertz frequencies to drive the lattice of complex materials. We will focus on the control of low energy collective properties of solids, which emerge on average when a high frequency vibration is driven and a new crystal structure induced. We first discuss the fundamentals of these lattice rearrangements, based on how anharmonic mode coupling transforms an oscillatory motion into a quasi-static deformation of the crystal structure. We then discuss experiments, in which selectively changing a bond angle turns an insulator into a metal, accompanied by changes in charge, orbital and magnetic order. We then address the case of light induced non-equilibrium superconductivity, a mysterious phenomenon observed in some cuprates and molecular materials when certain lattice vibrations are driven. Finally, we show that the dynamics of electronic and magnetic phase transitions in complex-oxide heterostructures follow distinctly new physical pathways in case of the resonant excitation of a substrate vibrational mode.

  1. Non-equilibrium control of complex solids by nonlinear phononics

    NASA Astrophysics Data System (ADS)

    Mankowsky, Roman; Först, Michael; Cavalleri, Andrea

    2016-06-01

    We review some recent advances in the use of optical fields at terahertz frequencies to drive the lattice of complex materials. We will focus on the control of low energy collective properties of solids, which emerge on average when a high frequency vibration is driven and a new crystal structure induced. We first discuss the fundamentals of these lattice rearrangements, based on how anharmonic mode coupling transforms an oscillatory motion into a quasi-static deformation of the crystal structure. We then discuss experiments, in which selectively changing a bond angle turns an insulator into a metal, accompanied by changes in charge, orbital and magnetic order. We then address the case of light induced non-equilibrium superconductivity, a mysterious phenomenon observed in some cuprates and molecular materials when certain lattice vibrations are driven. Finally, we show that the dynamics of electronic and magnetic phase transitions in complex-oxide heterostructures follow distinctly new physical pathways in case of the resonant excitation of a substrate vibrational mode.

  2. Double-hybrid density-functional theory applied to molecular crystals

    NASA Astrophysics Data System (ADS)

    Sharkas, Kamal; Toulouse, Julien; Maschio, Lorenzo; Civalleri, Bartolomeo

    2014-07-01

    We test the performance of a number of two- and one-parameter double-hybrid approximations, combining semilocal exchange-correlation density functionals with periodic local second-order Møller-Plesset (LMP2) perturbation theory, for calculating lattice energies of a set of molecular crystals: urea, formamide, ammonia, and carbon dioxide. All double-hybrid methods perform better on average than the corresponding Kohn-Sham calculations with the same functionals, but generally not better than standard LMP2. The one-parameter double-hybrid approximations based on the PBEsol density functional give lattice energies per molecule with an accuracy of about 6 kJ/mol, which is similar to the accuracy of LMP2. This conclusion is further verified on molecular dimers and on the hydrogen cyanide crystal.

  3. The effects of Raman scattering accompanied by the soliton excitation occurring in molecular crystals

    NASA Astrophysics Data System (ADS)

    Pang, X. F.

    2001-06-01

    A theoretical research is made for the effects of Raman scattering caused by the soliton excitation occurring in the organic molecular crystals, e.g., acetanilide, on the basis of vibration model of amide-I. The energy gap between the soliton state and the vibron state have been found by partial diagonalized method in second quantized representation, which is 18.1-33 cm -1. This result is approximately consistent with the red shift value obtained from the experiments, 16 cm -1. The differential cross-section of the Raman scattering, arising from the soliton excitation, has also been obtained. Finally, we derive some properties of the Raman scattering in such a case. This result establishes spectral signatures of the soliton in the molecular crystals, which may be observed in the experiment.

  4. Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

  5. Examination of surface nucleation during the growth of long alkane crystals by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Bourque, Alexander; Rutledge, Gregory

    2015-03-01

    Crystal growth from the melt of n-pentacontane (C50) was studied by molecular dynamics simulation using a validated united atom model. By quenching below the melting temperature of C50 (370 K), propagation of the crystal growth front into the C50 melt from a crystalline polyethylene surface was observed. By tracking the location of the midpoint in the orientational order parameter profile between the crystal and melt, crystal growth rates between 0.015-0.040 m/s were observed, for quench depths of 10 to 70 K below the melting point. In this work, surface nucleation is identified with the formation of 2D clusters of crystalline sites within layers parallel to the propagating growth front, by analogy to the formation of 3D clusters in primary, homogeneous nucleation. These surface nucleation events were tracked over several layers and numerous simulations, and a mean first passage time analysis was employed to estimate critical nucleus sizes, induction times and rates for surface nucleation. Based on new insights provided by the detailed molecular trajectories obtained from simulation, the classical theory proposed by Lauritzen and Hoffman is re-examined.

  6. Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human β-Defensin 2.

    PubMed

    Li, Jianguo; Hu, Zhongqiao; Beuerman, Roger; Verma, Chandra

    2017-04-06

    Human β-defensin 2 is a cysteine-rich antimicrobial peptide. In the crystal state, the N-terminal segment (residues 1-11) exhibits a helical conformation. However, a truncated form, with four amino acids removed from the N-terminus, adopts nonhelical conformations in solution, as shown by NMR. To explore the molecular origins of these different conformations, we performed Hamiltonian replica exchange molecular dynamics simulations of the peptide in solution and in the crystal state. It is found that backbone hydration and specific protein-protein interactions are key parameters that determine the peptide conformation. The helical conformation in the crystal state mainly arises from reduced hydration as well as a salt bridge between the peptide and a symmetry-related neighboring monomer in the crystal. When the extent of hydration is reduced and the salt bridge is reintroduced artificially, the peptide is successfully folded back to the helical conformation in solution. The findings not only shed light on the development of accurate force field parameters for protein molecules but also provide practical guidance in the design of functional proteins and peptides.

  7. Nonequilibrium interfaces in colloidal fluids

    NASA Astrophysics Data System (ADS)

    Bier, Markus; Arnold, Daniel

    2013-12-01

    The time-dependent structure, interfacial tension, and evaporation of an oversaturated colloid-rich (liquid) phase in contact with an undersaturated colloid-poor (vapor) phase of a colloidal dispersion is investigated theoretically during the early-stage relaxation, where the interface is relaxing towards a local equilibrium state while the bulk phases are still out of equilibrium. Since systems of this type exhibit a clear separation of colloidal and solvent relaxation time scales with typical times of interfacial tension measurements in between, they can be expected to be suitable for analogous experimental studies, too. The major finding is that, irrespective of how much the bulk phases differ from two-phase coexistence, the interfacial structure and the interfacial tension approach those at two-phase coexistence during the early-stage relaxation process. This is a surprising observation since it implies that the relaxation towards global equilibrium of the interface is not following but preceding that of the bulk phases. Scaling forms for the local chemical potential, the flux, and the dissipation rate exhibit qualitatively different leading order contributions depending on whether an equilibrium or a nonequilibrium system is considered. The degree of nonquilibrium between the bulk phases is found to not influence the qualitative relaxation behavior (i.e., the values of power-law exponents), but to determine the quantitative deviation of the observed quantities from their values at two-phase coexistence. Whereas the underlying dynamics differs between colloidal and molecular fluids, the behavior of quantities such as the interfacial tension approaching the equilibrium values during the early-stage relaxation process, during which nonequilibrium conditions of the bulk phases are not changed, can be expected to occur for both types of systems.

  8. Polarization Raman Microscopic Study of Molecular Alignment Behavior in Liquid Crystal/Polymer Composite Films

    NASA Astrophysics Data System (ADS)

    Murashige, Takeshi; Fujikake, Hideo; Sato, Hiroto; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2005-12-01

    We clarified that the molecular alignment of aggregated polymers is partially synchronized with liquid crystal (LC) director reorientation in an LC/polymer composite film. The molecular alignment behavior in composite films with LC- and polymer-rich regions formed by photopolymerization-induced phase separation was investigated using polarization Raman spectral microscopy. Raman scattering intensity induced by aligned side chains of polymers in the LC-rich region changed with LC director reorientation when voltage was applied to the composite film. It was confirmed for the first time that polymers capable of movement are formed in the LC-rich region.

  9. A molecular-field approximation for quantum crystals. Ph.D. Thesis; [considering ground state properties

    NASA Technical Reports Server (NTRS)

    Danilowicz, R.

    1973-01-01

    Ground-state properties of quantum crystals have received considerable attention from both theorists and experimentalists. The theoretical results have varied widely with the Monte Carlo calculations being the most successful. The molecular field approximation yields ground-state properties which agree closely with the Monte Carlo results. This approach evaluates the dynamical behavior of each pair of molecules in the molecular field of the other N-2 molecules. In addition to predicting ground-state properties that agree well with experiment, this approach yields data on the relative importance of interactions of different nearest neighbor pairs.

  10. Light quasiparticles dominate electronic transport in molecular crystal field-effect transistors

    SciTech Connect

    Li, Z. Q.; Podzorov, V.; Sai, N.; Martin, Michael C.; Gershenson, M. E.; Di Ventra, M.; Basov, D. N.

    2007-03-01

    We report on an infrared spectroscopy study of mobile holes in the accumulation layer of organic field-effect transistors based on rubrene single crystals. Our data indicate that both transport and infrared properties of these transistors at room temperature are governed by light quasiparticles in molecular orbital bands with the effective masses m[small star, filled]comparable to free electron mass. Furthermore, the m[small star, filled]values inferred from our experiments are in agreement with those determined from band structure calculations. These findings reveal no evidence for prominent polaronic effects, which is at variance with the common beliefs of polaron formation in molecular solids.

  11. Sub-nanometer Replica Molding of Molecular Steps on Ionic Crystals

    PubMed Central

    Elhadj, Selim; Rioux, Robert M.; Dickey, Michael D.; DeYoreo, James J.; Whitesides, George M.

    2010-01-01

    Replica molding with elastomeric polymers has been used routinely to replicate features less than 10 nm in size. Because the theoretical limit of this technique is set by polymer-surface interactions, atomic radii and accessible volumes, replication at sub-nm length scales should be possible. Using PDMS to create a mold and polyurethane to form the replica, we demonstrate replication of elementary steps 3-5 Å in height that define the minimum separation between molecular layers in the lattices of the ionic crystals potassium dihydrogen phosphate (KDP) and calcite (CaCO3). This work establishes the operation of replica molding at the molecular scale. PMID:20843061

  12. An Analysis of the NEXAFS Spectra of a molecular crystal: alpha-Glycine

    SciTech Connect

    Schwartz, Craig P.; Saykally, Richard J.; Prendergast, David

    2010-06-18

    The nitrogen K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectrum of alpha-crystalline glycine has been calculated for temperatures ranging from 0 K to 450 K. Significant temperature dependent spectral changes are predicted. The calculated room temperature spectrum is in good agreement with experiment. At high temperatures, molecular motions strongly influence the spectrum, as any unique spectrum from an individual instantaneous configuration does not resemble the experimental result or the average calculated spectrum; complex coupled motions in this prototypical molecular crystal underlie the observed spectral changes.

  13. Direct induction of molecular alignment in liquid crystal polymer network film by photopolymerization

    NASA Astrophysics Data System (ADS)

    Hisano, K.; Aizawa, M.; Ishizu, M.; Kurata, Y.; Shishido, A.

    2016-09-01

    Liquid crystal (LC) is the promising material for the fabrication of high-performance soft, flexible devices. The fascinating and useful properties arise from their cooperative effect that inherently allows the macroscopic integration and control of molecular alignment through various external stimuli. To date, light-matter interaction is the most attractive stimuli and researchers developed photoalignment through photochemical or photophysical reactions triggered by linearly polarized light. Here we show the new choice based on molecular diffusion by photopolymerization. We found that photopolymerization of a LC monomer and a crosslinker through a photomask enables to direct molecular alignment in the resultant LC polymer network film. The key generating the molecular alignment is molecular diffusion due to the difference of chemical potentials between irradiated and unirradiated regions. This concept is applicable to various shapes of photomask and two-dimensional molecular alignments can be fabricated depending on the spatial design of photomask. By virtue of the inherent versatility of molecular diffusion in materials, the process would shed light on the fabrication of various high-performance flexible materials with molecular alignment having controlled patterns.

  14. Liquid crystal alignment with a molecular template of imprinted polymer layer during phase separation

    NASA Astrophysics Data System (ADS)

    Kim, Hak-Rin; Jung, Jong-Wook; Lee, You-Jin; Kim, Jae-Hoon

    2006-03-01

    We developed a liquid crystal (LC) alignment method using a molecular template of an imprinted polymer layer during polymerization-induced phase separation. Our results showed that the nematic ordering of LC is transferred to the polymer chain ordering during an anisotropic phase separation, which produces an anisotropic azimuthal surface anchoring. Using in-plane field treatment during phase separation, a twisted nematic cell is demonstrated.

  15. Molecularly Dispersed Donors in Acceptor Molecular Crystals for Photon Upconversion under Low Excitation Intensity.

    PubMed

    Hosoyamada, Masanori; Yanai, Nobuhiro; Ogawa, Taku; Kimizuka, Nobuo

    2016-02-01

    For real-world applications of photon upconversion based on the triplet-triplet annihilation (TTA-UC), it is imperative to develop solid-state TTA-UC systems that work effectively under low excitation power comparable to solar irradiance. As an approach in this direction, aromatic crystals showing high triplet diffusivity are expected to serve as a useful platform. However, donor molecules inevitably tend to segregate from the host acceptor crystals, and this inhomogeneity results in the disappointing performance of crystalline state TTA-UC. In this work, a series of cast-film-forming acceptors was developed, which provide both regular acceptor alignment and soft domains of alkyl chains that accommodate donor molecules without segregation. A typical triplet sensitizer, Pt(II) octaethylporphyrin (PtOEP), was dispersed in these acceptor crystals without aggregation. As a result, efficient triplet energy transfer from the donor to the acceptor and diffusion of triplet excitons among regularly aligned anthracene chromophores occurred. It resulted in TTA-UC emission at low excitation intensities, comparable to solar irradiance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Role of supramolecular synthons in the formation of the supramolecular architecture of molecular crystals revisited from an energetic viewpoint.

    PubMed

    Shishkin, Oleg V; Zubatyuk, Roman I; Shishkina, Svitlana V; Dyakonenko, Viktoriya V; Medviediev, Volodymyr V

    2014-04-14

    Analysis of the strengths and directionality of intermolecular interactions in the crystals containing only one type of supramolecular synthon allows the suggestion of a general classification of molecular crystals depending on type of their basic structural motifs. All crystals may be divided on four classes namely (I) crystals with isotropic packing of the building units; (II) columnar crystals where the basic structural motif (BSM) is a chain/column; (III) layered crystals with layers as the BSM; (IV) columnar-layered crystals containing chains/columns as the primary basic structural motif and layers as the secondary BSM. Taking into account the participation of different supramolecular synthons in the formation of different levels of the organization of molecular crystals, they may be considered as basic (responsible for the formation of molecular complexes as building units of crystals), primary, secondary and auxiliary, which are involved in the agglomeration of molecules in primary or secondary basic structural motifs or in the packing of these motifs, respectively. The ranking of supramolecular synthons depends on values of energies of intermolecular interactions and it is individual for each crystal.

  17. Non-equilibrium in low-temperature plasmas

    NASA Astrophysics Data System (ADS)

    Taccogna, Francesco; Dilecce, Giorgio

    2016-11-01

    The wide range of applications of cold plasmas originates from their special characteristic of being a physical system out of thermodynamic equilibrium. This property enhances its reactivity at low gas temperature and allows to obtain macroscopic effects with a moderate energy consumption. In this review, the basic concepts of non-equilibrium in ionized gases are treated by showing why and how non-equilibrium functions of the degrees of freedom are formed in a variety of natural and man-made plasmas with particular emphasis on the progress made in the last decade. The modern point of view of a molecular basis of non-equilibrium and of a state-to-state kinetic approach is adopted. Computational and diagnostic techniques used to investigate the non-equilibrium conditions are also surveyed.

  18. Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations

    PubMed Central

    Ytreberg, F. Marty

    2009-01-01

    We compute the absolute binding affinities for two ligands bound to the FKBP protein using nonequilibrium unbinding simulations. The methodology is straightforward requiring little or no modification to many modern molecular simulation packages. The approach makes use of a physical pathway, eliminating the need for complicated alchemical decoupling schemes. We compare our nonequilibrium results to those obtained via a fully equilibrium approach and to experiment. The results of this study suggest that to obtain accurate results using nonequilibrium approaches one should use the stiff-spring approximation with the second cumulant expansion. From this study we conclude that nonequilibrium simulation could provide a simple means to estimate protein-ligand binding affinities. PMID:19405629

  19. Molecular Dynamics Simulations of Shock Wave Propagation across the Nitromethane Crystal-Melt Interface

    NASA Astrophysics Data System (ADS)

    Jiang, Shan; Sewell, Thomas D.; Thompson, Donald L.

    2015-06-01

    We are interested in understanding the fundamental processes that occur during propagation of shock waves across the crystal-melt interface in molecular substances. We have carried out molecular dynamics simulations of shock passage from the nitromethane (100)-oriented crystal into the melt and vice versa using the fully flexible, non-reactive Sorescu, Rice, and Thompson force field. A stable interface was established for a temperature near the melting point by using a combination of isobaric-isothermal (NPT) and isochoric-isothermal (NVT) simulations. The equilibrium bulk and interfacial regions were characterized using spatial-temporal distributions of molecular number density, kinetic and potential energy, and C-N bond orientations. Those same properties were calculated as functions of time during shock propagation. As expected, the local temperatures (intermolecular, intramolecular, and total) and stress states differed significantly between the liquid and crystal regions and depending on the direction of shock propagation. Substantial differences in the spatial distribution of shock-induced defect structures in the crystalline region were observed depending on the direction of shock propagation. Research supported by the U.S. Army Research Office.

  20. Role of molecule flexibility on the nucleation of dislocations in molecular crystals

    NASA Astrophysics Data System (ADS)

    Munday, Lynn B.; Mitchell, Robert L.; Knap, Jaroslaw; Chung, Peter W.

    2013-10-01

    We show that a molecule's flexibility described by changes to its conformation and orientation during deformation is vital for the proper representation of dislocation nucleation in molecular crystals. This is shown for the molecular crystal hexahydro-1,3,5-trinitro-s-triazine (RDX) by comparing direct atomistic simulations to two alternate forms of a continuum dislocation nucleation model for a crack tip loaded in pure shear. The atomistic simulations show the emission of partial dislocations. These are compared to continuum dislocation nucleation models based on generalized stacking fault (GSF) energy surfaces where the molecules are allowed to be either rigid or flexible. The rigid molecules are unable to represent the partial dislocations whereas the flexible molecules agree with the direct atomistic model to within 17% of the stress intensity factor for emission of the first partial dislocation and to within 1% for the second partial. This agreement first indicates that the molecule flexibility serves a critical role in the ductile behavior of the molecular crystal and, second, the continuum dislocation nucleation model represents the correct atomistic behavior, showing two partial dislocations connected by a stacking fault, when parameterized with GSF energy surfaces that account for the molecule flexibility.

  1. The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

    NASA Astrophysics Data System (ADS)

    Leiserowitz, Leslie; Marom, Noa; Distasio, Robert A., Jr.; Atalla, Viktor; Levchenko, Sergey; Kapishnikov, Sergey; Chelikowsky, James R.; Tkatchenko, Alexandre

    2012-02-01

    Molecular crystals often have several polymorphs that are close in energy (few meV per molecule), but possess very different physical and chemical properties. Treating polymorphism from first principles has been a long standing problem because conventional density-functional theory (DFT) lacks a proper description of long-range dispersion interactions that govern the structure and energetics of molecular crystals. Here we assess the effect of the many-body dispersion (MBD) energy on the structure and relative energies of the polymorphs of benchmark molecular crystals: glycine, alanine, and para-diiodobenzene. This is accomplished by using the recently developed first-principles DFT+MBD method [A. Tkatchenko, R.A. DiStasio Jr., R. Car, M. Scheffler, submitted], based on the earlier Tkatchenko-Scheffler (TS) dispersion correction [PRL 102, 073005 (2009)]. We show that the non-additive MBD energy plays a crucial role in making qualitatively and quantitatively accurate predictions for the structure and relative energies of polymorphs.

  2. Changes in molecular dynamics upon formation of a polymer dispersed liquid crystal.

    PubMed

    Brás, Ana R E; Viciosa, M Teresa; Rodrigues, Carla M; Dias, C J; Dionísio, Madalena

    2006-06-01

    The molecular dynamics during the formation of a polymer dispersed liquid crystal (PDLC) was followed by dielectric relaxation spectroscopy in the frequency range from 10(-1) to 2 x 10(6) Hz and over the temperature range from 158 to 273 K. The composite was produced by thermal polymerization induced phase separation of a mixture of triethyleneglycol dimethacrylate and the nematic liquid crystal, E7, in the proportion of 60:40 w/w. Both monomer and liquid crystal vitrify upon cooling having glass transition relaxation processes already characterized by some of us; yet E7 was previously studied in a narrower frequency range, so the present work updates its dielectric behavior. The starting mixture exhibits a rather complex dielectric spectrum due to the detection of multiple processes occurring simultaneously in the monomer and liquid crystal constituents. The PDLC formation occurs by mobility changes essentially in the liquid crystal tumbling motion, while the main relaxation of the monomer depletes upon polymerization. A low intense secondary process of E7 hardly detected in the bulk material is enhanced in both starting mixture and final composite allowing its characterization.

  3. Nanomechanical testing technique for millimeter-sized and smaller molecular crystals.

    PubMed

    Maughan, Michael R; Carvajal, M Teresa; Bahr, David F

    2015-01-01

    Large crystals are used as a control for the development of a mounting and nanoindentation testing technique for millimeter-sized and smaller molecular crystals. Indentation techniques causing either only elastic or elastic-plastic deformation produce similar results in assessing elastic modulus, however, the elastic indents are susceptible to surface angle and roughness effects necessitating larger sample sizes for similar confidence bounds. Elastic-plastic indentations give the most accurate results and could be used to determine the different elastic constants for anisotropic materials by indenting different crystal faces, but not by rotating the indenter about its axis and indenting the same face in a different location. The hardness of small and large crystals is similar, suggesting that defect content probed in this study is similar, and that small crystals can be compared directly to larger ones. The Young's modulus and hardness of the model test material, griseofulvin, are given for the first time to be 11.5GPa and 0.4GPa respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Crystallization studies on avian eggshell membranes: implications for the molecular factors controlling eggshell formation.

    PubMed

    Wu, T M; Rodriguez, J P; Fink, D J; Carrino, D A; Blackwell, J; Caplan, A I; Heuer, A H

    1995-02-01

    The avian eggshell is a natural biopolymer and mineral composite. It is a very useful model for biomimetic mineralization, since it is among the fastest forming hard tissues known. Isolated eggshell membranes, which were demineralized in vitro, were used to investigate the in vitro modulation of CaCO3 crystal deposition by organic matrix materials. Crystallization on the demineralized eggshell membrane occurred almost exclusively at the peripheries of residual calcium reserve assemblies, which contain a high concentration of sulfur. Similar structures are observed for eggshell membranes after natural demineralization. The characteristic rhombohedral crystal morphologies of the calcite crystals grown in this in vitro system are much less regular when grown in the presence of organic matrix or partially purified dermatan sulfate proteoglycans obtained from the eggshell. The effect of these macromolecules on the morphology and size of CaCO3 crystals is concentration-dependent. These studies indicate the complexity of the molecular and ionic interactions involved in the initiation and formation of the eggshell, with the focus on the role of the organic matrix.

  5. Protein crystallization and biosensor applications of hydrogel-based molecularly imprinted polymers.

    PubMed

    Reddy, Subrayal M; Phan, Quan T; El-Sharif, Hazim; Govada, Lata; Stevenson, Derek; Chayen, Naomi E

    2012-12-10

    We have characterized the imprinting capability of a family of acrylamide polymer-based molecularly imprinted polymers (MIPs) for bovine hemoglobin (BHb) and trypsin (Tryp) using spectrophotometric and quartz crystal microbalance (QCM) sensor techniques. Bulk gel characterization on acrylamide (AA), N-hydroxymethylacrylamide (NHMA), and N-isopropylacrylamide (NiPAM) gave varied selectivities when compared with nonimprinted polymers. We have also harnessed the ability of the MIPs to facilitate protein crystallization as a means of evaluating their selectivity for cognate and noncognate proteins. Crystallization trials indicated improved crystal formation in the order NiPAMcrystallization studies validated the hydrophilic efficacy of MIPS indicated in the QCM studies.

  6. Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata

    SciTech Connect

    Gavira, José A.; Jesus, Walleska de; Camara-Artigas, Ana; López-Garriga, Juan; García-Ruiz, Juan M.

    2006-03-01

    The haemoglobin II from the clam L. pectinata has been crystallized using counter-diffusion in single capillary in the presence of agarose to improve crystal quality. Initial phases have been obtained by molecular replacement. Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 73.92, c = 152.35 Å, and diffracted X-rays to a resolution of better than 2.0 Å. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (V{sub M}) of 3.15 Å{sup 3} Da{sup −1} and a solvent content of 61% by volume.

  7. Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates.

    PubMed

    Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

    2014-01-21

    We present a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. The formalism is based on combining Transition Path Theory with the results of nonequilibrium work relations, and shows that the equilibrium and nonequilibrium transition rates are in fact related. Aside from its fundamental importance, this allows for the calculation of relative equilibrium reaction rates with driven nonequilibrium simulations such as Steered Molecular Dynamics. The workings of the formalism are illustrated with a few typical numerical examples.

  8. Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An ab initio Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto

    2014-03-01

    Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.

  9. Nonequilibrium Interlayer Transport in Pulsed Laser Deposition

    SciTech Connect

    Tischler, Jonathan Zachary; Eres, Gyula; Larson, Ben C; Rouleau, Christopher M; Zschack, P.; Lowndes, Douglas H

    2006-01-01

    We use time-resolved surface x-ray diffraction measurements with microsecond range resolution to study the growth kinetics of pulsed laser deposited SrTiO3. Time-dependent surface coverages corresponding to single laser shots were determined directly from crystal truncation rod intensity transients. Analysis of surface coverage evolution shows that extremely fast nonequilibrium interlayer transport, which occurs concurrently with the arrival of the laser plume, dominates the deposition process. A much smaller fraction of material, which is governed by the dwell time between successive laser shots, is transferred by slow, thermally driven interlayer transport processes.

  10. Molecular theory of smectic ordering in liquid crystals with nanoscale segregation of different molecular fragments

    NASA Astrophysics Data System (ADS)

    Gorkunov, M. V.; Osipov, M. A.; Kapernaum, N.; Nonnenmacher, D.; Giesselmann, F.

    2011-11-01

    A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure.

  11. INTRODUCTION: Nonequilibrium Processes in Plasmas

    NASA Astrophysics Data System (ADS)

    Petrović, Zoran; Marić, Dragana; Malović, Gordana

    2009-07-01

    lead to new fundamental understanding is illustrated well in the paper by Uwe Czarnetzki which describes a new method for separate control of flux and energy of ions reaching the surface of electrodes. Deborah O'Connell from Belfast has shown space and phase resolved mode transitions in rf inductively coupled plasmas obtained by optical emission measurements. At the same time an application of a similar rf discharge for the treatment of paper was presented by Irina Filatova from Belarus. Many applications of non-equilibrium plasmas depend on the development of plasma sources operating at atmospheric pressure and one such source that promises to be prominent in medicine is described by Timo Gans. In a similar way, practical considerations require studies of the injection of liquids into plasmas and progress on the development of one such source is described by Mathew Goeckner and his colleagues from Dallas. From the Institute Jožef Štefan in Slovenia and the group of Miran Mozetič we have a detailed review of their work on functionalization of organic materials by oxygen plasmas. Even higher density plasmas, where the collective phenomena dominate, show different degrees of non-equilibrium and one example presented here by Zoltan Donko deals with two dimensional plasma dust crystals and liquids, while the lecture by Jovo Vranješ from Belgium deals with the treatment of collisions in multicomponent plasmas. Finally we have papers on the transport of pollutants. The association of the two fields started initially through joint interest in some of the methods for removal of NOx and SOx, from electrostatic precipitation of industrial dust to dielectric barrier discharges. The joint work continued on the application of flowing afterglow plasma combined with a hollow cathode discharge in order to achieve a proton transfer mass analysis of organic volatile compounds and also on the possibilities of applying similar methods for solving transport equations. In this volume we

  12. Efficient rotational cooling of Coulomb-crystallized molecular ions by a helium buffer gas.

    PubMed

    Hansen, A K; Versolato, O O; Kłosowski, L; Kristensen, S B; Gingell, A; Schwarz, M; Windberger, A; Ullrich, J; López-Urrutia, J R Crespo; Drewsen, M

    2014-04-03

    The preparation of cold molecules is of great importance in many contexts, such as fundamental physics investigations, high-resolution spectroscopy of complex molecules, cold chemistry and astrochemistry. One versatile and widely applied method to cool molecules is helium buffer-gas cooling in either a supersonic beam expansion or a cryogenic trap environment. Another more recent method applicable to trapped molecular ions relies on sympathetic translational cooling, through collisional interactions with co-trapped, laser-cooled atomic ions, into spatially ordered structures called Coulomb crystals, combined with laser-controlled internal-state preparation. Here we present experimental results on helium buffer-gas cooling of the rotational degrees of freedom of MgH(+) molecular ions, which have been trapped and sympathetically cooled in a cryogenic linear radio-frequency quadrupole trap. With helium collision rates of only about ten per second--that is, four to five orders of magnitude lower than in typical buffer-gas cooling settings--we have cooled a single molecular ion to a rotational temperature of 7.5(+0.9)(-0.7) kelvin, the lowest such temperature so far measured. In addition, by varying the shape of, or the number of atomic and molecular ions in, larger Coulomb crystals, or both, we have tuned the effective rotational temperature from about 7 kelvin to about 60 kelvin by changing the translational micromotion energy of the ions. The extremely low helium collision rate may allow for sympathetic sideband cooling of single molecular ions, and eventually make quantum-logic spectroscopy of buffer-gas-cooled molecular ions feasible. Furthermore, application of the present cooling scheme to complex molecular ions should enable single- or few-state manipulations of individual molecules of biological interest.

  13. Crystal and molecular structure of alpha-iodo-beta-chlorovinyl phenyl sulfone and ,US -dibromovinyl phenyl sulfone

    SciTech Connect

    Bel'skii, V.K.; Shainyan, B.A.; Mirskova, A.N.

    1986-09-01

    The authors discuss rearrangement and isomerization procedures occurring in the bromination, iodination, and chlorination of the title sulfones and assess their crystal and molecular structure using NMR spectroscopy and x-ray diffraction.

  14. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

    SciTech Connect

    He, Xiaoxia; Shen, Yan; Hung, Francisco R.; Santiso, Erik E.

    2015-09-28

    The homogeneous nucleation of crystals of the ionic liquid [dmim{sup +}][Cl{sup −}] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10{sup 10} cm{sup −3} s{sup −1} was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

  15. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

    NASA Astrophysics Data System (ADS)

    He, Xiaoxia; Shen, Yan; Hung, Francisco R.; Santiso, Erik E.

    2015-09-01

    The homogeneous nucleation of crystals of the ionic liquid [dmim+][Cl-] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 1010 cm-3 s-1 was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

  16. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt.

    PubMed

    He, Xiaoxia; Shen, Yan; Hung, Francisco R; Santiso, Erik E

    2015-09-28

    The homogeneous nucleation of crystals of the ionic liquid [dmim(+)][Cl(-)] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10(10) cm(-3) s(-1) was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

  17. Improvement of toughness by stereocomplex crystal formation in optically pure polylactides of high molecular weight.

    PubMed

    López-Rodríguez, N; Martínez de Arenaza, I; Meaurio, E; Sarasua, J R

    2014-09-01

    A solution casting method followed by thermal homogenization was performed for the preparation of 1:1 blends and non-blended films from poly(d-lactide) (PDLA) and poly(l-lactide) (PLLA) of three different molecular weights, and their thermal and mechanical properties were determined via differential scanning calorimetry (DSC) and tensile tests. According to the literature, when Mw is below 1.0×10(5)g/mol only stereocomplex crystallization takes place, and when it is higher, both homocrystallites and stereocomplex crystallites co-exist. In order to promote crystallization as a homocrystal in neat polylactides and to promote the stereoselective crystallization as stereocomplex in the case of non-blended films, and in turn, to achieve different degrees of crystallinity, several thermal treatments of annealing were carried out in this work. Highly stereocomplexed blends were found by the stereospecific thermal treatments. As a consequence, the toughness of 1:1 blends was found significantly enhanced over those of non-blended films, irrespective of molecular weight. For instance, in B2-5050 stereocomplexed blend having poly(l-lactide) and poly(d-lactide) of Mw=1.2×10(5)g/mol, tensile strength increased from 44.0±2.1MPa to 65.1±6.1MPa, and the elongation at break from 10.8±2.5% to 33.1±8.1% with respect to its non-blended poly(l-lactide) counterpart crystallized as homocrystal. This improvement in mechanical properties in stereocomplexed blends is not attributed to the inherent properties of the type of crystal polymorph but to the presence of a higher density of intercrystalline connections through a mobile amorphous phase, i.e. tie chains in the stereocomplexed supramolecular spherulitic entities that provide in the stereocomplexed samples enhanced strength and elongation at break at the same time. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea.

    PubMed

    Erba, Alessandro; Maul, Jefferson; Civalleri, Bartolomeo

    2016-01-31

    An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data.

  19. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  20. Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  1. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  2. Effects of molecular geometry on the properties of compressed diamondoid crystals

    DOE PAGES

    Yang, Fan; Lin, Yu; Baldini, Maria; ...

    2016-11-01

    Diamondoids are an intriguing group of carbon-based nanomaterials, which combine desired properties of inorganic nanomaterials and small hydrocarbon molecules with atomic-level uniformity. In this Letter, we report the first comparative study on the effect of pressure on a series of diamondoid crystals with systematically varying molecular geometries and shapes, including zero-dimensional (0D) adamantane; one-dimensional (1D) diamantane, [121]tetramantane, [123]tetramantane, and [1212]pentamantane; two-dimensional (2D) [12312]hexamantane; and three-dimensional (3D) triamantane and [1(2,3)4]pentamantane. We find the bulk moduli of these diamondoid crystals are strongly dependent on the diamondoids’ molecular geometry with 3D [1(2,3)4]pentamantane being the least compressible and 0D adamantane being the most compressible.more » These diamondoid crystals possess excellent structural rigidity and are able to sustain large volume deformation without structural failure even after repetitive pressure loading cycles. These properties are desirable for constructing cushioning devices. Furthermore, we also demonstrate that lower diamondoids outperform the conventional cushioning materials in both the working pressure range and energy absorption density.« less

  3. Effects of molecular geometry on the properties of compressed diamondoid crystals

    SciTech Connect

    Yang, Fan; Lin, Yu; Baldini, Maria; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Mao, Wendy L.

    2016-11-01

    Diamondoids are an intriguing group of carbon-based nanomaterials, which combine desired properties of inorganic nanomaterials and small hydrocarbon molecules with atomic-level uniformity. In this Letter, we report the first comparative study on the effect of pressure on a series of diamondoid crystals with systematically varying molecular geometries and shapes, including zero-dimensional (0D) adamantane; one-dimensional (1D) diamantane, [121]tetramantane, [123]tetramantane, and [1212]pentamantane; two-dimensional (2D) [12312]hexamantane; and three-dimensional (3D) triamantane and [1(2,3)4]pentamantane. We find the bulk moduli of these diamondoid crystals are strongly dependent on the diamondoids’ molecular geometry with 3D [1(2,3)4]pentamantane being the least compressible and 0D adamantane being the most compressible. These diamondoid crystals possess excellent structural rigidity and are able to sustain large volume deformation without structural failure even after repetitive pressure loading cycles. These properties are desirable for constructing cushioning devices. Furthermore, we also demonstrate that lower diamondoids outperform the conventional cushioning materials in both the working pressure range and energy absorption density.

  4. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  5. Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

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

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel; Bukusoglu, Emre; de Pablo, Juan; Abbott, Nicholas

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals that nanoscopic environments defined by LC defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic o-rings synthesized from Saturn-ring disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates.

  7. Topological defects in liquid crystals and molecular self-assembly (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Abbott, Nicholas L.

    2017-02-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals 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, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic "o-rings" synthesized from "Saturn-ring" disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates (e.g., polymer—surfactant complexes). Opportunities for the design of exquisitely responsive soft materials will be discussed using bacterial endotoxin as an example.

  8. Molecular-dynamics computer simulation of crystal growth and melting in Al50Ni50

    NASA Astrophysics Data System (ADS)

    Kerrache, A.; Horbach, J.; Binder, K.

    2008-03-01

    The melting and crystallization of Al50Ni50 are studied by means of molecular-dynamics computer simulations, using a potential of the embedded atom type to model the interactions between the particles. Systems in a slab geometry are simulated where the B2 phase of AlNi in the middle of an elongated simulation box is separated by two planar interfaces from the liquid phase, thereby considering the (100) crystal orientation. By determining the temperature dependence of the interface velocity, an accurate estimate of the melting temperature is provided. The value k=0.0025 m/s/K for the kinetic growth coefficient is found. This value is about two orders of magnitude smaller than that found in recent simulation studies of one-component metals. The classical Wilson-Frenkel model is not able to describe the crystal growth kinetics on a quantitative level. We argue that this is due to the neglect of diffusion processes in the liquid-crystal interface.

  9. Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations.

    PubMed

    Debela, Tekalign T; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

    2017-03-14

    The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

  10. Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

    2017-05-01

    The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

  11. Dissolution of Alkali Fluoride and Chloride Crystals in Water Studied by Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fukushima, N.; Tamura, Y.; Ohtaki, H.

    1991-02-01

    The dissolution of cubic crystals of NaF, KF, CsF, LiCl, NaCl, and KCl consisting of 32 cations and 32 anions in an isolated box containing 216 water molecules was studied at 298 K by molecular dynamics simulations. The ion-ion, ion-water and water-water interactions were described in terms of the Tosi-Fumi, Kistenmacher-Popkie-Clementi, and Matsuoka-Clementi-Yoshimine potentials, respectively. During the simulation periods of 12 ps for NaF, CsF and LiCl and 20 ps for KF, NaCl and KCl cations did not dissolve, while anions dissolved from the CsF, LiCl and NaCl crystals but not from the NaF, KF and KCl crystals. The mass effect in the dissolution of CsF was examined by giving the ceasium ions the atomic weight of the fluoride ion (18.998). In case of the "light" caesium ions in the crystal fluctuated less far and again fluoride ions but no caesium ions were dissolved.

  12. Comparison of the crystal structure and molecular models of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide (CMPO)

    SciTech Connect

    Rogers, R.D.; Rollins, A.N.; Gatrone, R.C.; Horwitz, E.P.

    1994-06-01

    The compound crystallizes in the space group P2{sub 1}/c with a=13. 446(6), b=22.280(7) {Angstrom}, b=92.07(4){degrees}, and D{sub calc}=1.05 g/cm{sup 3} for Z=8 (@20{degrees}C). Molecular mechanics, molecular dynamics, and MNDO calculations were also performed on CMPO utilizing the SYBYL{sup 2} suite of programs. Results from these calculations are compared to the crystal structure and to similar calculations performed on CMPO using ALCHEMY. The calculations agree fairly well with the crystal structure.

  13. Terahertz pulse generation in an organic crystal by optical rectification and resonant excitation of molecular charge transfer

    NASA Astrophysics Data System (ADS)

    Carey, John J.; Bailey, Ray T.; Pugh, D.; Sherwood, J. N.; Cruickshank, F. R.; Wynne, Klaas

    2002-12-01

    Organic molecular crystals that are extremely efficient at terahertz-pulse generation are in- vestigated. Terahertz pulses produced by optical rectification at 800 nm in (-)2-(α-methylbenzyl-amino)-5-nitropyridine have an order of magnitude higher power than those generated in the commonly used inorganic crystal ZnTe. The organic molecular crystals were also found to generate terahertz pulses when excited on resonance at 400 nm. This may pave the way for studying ultrafast charge-transport dynamics in three dimensions.

  14. Molecular dynamic simulations of the intergranular films between alumina and silicon nitride crystal grains

    NASA Astrophysics Data System (ADS)

    Zhang, Shenghong

    The intergranular films (IGFs) between the ceramics grains have very important effects on the structure and mechanical properties on the whole ceramics and have been studied for many decades. In the thesis, molecular dynamic (MD) computer simulations were applied to study the IGFs between the alumina and silicon nitride ceramic grains. Preferential adsorption of specific ions from the IGFs to the contacting surfaces of the alumina crystals was observed in the study of calcium-alumino-silicate glassy (CAS) IGFs formed between the combined basal and prism orientations of alpha-Al2O3 crystals. This segregation of specific ions to the interface enables formation of localized, ordered structures between the IGF and the crystals. However, the segregation behavior of the ions is anisotropic, depending on the orientation of the alpha-Al2O 3 crystals. Self-diffusion of calcium ions between these CAS IGFs was also carried out by MD simulations. The results show that the diffusion coefficients adjacent to the interfaces are smaller and the activation energies are much higher than those in the interior of the IGF and in bulk glasses. It was also suggested that Ca transport is mainly though the interior of the IGF and implies that diffusion would be significantly inhibited by sufficiently thin IGFs. The growth of the alumina ceramic grains was simulated in the contacting with IGFs containing high concentrations of aluminum ions. Five different compositions in the IGFs were studied. Results show preferential growth along the [1120] of the (1120) surface in comparison to growth along the [0001] direction on the (0001) surface for compositions near a Ca/Al ratio of 0.5. The simulations also show the mechanism by which Ca ions in the IGF inhibit growth on the basal surface. The simulations provide an atomistic view of attachment onto crystal surfaces, affecting grain growth in alumina. The dissolution of the alumina crystal grains in the silicate melts is another important issue in

  15. Light-induced molecular adsorption and reorientation at polyvinylcinnamate-fluorinated/liquid-crystal interface

    SciTech Connect

    Francescangeli, O.; Lucchetti, L.; Simoni, F.; Stanic, V.; Mazzulla, A.

    2005-01-01

    We have carried out a detailed experimental study, by means of x-ray reflectometry (XRR) and half-leaky guided mode (HLGM) optical characterization, of the light-induced molecular adsorption and reorientation at the polyvinylcinnamate-fluorinated (PVCN-F)/liquid-crystal (LC) interface of a LC cell doped with the azo-dye methyl red (MR). The XRR data allowed characterizing the microscopic structure of the adsorbed dye layer both before irradiation (dark adsorption) and after irradiation (light-induced adsorption). The HLGM optical characterization has made possible the experimental determination of the nematic director profile in the LC cell and evaluation of the effects of light-induced adsorption on the LC anchoring conditions. The experimental findings have confirmed the formation of a dark-adsorbed layer and are in agreement with the absorption model previously proposed to account for the complex phenomenology related to light-induced anchoring and reorientation in dye-doped liquid crystals.

  16. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

  17. Critical CuI buffer layer surface density for organic molecular crystal orientation change

    SciTech Connect

    Ahn, Kwangseok; Kim, Jong Beom; Lee, Dong Ryeol; Kim, Hyo Jung; Lee, Hyun Hwi

    2015-01-21

    We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 −2) by a CuI buffer layer with a very low surface density, so low that a large proportion of the substrate surface is bare.

  18. Anisotropy effects in phonon-assisted charge-carrier transport in organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Hannewald, K.; Bobbert, P. A.

    2004-02-01

    We present a theoretical description of polaron dc conductivities in organic molecular crystals. Our approach is based on a rigorous evaluation of the Kubo formula for electrical conductivity within a mixed Holstein-Peierls model. It generalizes the result of Holstein’s local-coupling theory by treating both local and nonlocal electron-phonon interactions nonperturbatively. The general theory is supplemented by an application to a simplified model crystal in order to emphasize the essential physics. Accompanied by an illustrative numerical example, special emphasis is put on the emergence of anisotropy effects in the temperature dependence of the conductivity tensor. These anisotropy effects are shown to originate from phonon-assisted currents due to the nonlocal electron-lattice interaction which demonstrates the importance to go beyond local-coupling theories in order to describe the experimental observations.

  19. Photoinduced reversible switching of porosity in molecular crystals based on star-shaped azobenzene tetramers.

    PubMed

    Baroncini, Massimo; d'Agostino, Simone; Bergamini, Giacomo; Ceroni, Paola; Comotti, Angiolina; Sozzani, Piero; Bassanetti, Irene; Grepioni, Fabrizia; Hernandez, Taylor M; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-08-01

    The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of great interest for separation, catalysis, optoelectronics, holography, mechanical actuation and solar energy conversion. Here, we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, the porosity of which can be tuned by changing the peripheral substituents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties such as birefringence as well as the capture of CO2 from the gas phase. The linear design, structural versatility and synthetic accessibility make this new family of materials potentially interesting for technological applications.

  20. First principles calculation of the mechanical compression of two organic molecular crystals.

    PubMed

    Zerilli, Frank J; Kuklja, Maija M

    2006-04-20

    The mechanical compression curves for the organic molecular crystals 1,1-diamino-2,2-dinitroethylene and beta-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (beta-HMX) are calculated using the Hartree-Fock approximation to the solutions of the many-body Schrödinger equation for a periodic system as implemented in the computer program CRYSTAL. No correction was made for basis set superposition error. The equilibrium lattice parameters are reproduced to within 1% of reported experimental values. Pressure values on the isotherm also agree well with reported experimental values. To obtain accurate results, the relaxation of all the atomic coordinates as well as the lattice parameters under a fixed volume constraint was required.

  1. Tailoring molecular specificity toward a crystal facet: a lesson from biorecognition toward Pt{111}.

    PubMed

    Ruan, Lingyan; Ramezani-Dakhel, Hadi; Chiu, Chin-Yi; Zhu, Enbo; Li, Yujing; Heinz, Hendrik; Huang, Yu

    2013-02-13

    Surfactants with preferential adsorption to certain crystal facets have been widely employed to manipulate morphologies of colloidal nanocrystals, while mechanisms regarding the origin of facet selectivity remain an enigma. Similar questions exist in biomimetic syntheses concerning biomolecular recognition to materials and crystal surfaces. Here we present mechanistic studies on the molecular origin of the recognition toward platinum {111} facet. By manipulating the conformations and chemical compositions of a platinum {111} facet specific peptide, phenylalanine is identified as the dominant motif to differentiate {111} from other facets. The discovered recognition motif is extended to convert nonspecific peptides into {111} specific peptides. Further extension of this mechanism allows the rational design of small organic molecules that demonstrate preferential adsorption to the {111} facets of both platinum and rhodium nanocrystals. This work represents an advance in understanding the organic-inorganic interfacial interactions in colloidal systems and paves the way to rational and predictable nanostructure modulations for many applications.

  2. High breakdown single-crystal GaN p-n diodes by molecular beam epitaxy

    SciTech Connect

    Qi, Meng; Zhao, Yuning; Yan, Xiaodong; Li, Guowang; Verma, Jai; Fay, Patrick; Nomoto, Kazuki; Zhu, Mingda; Hu, Zongyang; Protasenko, Vladimir; Song, Bo; Xing, Huili Grace; Jena, Debdeep; Bader, Samuel

    2015-12-07

    Molecular beam epitaxy grown GaN p-n vertical diodes are demonstrated on single-crystal GaN substrates. A low leakage current <3 nA/cm{sup 2} is obtained with reverse bias voltage up to −20 V. With a 400 nm thick n-drift region, an on-resistance of 0.23 mΩ cm{sup 2} is achieved, with a breakdown voltage corresponding to a peak electric field of ∼3.1 MV/cm in GaN. Single-crystal GaN substrates with very low dislocation densities enable the low leakage current and the high breakdown field in the diodes, showing significant potential for MBE growth to attain near-intrinsic performance when the density of dislocations is low.

  3. Magnetic properties, crystal and molecular stucture of (NBu 4) 2[ReCl 4(ox)

    NASA Astrophysics Data System (ADS)

    Tomkiewicz, A.; Bartczak, T. J.; Kruszyński, R.; Mroziński, J.

    2001-09-01

    The synthesis, structure and magnetic properties of the rhenium(IV) complex (NBu4)2[ReCl4(ox)] is reported. The crystal and molecular structure (NBu4)2[ReCl4(ox)] has been solved by the heavy atom method and refined anisotropically to R1=0.049 for 5636 unique observed reflections. The title compound crystallizes in the monoclinic space group P21/n with Z=4. The Re atom is of six-coordinate distorted octahedral configuration being bonded to one bidentate oxalate group and four chloride anions. The asymmetric unit contains one [ReCl4(ox)]- 2 anion and two [NBu4]+ cations. The magnetic behavior of (NBu4)2[ReCl4(ox)] has been investigated over the temperature range 1.72-300 K. This measurement revealed that examined compound is magnetically diluted with the great value of zero-field splitting parameter D=53 cm-1.

  4. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal.

    PubMed

    Miller, Nichole Cates; Cho, Eunkyung; Junk, Matthias J N; Gysel, Roman; Risko, Chad; Kim, Dongwook; Sweetnam, Sean; Miller, Chad E; Richter, Lee J; Kline, R Joseph; Heeney, Martin; McCulloch, Iain; Amassian, Aram; Acevedo-Feliz, Daniel; Knox, Christopher; Hansen, Michael Ryan; Dudenko, Dmytro; Chmelka, Bradley F; Toney, Michael F; Brédas, Jean-Luc; McGehee, Michael D

    2012-11-27

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels.

  5. Temperature dependence of Raman spectroscopy of molecular iodine trapped in zeolite crystals

    NASA Astrophysics Data System (ADS)

    Guo, Wenhao; Wang, Dingdi; Hu, Juanmei; Tang, Zikang; Du, Shengwang

    2012-02-01

    Molecular iodine has been pursued for many practical applications, such as molecular clock, molecule-based quantum information processing, due to its narrow-linewidth hyperfine optical transitions. But because of its low vapor pressure, the experimental setup employing a free-space-based iodine vapor cell is very space-consuming. Recently, it is reported that the iodine molecule can be loaded into the channels of zeolite crystals, the density there could be orders improved and its space orientation can be precisely controlled. It may drastically reduce the size of molecular iodine experiment setup, and have many potential applications in microchip technology. We have studied the Raman spectroscopy of iodine molecule confined in zeolite crystals, AlPO4-5 (AFI) and AlPO4-11 (AEL), under different temperatures. The results show that in AEL, where the molecules are intensely confined, the ground vibrational states are close to that of an ideal 1D harmonic oscillator, while in AFI, where the molecules have a bit more freedom, they vibrate like in the free space, but with a loosened spring. And we come up a reasonable theoretical model to explain the Raman width dependence on temperature for these systems

  6. Bond length estimates for oxide crystals with a molecular power law expression

    NASA Astrophysics Data System (ADS)

    Gibbs, G. V.; Ross, Nancy L.; Cox, David F.

    2015-07-01

    A molecular power law bond length regression expression, R(M-O) = 1.39( s/ r)-0.22, defined in terms of the quotient, s/ r, where s is the averaged Pauling bond strength for the bonded interaction comprising a given molecular coordination polyhedron and r is the periodic table row number for the M atom, serves to replicate the bulk of the 470 individual experimental M-O average bond lengths estimated with Shannon's (Acta Crystallogr A 32(5):751-767, 1976) crystal radii for oxides to within 0.10 Å. The success of the molecular expression is ascribed to a one-to-one deep-seated connection that obtains between the electron density accumulated between bonded pairs of atoms and the average Pauling bond strength. It also implies that the bonded interactions that constitute oxide crystals are governed in large part by local forces. Although the expression reproduces the bond lengths involving rare earth atoms typically to within ~0.05 Å, it does not reproduce the lanthanide ionic radius contraction. It also fails to reproduce the experimental bond lengths for selected transition cations like Cu1+, Ag1+ and VILSFe2+ and for cations like IVK+, VIBa2+ and IIU6+.

  7. Molecular characterization and genetic diversity of insecticidal crystal protein genes in native Bacillus thuringiensis isolates.

    PubMed

    Mahadeva Swamy, H M; Asokan, R; Mahmood, Riaz; Nagesha, S N

    2013-04-01

    The Western Ghats of Karnataka natural ecosystem are among the most diverse and is one of the eight hottest hotspots of biological diversity in the world, that runs along the western part of India through four states including Karnataka. Bacillus thuringiensis (Bt) strains were isolated from soils of Western Ghats of Karnataka and characterized by molecular and analytical methods as a result of which 28 new Bt-like isolates were identified. Bt strains were isolated from soil samples using sodium acetate selection method. The morphology of crystals was studied using light and phase contrast microscopy. Isolates were further characterized for insecticidal cry gene by PCR, composition of toxins in bacterial crystals by SDS-PAGE cloning, sequencing and evaluation of toxicity was done. As a result 28 new Bt-like isolates were identified. Majority of the isolates showed the presence of a 55 kDa protein bands on SDS-PAGE while the rest showed 130, 73, 34, and 25 kDa bands. PCR analysis revealed predominance of Coleopteran-active cry genes in these isolates. The variations in the nucleotide sequences, crystal morphology, and mass of crystal protein(s) purified from the Bt isolates revealed genetic and molecular diversity. Three strains containing Coleopteran-active cry genes showed higher activity against larvae Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) than B. thuringiensis subsp. Morrisoni. Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production.

  8. Thermal conductivity calculation in anisotropic crystals by molecular dynamics: Application to α-Fe2O3.

    PubMed

    Severin, Jonathan; Jund, Philippe

    2017-02-07

    In this work, we aim to study the thermal properties of materials using classical molecular dynamics simulations and specialized numerical methods. We focus primarily on the thermal conductivity κ using non-equilibrium molecular dynamics (NEMD) to study the response of a crystalline solid, namely hematite (α-Fe2O3), to an imposed heat flux as is the case in real life applications. We present a methodology for the calculation of κ as well as an adapted potential for hematite. Taking into account the size of the simulation box, we show that not only the longitudinal size (in the direction of the heat flux) but also the transverse size plays a role in the determination of κ and should be converged properly in order to have reliable results. Moreover we propose a comparison of thermal conductivity calculations in two different crystallographic directions to highlight the spatial anisotropy and we investigate the non-linear temperature behavior typically observed in NEMD methods.

  9. Thermal conductivity calculation in anisotropic crystals by molecular dynamics: Application to α-Fe2O3

    NASA Astrophysics Data System (ADS)

    Severin, Jonathan; Jund, Philippe

    2017-02-01

    In this work, we aim to study the thermal properties of materials using classical molecular dynamics simulations and specialized numerical methods. We focus primarily on the thermal conductivity κ using non-equilibrium molecular dynamics (NEMD) to study the response of a crystalline solid, namely hematite (α -Fe2O3 ), to an imposed heat flux as is the case in real life applications. We present a methodology for the calculation of κ as well as an adapted potential for hematite. Taking into account the size of the simulation box, we show that not only the longitudinal size (in the direction of the heat flux) but also the transverse size plays a role in the determination of κ and should be converged properly in order to have reliable results. Moreover we propose a comparison of thermal conductivity calculations in two different crystallographic directions to highlight the spatial anisotropy and we investigate the non-linear temperature behavior typically observed in NEMD methods.

  10. Anisotropy in surface-initiated melting of the triclinic molecular crystal 1,3,5-triamino-2,4,6-trinitrobenzene: A molecular dynamics study.

    PubMed

    Mathew, N; Sewell, Thomas D; Thompson, Donald L

    2015-09-07

    Surface-initiated melting of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a triclinic molecular crystal, was investigated using molecular dynamics simulations. Simulations were performed for the three principal crystallographic planes exposed to vacuum, with the normal vectors to the planes given by b × c, c × a, and a × b (where a, b, and c define the edge vectors of the unit cell), denoted as (100), (010), and (001), respectively. The best estimate of the normal melting temperature for TATB is 851 ± 5 K. The nature and extent of disordering of the crystal-vacuum interface depend on the exposed crystallographic face, with the (001) face exhibiting incomplete melting and superheating. This is attributed to the anisotropy of the inter-molecular hydrogen bonding and the propensity of the crystal to form stacking faults in directions approximately perpendicular to the (100) and (010) faces. For all three crystal orientations, formation of molecular vacancies in the lattice at the crystal-vacuum (or crystal-quasi-liquid layer) interface precedes the complete loss of order at the interface.

  11. Anisotropy in surface-initiated melting of the triclinic molecular crystal 1,3,5-triamino-2,4,6-trinitrobenzene: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Mathew, N.; Sewell, Thomas D.; Thompson, Donald L.

    2015-09-01

    Surface-initiated melting of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a triclinic molecular crystal, was investigated using molecular dynamics simulations. Simulations were performed for the three principal crystallographic planes exposed to vacuum, with the normal vectors to the planes given by b × c, c × a, and a × b (where a, b, and c define the edge vectors of the unit cell), denoted as (100), (010), and (001), respectively. The best estimate of the normal melting temperature for TATB is 851 ± 5 K. The nature and extent of disordering of the crystal-vacuum interface depend on the exposed crystallographic face, with the (001) face exhibiting incomplete melting and superheating. This is attributed to the anisotropy of the inter-molecular hydrogen bonding and the propensity of the crystal to form stacking faults in directions approximately perpendicular to the (100) and (010) faces. For all three crystal orientations, formation of molecular vacancies in the lattice at the crystal-vacuum (or crystal-quasi-liquid layer) interface precedes the complete loss of order at the interface.

  12. MOLECULAR ORBITALS AND ELECTRON-TRANSFER SPECTRA IN RUTILE. GROWTH OF CRYSTALS BY FLAME FUSION,

    DTIC Science & Technology

    CRYSTAL GROWTH , *TITANIUM COMPOUNDS, *ABSORPTION, SINGLE CRYSTALS , OXIDES, MEASUREMENT, ELECTRON TRANSITIONS, SPECTROPHOTOMETERS, ULTRAVIOLET...RADIATION, POLARIZATION, CRYSTAL STRUCTURE, SYMMETRY(CRYSTALLOGRAPHY), YTTRIUM COMPOUNDS, ALUMINUM COMPOUNDS.

  13. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    PubMed

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  14. Excitation of rotons in parahydrogen crystals: The laser-induced-molecular-alignment mechanism

    NASA Astrophysics Data System (ADS)

    Lindgren, Johan; Kiljunen, Toni

    2013-10-01

    Solid parahydrogen (p-H2) is known to support long-lived coherences, of the order of 100 ps, which enables high-resolution spectroscopy in the time domain. Rotational Raman-type excitations to sublevels of J=2 are delocalized due to electric-quadrupole-quadrupole coupling in p-H2 crystals, and the resulting states can be characterized as rotons. Wave packets of rotons exhibit molecular alignment with respect to laboratory coordinates. Here the concept of field-free molecular alignment, induced by strong ultrashort laser pulses, is extended into a molecular solid case. We derive a solid-state analog for the gas-phase alignment measure and illustrate the time-dependent alignment degree in p-H2 crystals by numerical simulations. To underscore the Raman gain effect of the solid, general properties of the field-free alignment are revisited by comparing gaseous p-H2 with N2. The interplay between the polarization direction of the excitation pulses and the axis directionality of the crystal is shown to affect the alignment dynamics via the spatial (M=0,±1,±2) composition of the roton wave packets. We simulate experimental traces by incorporating the induced alignment degree in the calculation of heterodyne-detected realization of femtosecond pump-probe optical Kerr effect spectroscopy. With the help of dispersed, two-dimensional resolved images of the calculated signal we reproduce the experiment as a whole. To that end, the effects of probe chirp, shape, and power must be explored in detail. We find good agreement with previous experiments and unravel the ambiguity of tracing back the wave-packet composition from the signal; in particular, we find that the effect of quantum phase factors of all the components should be taken into account when explaining the signal properties.

  15. How the Molecular Packing Affects the Room Temperature Phosphorescence in Pure Organic Compounds: Ingenious Molecular Design, Detailed Crystal Analysis, and Rational Theoretical Calculations.

    PubMed

    Xie, Yujun; Ge, Yuwei; Peng, Qian; Li, Conggang; Li, Qianqian; Li, Zhen

    2017-02-21

    Long-lived phosphorescence at room temperature (RTP) from pure organic molecules is rare. Recent research reveals various crystalline organic molecules can realize RTP with lifetimes extending to the magnitude of second. There is little research on how molecular packing affecting RTP. Three compounds are designed with similar optical properties in solution, but tremendously different solid emission characteristics. By investigating the molecular packing arrangement in single crystals, it is found that the packing style of the compact face to face favors of long phosphorescence lifetime and high photoluminescence efficiency, with the lifetime up to 748 ms observed in the crystal of CPM ((9H-carbazol-9-yl)(phenyl)methanone). Theoretical calculation analysis also reveals this kind of packing style can remarkably reduce the singlet excited energy level and prompt electron communication between dimers. Surprisingly, CPM has two very similar single crystals, labeled as CPM and CPM-A, with almost identical crystal data, and the only difference is that molecules in CPM-A crystal take a little looser packing arrangement. X-ray diffraction and cross-polarization under magic spinning (13) C NMR spectra double confirm that they are different crystals. Interestingly, CPM-A crystal shows negligible RTP compared to the CPM crystal, once again proving that the packing style is critical to the RTP property.

  16. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  17. Detection of Non-Equilibrium Fluctuations in Active Gels

    NASA Astrophysics Data System (ADS)

    Bacanu, Alexandru; Broedersz, Chase; Gladrow, Jannes; Mackintosh, Fred; Schmidt, Christoph; Fakhri, Nikta

    Active force generation at the molecular scale in cells can result in stochastic non-equilibrium dynamics on mesoscpopic scales. Molecular motors such as myosin can drive steady-state stress fluctuations in cytoskeletal networks. Here, we present a non-invasive technique to probe non-equilibrium fluctuations in an active gel using single-walled carbon nanotubes (SWNTs). SWNTs are semiflexible polymers with intrinsic fluorescence in the near infrared. Both thermal and active motor-induced forces in the network induce transverse fluctuations of SWNTs. We demonstrate that active driven shape fluctuations of the SWNTs exhibit dynamics that reflect the non-equilibrium activity, in particular the emergence of correlations between the bending modes. We discuss the observation of breaking of detailed balance in this configurational space of the SWNT probes. Supported by National Defense Science and Engineering Graduate Student Fellowship (NDSEG).

  18. Elastic anisotropy of shocked aluminum single crystals: Use of molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zimmerman, J. A.; Winey, J. M.; Gupta, Y. M.

    2011-05-01

    Molecular dynamics (MD) calculations were used to examine shock wave propagation along [100], [111], and [110] directions in aluminum single crystals. Four different embedded-atom method (EAM) potentials were used to obtain wave profiles in ideal (defect-free) crystals shocked to peak longitudinal stresses approaching 13 GPa. Due to the lack of defects in the simulated crystals, the peak stresses considered, and the short time scales examined, inelastic deformation was not observed in the MD simulations. Time-averaged and spatially averaged continuum variables were determined from the MD simulations to compare results from different potentials and to provide a direct comparison with results from nonlinear elastic continuum calculations that incorporated elastic constants up to fourth order. These comparisons provide a basis for selecting the optimal potential from among the four potentials examined. MD results for shocks along the [100] direction show significant differences for stresses and densities determined from simulations using different EAM potentials. In contrast, the continuum variables for shocks along the [111] and [110] directions show smaller differences for three of the four potentials examined. Comparisons with the continuum calculations show that the potential developed recently by Winey, Kubota, and Gupta [Modell. Simul. Mater. Sci. Eng.0965-039310.1088/0965-0393/17/5/055004 17, 055004 (2009)] provides the best overall agreement between the MD simulations and the continuum calculations. As such, this potential is recommended for MD simulations of shock wave propagation in aluminum single crystals. Extending the current findings to elastic-plastic deformation would be desirable. More generally, our work demonstrates that MD simulations of elastic shock waves in defect-free single crystals, in combination with nonlinear elastic continuum calculations, constitute an important step in establishing the applicability of classical MD potentials for

  19. Nonequilibrium thermodynamics of spacetime.

    PubMed

    Eling, Christopher; Guedens, Raf; Jacobson, Ted

    2006-03-31

    It has previously been shown that the Einstein equation can be derived from the requirement that the Clausius relation dS=deltaQ/T hold for all local acceleration horizons through each spacetime point, where is one-quarter the horizon area change in Planck units and deltaQ and T are the energy flux across the horizon and the Unruh temperature seen by an accelerating observer just inside the horizon. Here we show that a curvature correction to the entropy that is polynomial in the Ricci scalar requires a nonequilibrium treatment. The corresponding field equation is derived from the entropy balance relation dS=deltaQ/T+diS, where diS is a bulk viscosity entropy production term that we determine by imposing energy-momentum conservation. Entropy production can also be included in pure Einstein theory by allowing for shear viscosity of the horizon.

  20. Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen

    PubMed Central

    Pandian, Ramasamy P.; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M.; Hammel, P. Chris; Manoharan, Periakaruppan T.; Kuppusamy, Periannan

    2009-01-01

    The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å2 in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å2) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO2 with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy. PMID:19809598