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Sample records for polarized atomistic molecular

  1. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

    PubMed Central

    Bjelkmar, Pär; Niemelä, Perttu S.; Vattulainen, Ilpo; Lindahl, Erik

    2009-01-01

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations. PMID:19229308

  2. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  3. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  4. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    PubMed

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  6. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    PubMed

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-10-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  7. PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

    PubMed Central

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-01-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  8. Molecular cooperativity and compatibility via full atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kwan Yang, Kenny

    Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

  9. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

    SciTech Connect

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R.

    2014-04-07

    An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

  10. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    SciTech Connect

    Jay A Brandes

    2009-09-23

    This was a grant to support travel for scientists to present data and interact with others in their field. Specifically, speakers presented their data in a session entitled “Interfacial Phenomena: Linking Atomistic and Macroscopic Properties: Theoretical and Experimental Studies of the Structure and Reactivity of Mineral Surfaces”. The session ran across three ½ day periods, March 30-31 2004. The session’s organizers were David J. Wesolowski andGordon E. Brown Jr. There were a total of 30 talks presented.

  11. Molecular content of polar-ring galaxies

    NASA Astrophysics Data System (ADS)

    Combes, F.; Moiseev, A.; Reshetnikov, V.

    2013-06-01

    We have searched for CO lines in a sample of 21 new morphologically determined polar-ring galaxies (of which nine are kinematically confirmed), obtained from a wide search in the Galaxy Zoo project by Moiseev and collaborators. Polar-ring galaxies (PRGs) are a unique class of objects, tracing special episodes in the galaxy mass assembly: they can be formed through galaxy interaction and merging, but also through accretion from cosmic filaments. Furthermore, they enable the study of dark matter haloes in three dimensions. The polar ring itself is a sub-system rich in gas, where molecular gas is expected, and new stars are formed. Among the sample of 21 PRGs, we have detected five CO-rich systems, that can now be followed up with higher spatial resolution. Their average molecular mass is 9.4 × 109M⊙, and their average gas fraction is 27% of their baryonic mass, with a range from 15 to 43%, implying that they have just accreted a large amount of gas. The position of the detected objects in the velocity-magnitude diagram is offset from the Tully-Fisher relation of normal spirals, as was already found for PRGs. This work is part of our multi-wavelength project to determine the detailed morphology and dynamics of PRGs, test through numerical models their formation scenario, and deduce their dark matter content and 3D-shape. Based on observations carried out with the IRAM 30 m telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).Spectra of detections are available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (ftp://130.79.128.5">130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/554/A11

  12. Atomistic Molecular Dynamics Simulations of Crude Oil/Brine Displacement in Calcite Mesopores.

    PubMed

    Sedghi, Mohammad; Piri, Mohammad; Goual, Lamia

    2016-04-12

    Unconventional reservoirs such as hydrocarbon-bearing shale formations and ultratight carbonates generate a large fraction of oil and gas production in North America. The characteristic feature of these reservoirs is their nanoscale porosity that provides significant surface areas between the pore walls and the occupying fluids. To better assess hydrocarbon recovery from these formations, it is crucial to develop an improved insight into the effects of wall-fluid interactions on the interfacial phenomena in these nanoscale confinements. One of the important properties that controls the displacement of fluids inside the pores is the threshold capillary pressure. In this study, we present the results of an integrated series of large-scale molecular dynamics (MD) simulations performed to investigate the effects of wall-fluid interactions on the threshold capillary pressures of oil-water/brine displacements in a calcite nanopore with a square cross section. Fully atomistic models are utilized to represent crude oil, brine, and calcite in order to accommodate electrostatic interactions and H-bonding between the polar molecules and the calcite surface. To this end, we create mixtures of various polar and nonpolar organic molecules to better represent the crude oil. The interfacial tension between oil and water/brine and their contact angle on calcite surface are simulated. We study the effects of oil composition, water salinity, and temperature and pressure conditions on these properties. The threshold capillary pressure values are also obtained from the MD simulations for the calcite nanopore. We then compare the MD results against those generated using the Mayer-Stowe-Princen (MSP) method and explain the differences. PMID:27010399

  13. Hybrid Atomistic and Coarse-Grained Molecular Dynamics Simulations of Polyethylene Glycol (PEG) in Explicit Water.

    PubMed

    Stanzione, Francesca; Jayaraman, Arthi

    2016-05-01

    In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869

  14. Ultrathin Molecular-Layer-by-Layer Polyamide Membranes: Insights from Atomistic Molecular Simulations.

    PubMed

    Liyana-Arachchi, Thilanga P; Sturnfield, James F; Colina, Coray M

    2016-09-01

    In this study, we present an atomistic simulation study of several physicochemical properties of polyamide (PA) membranes formed from interfacial polymerization or from a molecular-layer-by-layer (mLbL) on a silicon wafer. These membranes are composed of meta-phenylenediamine (MPD) and benzene-1,3,5-tricarboxylic acid chloride (TMC) for potential reverse osmosis (RO) applications. The mLbL membrane generation procedure and the force field models were validated, by comparison with available experimental data, for hydrated density, membrane swelling, and pore size distributions of PA membranes formed by interfacial polymerization. Physicochemical properties such as density, free volume, thickness, the degree of cross-linking, atomic compositions, and average molecular orientation (which is relevant for the mLbL membranes) are compared for these different processes. The mLbL membranes are investigated systematically with respect to TMC monomer growth rate per substrate surface area, MPD/TMC ratio, and the number of mLbL deposition cycles. Atomistic simulations show that the mLbL deposition generates membranes with a constant film growth if both the TMC monomer growth rate and MPD/TMC monomer ratio are kept constant. The film growth rate increases with TMC monomer growth rate or MPD/TMC ratio. Furthermore, it was found on one hand that the mLbL membrane density and free volume varies significantly with respect to the TMC monomer growth rate, while on the other hand the degree of cross-linking and the atomic composition varies considerably with the MPD/TMC ratio. Additionally, it was found that both TMC and MPD orient at a tilted angle with respect to the substrate surface, where their angular distribution and average angle orientation depend on both the TMC growth rate and the number of deposition cycles. This study illustrates that molecular simulations can play a crucial role in the understanding of structural properties that can empower the design of the next

  15. Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

    NASA Astrophysics Data System (ADS)

    Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

    2013-04-01

    Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

  16. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

    PubMed

    Zhang, Wenjun; Wang, Ming L; Cranford, Steven W

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  17. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    PubMed Central

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  18. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  19. Atomistic Molecular Dynamics Simulations of the Electrical Double

    NASA Astrophysics Data System (ADS)

    Li, Zifeng; Milner, Scott; Fichthorn, Kristen

    2015-03-01

    The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

  20. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

    PubMed Central

    Maffeo, Christopher; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

    The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures. PMID:26980283

  1. Atomistic simulation based prediction of the solvent effect on the molecular mobility and glass transition of poly (methyl methacrylate)

    NASA Astrophysics Data System (ADS)

    Mishra, Shawn; Keten, Sinan

    2013-01-01

    We present an investigation of the retained solvent effect on the glass transition temperature (Tg) of poly(methyl methacrylate) (PMMA) through all-atom molecular dynamics simulations. Addition of a weakly interactive solvent, tetrahydrofuran (THF), causes a depression of the PMMA Tg that can be identified through an analysis of the mean squared displacement of the polymer chains from atomistic trajectories. Our results are in very good agreement with an atomistically informed theoretical model based on free volume theory and demonstrate the applicability of molecular simulation to discern solvent effects on polymer thermomechanical behavior in silico.

  2. Fully atomistic molecular dynamics simulation of nanosilica-filled crosslinked polybutadiene

    NASA Astrophysics Data System (ADS)

    Pavlov, Alexander S.; Khalatur, Pavel G.

    2016-06-01

    We report on the first fully atomistic simulation of sulfur-crosslinked cis-1,4-polybutadiene (PB) rubbers, both unfilled and nanosilica-filled. A well-integrated network is built by crosslinking the coarse-grained precursor PB chains. The initial configurations for subsequent molecular dynamics simulations are obtained by reverse mapping of well-equilibrated coarse-grained systems. Thermal and mechanical properties of the PB-based elastomers are predicted in reasonable agreement with experiment. The inclusion of silica nanoparticles into the model rubber increases the glass transition temperature and elastic modulus. Under tensile loading conditions, the formation of structural defects (microcavities) within the polymer bulk is observed for nanocomposite at the elastomer/nanoparticle interfaces.

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

    NASA Astrophysics Data System (ADS)

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

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

  4. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    PubMed

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  5. Atomistic mechanisms of amorphization during nanoindentation of SiC: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Szlufarska, Izabela; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2005-05-01

    Atomistic mechanisms underlying the nanoindentation-induced amorphization in SiC crystal has been studied by molecular dynamics simulations on parallel computers. The calculated load-displacement curve consists of a series of load drops, corresponding to plastic deformation, in addition to a shoulder at a smaller displacement, which is fully reversible upon unloading. The peaks in the load-displacement curve are shown to reflect the crystalline structure and dislocation activities under the surface. The evolution of indentation damage and defect accumulation are also discussed in terms of bond angles, local pressure, local shear stress, and spatial rearrangements of atoms. These structural analyses reveal that the defect-stimulated growth and coalescence of dislocation loops are responsible for the crystalline-to-amorphous transition. The shortest-path-ring analysis is effectively employed to characterize nanoindentation-induced structural transformations and dislocation activities.

  6. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    PubMed Central

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  7. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V

    2015-09-01

    Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936

  8. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    PubMed

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  9. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

    PubMed

    Oakes, V; Furini, S; Domene, C

    2016-01-01

    The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. PMID:27586285

  10. Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study

    PubMed Central

    Telesco, Shannon E.; Radhakrishnan, Ravi

    2009-01-01

    HER2 (ErbB2/Neu) is a receptor tyrosine kinase belonging to the epidermal growth factor receptor (EGFR)/ErbB family and is overexpressed in 20–30% of human breast cancers. Although several crystal structures of ErbB kinases have been solved, the precise mechanism of HER2 activation remains unknown, and it has been suggested that HER2 is unique in its requirement for phosphorylation of Y877, a key tyrosine residue located in the activation loop. To elucidate mechanistic details of kinase domain regulation, we performed molecular dynamics simulations of a homology-modeled HER2 kinase structure in active and inactive conformations. Principal component analysis of the atomistic fluctuations reveals a tight coupling between the activation loop and catalytic loop that may contribute to alignment of residues required for catalysis in the active kinase. The free energy perturbation method is also employed to predict a role for phosphorylated Y877 in stabilizing the kinase conformations. Finally, simulation results are presented for a HER2/EGFR heterodimer and reveal that the dimeric interface induces a rearrangement of the αC helix toward the active conformation. Elucidation of the molecular regulatory mechanisms in HER2 will help establish structure-function relationships in the wild-type kinase, as well as predict mutations with a propensity for constitutive activation in HER2-mediated cancers. PMID:19289058

  11. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

    PubMed Central

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210

  12. Function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

    SciTech Connect

    Nutt, David; Smith, Jeremy C

    2008-10-01

    Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.

  13. Atomistic Molecular Dynamics Simulations of Charged Latex Particle Surfaces in Aqueous Solution.

    PubMed

    Li, Zifeng; Van Dyk, Antony K; Fitzwater, Susan J; Fichthorn, Kristen A; Milner, Scott T

    2016-01-19

    Charged particles in aqueous suspension form an electrical double layer at their surfaces, which plays a key role in suspension properties. For example, binder particles in latex paint remain suspended in the can because of repulsive forces between overlapping double layers. Existing models of the double layer assume sharp interfaces bearing fixed uniform charge, and so cannot describe aqueous binder particle surfaces, which are soft and diffuse, and bear mobile charge from ionic surfactants as well as grafted multivalent oligomers. To treat this industrially important system, we use atomistic molecular dynamics simulations to investigate a structurally realistic model of commercial binder particle surfaces, informed by extensive characterization of particle synthesis and surface properties. We determine the interfacial profiles of polymer, water, bound and free ions, from which the charge density and electrostatic potential can be calculated. We extend the traditional definitions of the inner and outer Helmholtz planes to our diffuse interfaces. Beyond the Stern layer, the simulated electrostatic potential is well described by the Poisson-Boltzmann equation. The potential at the outer Helmholtz plane compares well to the experimental zeta potential. We compare particle surfaces bearing two types of charge groups, ionic surfactant and multivalent oligomers, with and without added salt. Although the bare charge density of a surface bearing multivalent oligomers is much higher than that of a surfactant-bearing surface at realistic coverage, greater counterion condensation leads to similar zeta potentials for the two systems. PMID:26735020

  14. Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

    SciTech Connect

    Lee, One-Sun; Stupp, Samuel I.; Schatz, George C.

    2011-01-01

    Relaxation of a self-assembled structure of 144 peptide amphiphile (PA) molecules into cylindrical nanofibers is studied using atomistic molecular dynamics simulations including explicit water with physiological ion concentration. The PA for these studies includes a hydrophobic alkyl chain that is attached to the N-terminus of the sequence SLSLAAAEIKVAV. The self-assembly is initiated with PA molecules in a roughly cylindrical configuration, as suggested from previous experimental and theoretical investigations, and the cylindrical configuration that results is found to be stable during 40 ns simulations. In the converged structure of the resulting nanofiber, the cylinder radius is ~44 Å, a result that is consistent with experimental results. Water and sodium ions can penetrate into the peptide portion of the fiber but not between the alkyl chains. Even though each PA has an identical sequence, a broad distribution of secondary structure is found in the converged structure of the nanofiber. The β-sheet population for the SLSL and IKV segments of the peptide is ~25%, which is consistent with previous circular dichroism results. We also found that the epitope sequence IKVAV is located on the surface of the nanofiber, as designed for the promotion of the neurite growth. Our findings will be useful for designing new PA fibers that have improved bioactive properties.

  15. Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis.

    PubMed

    Sutthibutpong, Thana; Noy, Agnes; Harris, Sarah

    2016-01-01

    While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA. PMID:27283311

  16. Communication: Phase diagram of C36 by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    NASA Astrophysics Data System (ADS)

    Abramo, M. C.; Caccamo, C.; Costa, D.; Munaò, G.

    2014-09-01

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. We first show that free energies obtained via thermodynamic integrations along isotherms displaying "van der Waals loops," are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C36, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400-1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C36 fullerite and of its liquid state, at variance with what previously experienced for C60.

  17. Polarization effects in molecular mechanical force fields.

    PubMed

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594

  18. Polarization effects in molecular mechanical force fields

    PubMed Central

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2014-01-01

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594

  19. ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

    PubMed

    Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

    2010-04-15

    We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. PMID:19824035

  20. Understanding polarization properties of InAs quantum dots by atomistic modeling of growth dynamics

    SciTech Connect

    Tasco, Vittorianna; Todaro, Maria Teresa; De Giorgi, Milena; Passaseo, Adriana; Usman, Muhammad

    2013-12-04

    A model for realistic InAs quantum dot composition profile is proposed and analyzed, consisting of a double region scheme with an In-rich internal core and an In-poor external shell, in order to mimic the atomic scale phenomena such as In-Ga intermixing and In segregation during the growth and overgrowth with GaAs. The parameters of the proposed model are derived by reproducing the experimentally measured polarization data. Further understanding is developed by analyzing the strain fields which suggests that the two-composition model indeed results in lower strain energies than the commonly applied uniform composition model.

  1. Molecular and intermolecular effects in collagen fibril mechanics: a multiscale analytical model compared with atomistic and experimental studies.

    PubMed

    Marino, Michele

    2016-02-01

    Both atomistic and experimental studies reveal the dependence of collagen fibril mechanics on biochemical and biophysical features such as, for instance, cross-link density, water content and protein sequence. In order to move toward a multiscale structural description of biological tissues, a novel analytical model for collagen fibril mechanics is herein presented. The model is based on a multiscale approach that incorporates and couples: thermal fluctuations in collagen molecules; the uncoiling of collagen triple helix; the stretching of molecular backbone; the straightening of the telopeptide in which covalent cross-links form; slip-pulse mechanisms due to the rupture of intermolecular weak bonds; molecular interstrand delamination due to the rupture of intramolecular weak bonds; the rupture of covalent bonds within molecular strands. The effectiveness of the proposed approach is verified by comparison with available atomistic results and experimental data, highlighting the importance of cross-link density in tuning collagen fibril mechanics. The typical three-region shape and hysteresis behavior of fibril constitutive response, as well as the transition from a yielding-like to a brittle-like behavior, are recovered with a special insight on the underlying nanoscale mechanisms. The model is based on parameters with a clear biophysical and biochemical meaning, resulting in a promising tool for analyzing the effect of pathological or pharmacological-induced histochemical alterations on the functional mechanical response of collagenous tissues. PMID:26220454

  2. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

    SciTech Connect

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; Opper, Kathleen L.; Wagener, Kenneth B.; Stevens, Mark J.; Frischknecht, Amalie Lucile; Winey, Karen I.

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. In these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average

  3. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

    DOE PAGESBeta

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; Opper, Kathleen L.; Wagener, Kenneth B.; Stevens, Mark J.; Frischknecht, Amalie Lucile; Winey, Karen I.

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the

  4. A DMPA Langmuir monolayer study: from gas to solid phase. An atomistic description by molecular dynamics Simulation.

    PubMed

    Giner-Casares, J J; Camacho, L; Martín-Romero, M T; Cascales, J J López

    2008-03-01

    In this work, a DMPA Langmuir monolayer at the air/water interface was studied by molecular dynamics simulations. Thus, an atomistic picture of a Langmuir monolayer was drawn from its expanded gas phase to its final solid condensed one. In this sense, some properties of monolayers that were traditionally poorly or even not reproduced in computer simulations, such as lipid domain formation or pressure-area per lipid isotherm, were properly reproduced in this work. Thus, the physical laws that control the lipid domain formation in the gas phase and the structure of lipid monolayers from the gas to solid condensed phase were studied. Thanks to the atomistic information provided by the molecular dynamics simulations, we were able to add valuable information to the experimental description of these processes and to access experimental data related to the lipid monolayers in their expanded phase, which is difficult or inaccessible to study by experimental techniques. In this sense, properties such as lipids head hydration and lipid structure were studied. PMID:18225932

  5. Molecular hydrogen polarization images of OMC-1

    SciTech Connect

    Burton, M.G.; Minchin, N.R.; Hough, J.H.; Aspin, C.; Axon, D.J. California Univ., Irvine Hatfield Polytechnic Joint Astronomy Centre, Hilo, HI Nuffield Radio Astronomy Labs., Jodrell Bank )

    1991-07-01

    An image of the polarization of the shocked H2 v = 1-0 S(1) line emission in the core of OMC-1 has been obtained. Along the molecular outflow of the source, the line is dichroically polarized by a medium of aligned grains located between the earth and the shock fronts. The polarization pattern traces the magnetic field direction, which is parallel to the outflow axis and to the large-scale field direction determined from far-IR continuum measurements. Close to the IR source IRc2, the likely source of the outflow, the aligned vectors twist, indicating that the magnetic field direction changes. Modeling the line ratios of scattered H2 lines in the reflection nebula, it is concluded that the size distribution of grains there is typical of the small grains in the diffuse interstellar medium. By contrast, the scattered continuum radiation from the core region suggests that the grains there are larger than this. 33 refs.

  6. Molecular hydrogen polarization images of OMC-1

    NASA Technical Reports Server (NTRS)

    Burton, Michael G.; Minchin, N. R.; Hough, J. H.; Aspin, C.; Axon, D. J.

    1991-01-01

    An image of the polarization of the shocked H2 v = 1-0 S(1) line emission in the core of OMC-1 has been obtained. Along the molecular outflow of the source, the line is dichroically polarized by a medium of aligned grains located between the earth and the shock fronts. The polarization pattern traces the magnetic field direction, which is parallel to the outflow axis and to the large-scale field direction determined from far-IR continuum measurements. Close to the IR source IRc2, the likely source of the outflow, the aligned vectors twist, indicating that the magnetic field direction changes. Modeling the line ratios of scattered H2 lines in the reflection nebula, it is concluded that the size distribution of grains there is typical of the small grains in the diffuse interstellar medium. By contrast, the scattered continuum radiation from the core region suggests that the grains there are larger than this.

  7. Order and conformation of biphenyl in cyanobiphenyl liquid crystals: a combined atomistic molecular dynamics and 1H NMR study.

    PubMed

    Pizzirusso, Antonio; Di Pietro, Maria Enrica; De Luca, Giuseppina; Celebre, Giorgio; Longeri, Marcello; Muccioli, Luca; Zannoni, Claudio

    2014-05-19

    The alignment of biphenyl (2P) in the liquid-crystal phases of 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4-n-octyl-4'-cyanobiphenyl (8CB) is investigated by using a combination of predictive atomistic molecular dynamics (MD) simulations and (1)H liquid-crystal nuclear magnetic resonance (LXNMR) residual dipolar coupling measurements. A detailed comparison and validation of the MD results with LXNMR is provided, showing a good agreement between the simulated and experimental dipolar couplings at the same reduced temperature. MD is then used to examine the location of 2P in the smectic phase, which is unavailable to LXNMR, and 2P is found to be rather uniformly distributed. The combination of MD and NMR spectroscopy provides detailed information about the order, interconnection between orientation and conformation, local positional order, and interactions with the liquid-crystalline solvent. PMID:24692106

  8. Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics.

    PubMed

    Booth, Jonathan J; Shalashilin, Dmitrii V

    2016-02-01

    The results of boxed dynamics (BXD) fully atomistic simulations of protein unfolding by atomic force microscopy (AFM) in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on a time scale which is too long for standard atomistic molecular dynamics (MD) simulations, which are usually performed with the addition of forces which exceed those of experiment by many orders of magnitude. BXD can reach the time scale of slow unfolding and sample the very high free energy unfolding pathway, reproducing the experimental dependence of pulling force against extension and extension against time. Calculations show the presence of the pulling force "humps" previously observed in the VC AFM experiments and allow the identification of intermediate protein conformations responsible for them. Fully atomistic BXD simulations can estimate the rate of unfolding in the FC experiments up to the time scale of seconds. PMID:26760898

  9. Atomistic and molecular effects in electric double layers at high surface charges

    SciTech Connect

    Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

    2015-06-16

    Here, the Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities provided by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.

  10. Atomistic and molecular effects in electric double layers at high surface charges

    DOE PAGESBeta

    Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

    2015-06-16

    Here, the Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities providedmore » by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.« less

  11. Atomistic and Molecular Effects in Electric Double Layers at High Surface Charges

    SciTech Connect

    Templeton, Jeremy Alan; Lee, Jonathan; Mani, Ali

    2015-06-16

    The Poisson–Boltzmann theory for electrolytes near a charged surface is known to be invalid due to unaccounted physics associated with high ion concentration regimes. In order to investigate this regime, fluids density functional theory (f-DFT) and molecular dynamics (MD) simulations were used to determine electric surface potential as a function of surface charge. Based on these detailed computations, for electrolytes with nonpolar solvent, the surface potential is shown to depend quadratically on the surface charge in the high charge limit. We demonstrate that modified Poisson–Boltzmann theories can model this limit if they are augmented with atomic packing densities provided by MD. However, when the solvent is a highly polar molecule water an intermediate regime is identified in which a constant capacitance is realized. Simulation results demonstrate the mechanism underlying this regime, and for the salt water system studied here, it persists throughout the range of physically realistic surface charge densities so the potential’s quadratic surface charge dependence is not obtained.

  12. Parallel Atomistic Simulations

    SciTech Connect

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  13. Modulation of electronic and self-assembly properties of a donor-acceptor-donor-based molecular materials via atomistic approach.

    PubMed

    Dhar, Joydeep; Swathi, K; Karothu, Durga Prasad; Narayan, K S; Patil, Satish

    2015-01-14

    The performance of molecular materials in optoelectronic devices critically depends upon their electronic properties and solid-state structure. In this report, we have synthesized sulfur and selenium based (T4BT and T4BSe) donor-acceptor-donor (D-A-D) organic derivatives in order to understand the structure-property correlation in organic semiconductors by selectively tuning the chalcogen atom. The photophysical properties exhibit a significant alteration upon varying a single atom in the molecular structure. A joint theoretical and experimental investigation suggests that replacing sulfur with selenium significantly reduces the band gap and molar absorption coefficient because of lower electronegativity and ionization potential of selenium. Single-crystal X-ray diffraction analysis showed differences in their solid-state packing and intermolecular interactions. Subsequently, difference in the solid-state packing results variation in self-assembly. Micorstructural changes within these materials are correlated to their electrical resistance variation, investigated by conducting probe atomic force microscopy (CP-AFM) measurements. These results provide useful guidelines to understand the fundamental properties of D-A-D materials prepared by atomistic modulation. PMID:25532139

  14. Prediction of cosolvent effect on solvation free energies and solubilities of organic compounds in supercritical carbon dioxide based on fully atomistic molecular simulations.

    PubMed

    Frolov, Andrey I; Kiselev, Michael G

    2014-10-01

    The solubility of organic compounds in supercritical fluids can be dramatically affected by addition of a suitable cosolvent (entrainer) at small concentrations. This makes the screening of the best-suited cosolvent an important task for the supercritical technology. The present study aims to improve our fundamental understanding of solvation in supercritical CO2 with cosolvents. We address the following questions: (1) How does the solvation free energy depend on the chemical class of an organic solute and the chemical nature of co-solvents? (2) Which intermolecular interactions determine the effect of a cosolvent on the solubility of organic compounds? We performed extensive calculations of solvation free energies of monofunctional organic molecules at infinite dilution in supercritical media by the Bennett's acceptance ratio method based on fully atomistic molecular dynamics sampling. Sixteen monofunctional organic molecules were solvated in pure sc-CO2 and sc-CO2 with addition of 6 molar % of cosolvents of different chemical nature: ethanol, acetone, and n-hexane. Cosolvent-induced solubility enhancement (CISE) factors were also calculated. It was found that formation of significant number of hydrogen bonds between a solute and cosolvent molecules leads to a profound solubility enhancement. The cosolvent effect is proportional to the number of hydrogen bonds. When polar cosolvents do not form hydrogen bonds with solutes, the CISE correlates with the dipole moment of solute molecules. However, the electrostatic interactions have a small impact on the solubility enhancement compared to hydrogen bonding. Addition of a nonpolar cosolvent, n-hexane, has a very little effect on the solvation Gibbs free energy of studied small organic molecules. The observed trends were discussed in line with available experimental data. PMID:25181254

  15. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    NASA Astrophysics Data System (ADS)

    Langeloth, Michael; Sugii, Taisuke; Böhm, Michael C.; Müller-Plathe, Florian

    2015-12-01

    We investigate the volumetric glass transition temperature Tg in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that Tg increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition Tg in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that Tg is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  16. Communication: Phase diagram of C{sub 36} by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    SciTech Connect

    Abramo, M. C.; Caccamo, C. Costa, D.; Munaò, G.

    2014-09-07

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C{sub 36}. We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C{sub 36}, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C{sub 36} fullerite and of its liquid state, at variance with what previously experienced for C{sub 60}.

  17. Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

    PubMed Central

    Abriata, Luciano A.; Dal Peraro, Matteo

    2015-01-01

    Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027

  18. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    SciTech Connect

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

    2015-12-28

    We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  19. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Berdiyorov, G.; Harrabi, K.; Mehmood, U.; Peeters, F. M.; Tabet, N.; Zhang, J.; Hussein, I. A.; McLachlan, M. A.

    2015-07-01

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C60 and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C60 is an order of magnitude larger than the one for PCBM.

  20. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    SciTech Connect

    Berdiyorov, G. Tabet, N.; Harrabi, K.; Mehmood, U.; Hussein, I. A.; Peeters, F. M.; Zhang, J.; McLachlan, M. A.

    2015-07-14

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.

  1. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  2. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.

    PubMed

    Pasi, Marco; Lavery, Richard

    2016-06-20

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA-core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA-core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  3. Atomistic simulation of solid-liquid coexistence for molecular systems: Application to triazole and benzene

    NASA Astrophysics Data System (ADS)

    Eike, David M.; Maginn, Edward J.

    2006-04-01

    A method recently developed to rigorously determine solid-liquid equilibrium using a free-energy-based analysis has been extended to analyze multiatom molecular systems. This method is based on using a pseudosupercritical transformation path to reversibly transform between solid and liquid phases. Integration along this path yields the free energy difference at a single state point, which can then be used to determine the free energy difference as a function of temperature and therefore locate the coexistence temperature at a fixed pressure. The primary extension reported here is the introduction of an external potential field capable of inducing center of mass order along with secondary orientational order for molecules. The method is used to calculate the melting point of 1-H-1,2,4-triazole and benzene. Despite the fact that the triazole model gives accurate bulk densities for the liquid and crystal phases, it is found to do a poor job of reproducing the experimental crystal structure and heat of fusion. Consequently, it yields a melting point that is 100K lower than the experimental value. On the other hand, the benzene model has been parametrized extensively to match a wide range of properties and yields a melting point that is only 20K lower than the experimental value. Previous work in which a simple "direct heating" method was used actually found that the melting point of the benzene model was 50K higher than the experimental value. This demonstrates the importance of using proper free energy methods to compute phase behavior. It also shows that the melting point is a very sensitive measure of force field quality that should be considered in parametrization efforts. The method described here provides a relatively simple approach for computing melting points of molecular systems.

  4. Liquid state DNP at high magnetic fields: Instrumentation, experimental results and atomistic modelling by molecular dynamics simulations.

    PubMed

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

    Dynamic nuclear polarization (DNP) at high magnetic fields has recently become one of the major research areas in magnetic resonance spectroscopy and imaging. Whereas much work has been devoted to experiments where the polarization transfer from the electron spin to the nuclear spin is performed in the solid state, only a few examples exist of experiments where the polarization transfer is performed in the liquid state. Here we describe such experiments at a magnetic field of 9.2 T, corresponding to a nuclear Larmor frequency of 400 MHz for proton spins and an excitation frequency of 263 GHz for the electron spins. The technical requirements to perform such experiments are discussed in the context of the double resonance structures that we have implemented. The experimental steps that allowed access to the enhancement factors for proton spins of several organic solvents with nitroxide radicals as polarizing agents are described. A computational scheme for calculating the coupling factors from molecular dynamics (MD) simulations is outlined and used to highlight the limitations of the classical models based on translational and rotational motion that are typically employed to quantify the observed coupling factors. The ability of MD simulations to predict enhancements for a variety of radicals and solvent molecules at any magnetic field strength should prove useful in optimizing experimental conditions for DNP in the liquid state. PMID:26920832

  5. Liquid state DNP at high magnetic fields: Instrumentation, experimental results and atomistic modelling by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

    Dynamic nuclear polarization (DNP) at high magnetic fields has recently become one of the major research areas in magnetic resonance spectroscopy and imaging. Whereas much work has been devoted to experiments where the polarization transfer from the electron spin to the nuclear spin is performed in the solid state, only a few examples exist of experiments where the polarization transfer is performed in the liquid state. Here we describe such experiments at a magnetic field of 9.2 T, corresponding to a nuclear Larmor frequency of 400 MHz for proton spins and an excitation frequency of 263 GHz for the electron spins. The technical requirements to perform such experiments are discussed in the context of the double resonance structures that we have implemented. The experimental steps that allowed access to the enhancement factors for proton spins of several organic solvents with nitroxide radicals as polarizing agents are described. A computational scheme for calculating the coupling factors from molecular dynamics (MD) simulations is outlined and used to highlight the limitations of the classical models based on translational and rotational motion that are typically employed to quantify the observed coupling factors. The ability of MD simulations to predict enhancements for a variety of radicals and solvent molecules at any magnetic field strength should prove useful in optimizing experimental conditions for DNP in the liquid state.

  6. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Garrido, J. M.; Algaba, J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.; Blas, F. J.

    2016-04-01

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  7. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation.

    PubMed

    Garrido, J M; Algaba, J; Míguez, J M; Mendiboure, B; Moreno-Ventas Bravo, A I; Piñeiro, M M; Blas, F J

    2016-04-14

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  8. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations.

    PubMed

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

    Given the importance of plasmalogens in cellular membranes and neurodegenerative diseases, a better understanding of how plasmalogens affect the lipid membrane properties is needed. Here we carried out molecular dynamics simulations to study a lipid membrane comprised of ethanolamine plasmalogens (PE-plasmalogens). We compared the results to the PE-diacyl counterpart and palmitoyl-oleyl-phosphatidylcholine (POPC) bilayers. Results show that PE-plasmalogens form more compressed, thicker, and rigid lipid bilayers in comparison with the PE-diacyl and POPC membranes. The results also point out that the vinyl-ether linkage increases the ordering of sn-1 chain substantially and the ordering of the sn-2 chain to a minor extent. Further, the vinyl-ether linkage changes the orientation of the lipid head group, but it does not cause changes in the head group and glycerol backbone tilt angles with respect to the bilayer normal. The vinyl-ether linkage also packs the proximal regions of the sn-1 and sn-2 chains more closely together which also decreases the distance between the rest of the sn-1 and sn-2 chains. PMID:26522077

  9. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations

    PubMed Central

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

    Given the importance of plasmalogens in cellular membranes and neurodegenerative diseases, a better understanding of how plasmalogens affect the lipid membrane properties is needed. Here we carried out molecular dynamics simulations to study a lipid membrane comprised of ethanolamine plasmalogens (PE–plasmalogens). We compared the results to the PE–diacyl counterpart and palmitoyl-oleyl-phosphatidylcholine (POPC) bilayers. Results show that PE–plasmalogens form more compressed, thicker, and rigid lipid bilayers in comparison with the PE–diacyl and POPC membranes. The results also point out that the vinyl–ether linkage increases the ordering of sn-1 chain substantially and the ordering of the sn-2 chain to a minor extent. Further, the vinyl–ether linkage changes the orientation of the lipid head group, but it does not cause changes in the head group and glycerol backbone tilt angles with respect to the bilayer normal. The vinyl–ether linkage also packs the proximal regions of the sn-1 and sn-2 chains more closely together which also decreases the distance between the rest of the sn-1 and sn-2 chains. PMID:26522077

  10. Atomistic structure of amorphous silicon nitride from classical molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ippolito, Mariella; Meloni, Simone

    2011-04-01

    By means of molecular dynamics simulations based on the Billeter [S. R. Billeter, A. Curioni, D. Fischer, and W. Andreoni, Phys. Rev. BPRLTAO1098-012110.1103/PhysRevB.73.155329 73, 155329 (2006)] environment-dependent classical force field we studied the structural features of SiNx samples at various stoichiometries. Our results are in good agreement with experimental data and are able to reproduce some features which so far were not reproduced by simulations. In particular, we identified units containing N-N bonds, which are thought to be responsible for an unassigned peak in the radial distribution function obtained from neutron diffraction data and signals observed in electron spin resonance, x-ray photoemission spectroscopy, electron-energy-loss spectroscopy, and optical absorption experiments. We have identified defects which are thought to be responsible for the high concentration of charge traps that makes this material suitable for building nonvolatile memory devices. We analyzed the dependency of the concentration of these defects with the stoichiometry of the sample.

  11. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    NASA Astrophysics Data System (ADS)

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-05-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

  12. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations.

    PubMed

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-01-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user's specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program. PMID:27188541

  13. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    PubMed Central

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-01-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program. PMID:27188541

  14. TOPICAL REVIEW: Polarization effects in molecular mechanical force fields

    NASA Astrophysics Data System (ADS)

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2009-08-01

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations.

  15. Submillimeter Polarization Spectrum in the Vela C Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Gandilo, Natalie N.; Ade, Peter A. R.; Angilè, Francesco E.; Ashton, Peter; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fissel, Laura M.; Fukui, Yasuo; Galitzki, Nicholas; Klein, Jeffrey; Korotkov, Andrei L.; Li, Zhi-Yun; Martin, Peter G.; Matthews, Tristan G.; Moncelsi, Lorenzo; Nakamura, Fumitaka; Netterfield, Calvin B.; Novak, Giles; Pascale, Enzo; Poidevin, Frédérick; Santos, Fabio P.; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Diego Soler, Juan; Thomas, Nicholas E.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

    2016-06-01

    Polarization maps of the Vela C molecular cloud were obtained at 250, 350, and 500 μm during the 2012 flight of the balloon-borne telescope BLASTPol. These measurements are used in conjunction with 850 μm data from Planck to study the submillimeter spectrum of the polarization fraction for this cloud. The spectrum is relatively flat and does not exhibit a pronounced minimum at λ ∼ 350 μm as suggested by previous measurements of other molecular clouds. The shape of the spectrum does not depend strongly on the radiative environment of the dust, as quantified by the column density or the dust temperature obtained from Herschel data. The polarization ratios observed in Vela C are consistent with a model of a porous clumpy molecular cloud being uniformly heated by the interstellar radiation field.

  16. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

    PubMed

    Wassenaar, Tsjerk A; Ingólfsson, Helgi I; Priess, Marten; Marrink, Siewert J; Schäfer, Lars V

    2013-04-01

    Hybrid molecular dynamics simulations of atomistic (AA) solutes embedded in coarse-grained (CG) environment can substantially reduce the computational cost with respect to fully atomistic simulations. However, interfacing both levels of resolution is a major challenge that includes a balanced description of the relevant interactions. This is especially the case for polar solvents such as water, which screen the electrostatic interactions and thus require explicit electrostatic coupling between AA and CG subsystems. Here, we present and critically test computationally efficient hybrid AA/CG models. We combined the Gromos atomistic force field with the MARTINI coarse-grained force field. To enact electrostatic coupling, two recently developed CG water models with explicit electrostatic interactions were used: the polarizable MARTINI water model and the BMW model. The hybrid model was found to be sensitive to the strength of the AA-CG electrostatic coupling, which was adjusted through the relative dielectric permittivity εr(AA-CG). Potentials of mean force (PMFs) between pairs of amino acid side chain analogues in water and partitioning free enthalpies of uncharged amino acid side chain analogues between apolar solvent and water show significant differences between the hybrid simulations and the fully AA or CG simulations, in particular for charged and polar molecules. For apolar molecules, the results obtained with the hybrid AA/CG models are in better agreement with the fully atomistic results. The structures of atomistic ubiquitin solvated in CG water and of a single atomistic transmembrane α-helix and the transmembrane portion of an atomistic mechanosensitive channel in CG lipid bilayers were largely maintained during 50-100 ns of AA/CG simulations, partly due to an overstabilization of intramolecular interactions. This work highlights some key challenges on the way toward hybrid AA/CG models that are both computationally efficient and sufficiently accurate for

  17. A long-range electric field solver for molecular dynamics of fluid-solid interfaces based on atomistic-to-continuum modeling.

    SciTech Connect

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan

    2010-11-01

    Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anisotropic electric fields, as occur at charged fluid/solid interfaces, in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. Our model represents the electric potential on a finite element mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. A Calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  19. Molecular Rationale for Improved Dynamic Nuclear Polarization of Biomembranes.

    PubMed

    Smith, Adam N; Twahir, Umar T; Dubroca, Thierry; Fanucci, Gail E; Long, Joanna R

    2016-08-18

    Dynamic nuclear polarization (DNP) enhanced solid-state NMR can provide orders of magnitude in signal enhancement. One of the most important aspects of obtaining efficient DNP enhancements is the optimization of the paramagnetic polarization agents used. To date, the most utilized polarization agents are nitroxide biradicals. However, the efficiency of these polarization agents is diminished when used with samples other than small molecule model compounds. We recently demonstrated the effectiveness of nitroxide labeled lipids as polarization agents for lipids and a membrane embedded peptide. Here, we systematically characterize, via electron paramagnetic (EPR), the dynamics of and the dipolar couplings between nitroxide labeled lipids under conditions relevant to DNP applications. Complemented by DNP enhanced solid-state NMR measurements at 600 MHz/395 GHz, a molecular rationale for the efficiency of nitroxide labeled lipids as DNP polarization agents is developed. Specifically, optimal DNP enhancements are obtained when the nitroxide moiety is attached to the lipid choline headgroup and local nitroxide concentrations yield an average e(-)-e(-) dipolar coupling of 47 MHz. On the basis of these measurements, we propose a framework for development of DNP polarization agents optimal for membrane protein structure determination. PMID:27434371

  20. Polarization of far-infrared radiation from molecular clouds

    SciTech Connect

    Novak, G.; Gonatas, D.P.; Hildebrand, R.H.; Platt, S.R.; Dragovan, M. AT T Bell Laboratories, Murray Hill, NJ )

    1989-10-01

    The paper reports measurements of the polarization of far-infrared emission from dust in nine molecular clouds. Detections were obtained in Mon R2, in the Kleinmann-Low (KL) nebula in Orion, and in Sgr A. Upper limits were set for six other clouds. A comparison of the 100 micron polarization of KL with that previously measured at 270 microns provides new evidence that the polarization is due to emission from magnetically aligned dust grains. Comparing the results for Orion with measurements at optical wavelengths, it is inferred that the magnetic field direction in the outer parts of the Orion cloud is the same as that in the dense core. This direction is nearly perpendicular to the ridge of molecular emission and is parallel to both the molecular outflow in KL and the axis of rotation of the cloud core. In Mon R2, the field direction which the measurements imply does not agree withthat derived from 0.9-2.2 micron polarimetry. The discrepancy is attributed to scattering in the near-infrared. In Orion and Sgr A, where comparisons are possible, the measurements are in good agreement with 10 micron polarization measurements. 55 refs.

  1. Polarization of far-infrared radiation from molecular clouds

    NASA Technical Reports Server (NTRS)

    Novak, G.; Gonatas, D. P.; Hildebrand, R. H.; Platt, S. R.; Dragovan, M.

    1989-01-01

    The paper reports measurements of the polarization of far-infrared emission from dust in nine molecular clouds. Detections were obtained in Mon R2, in the Kleinmann-Low (KL) nebula in Orion, and in Sgr A. Upper limits were set for six other clouds. A comparison of the 100 micron polarization of KL with that previously measured at 270 microns provides new evidence that the polarization is due to emission from magnetically aligned dust grains. Comparing the results for Orion with measurements at optical wavelengths, it is inferred that the magnetic field direction in the outer parts of the Orion cloud is the same as that in the dense core. This direction is nearly perpendicular to the ridge of molecular emission and is parallel to both the molecular outflow in KL and the axis of rotation of the cloud core. In Mon R2, the field direction which the measurements imply does not agree withthat derived from 0.9-2.2 micron polarimetry. The discrepancy is attributed to scattering in the near-infrared. In Orion and Sgr A, where comparisons are possible, the measurements are in good agreement with 10 micron polarization measurements.

  2. NON-ZEEMAN CIRCULAR POLARIZATION OF MOLECULAR ROTATIONAL SPECTRAL LINES

    SciTech Connect

    Houde, Martin; Jones, Scott; Rajabi, Fereshte; Hezareh, Talayeh

    2013-02-10

    We present measurements of circular polarization from rotational spectral lines of molecular species in Orion KL, most notably {sup 12}CO (J = 2 {yields} 1), obtained at the Caltech Submillimeter Observatory with the Four-Stokes-Parameter Spectral Line Polarimeter. We find levels of polarization of up to 1%-2% in general; for {sup 12}CO (J = 2 {yields} 1) this level is comparable to that of linear polarization also measured for that line. We present a physical model based on resonant scattering in an attempt to explain our observations. We discuss how slight differences in scattering amplitudes for radiation polarized parallel and perpendicular to the ambient magnetic field, responsible for the alignment of the scattering molecules, can lead to the observed circular polarization. We also show that the effect is proportional to the square of the magnitude of the plane of the sky component of the magnetic field and therefore opens up the possibility of measuring this parameter from circular polarization measurements of Zeeman insensitive molecules.

  3. A Molecular Switch for the Orientation of Epithelial Cell Polarization

    PubMed Central

    Bryant, David M.; Roignot, Julie; Datta, Anirban; Overeem, Arend W.; Kim, Minji; Yu, Wei; Peng, Xiao; Eastburn, Dennis J.; Ewald, Andrew J.; Werb, Zena; Mostov, Keith E.

    2014-01-01

    SUMMARY The formation of epithelial tissues containing lumens requires not only the apical-basolateral polarization of cells, but also the coordinated orientation of this polarity such that the apical surfaces of neighboring cells all point toward the central lumen. Defects in extracellular matrix (ECM) signaling lead to inverted polarity so that the apical surfaces face the surrounding ECM. We report a molecular switch mechanism controlling polarity orientation. ECM signals through a β1-integrin/FAK/p190RhoGAP complex to down-regulate a RhoA/ROCK/Ezrin pathway at the ECM interface. PKCβII phosphorylates the apical identity-promoting Podocalyxin/NHERF1/Ezrin complex, removing Podocalyxin from the ECM-abutting cell surface and initiating its transcytosis to an apical membrane initiation site for lumen formation. Inhibition of this switch mechanism results in the retention of Podocalyxin at the ECM interface and the development instead of collective front-rear polarization and motility. Thus, ECM-derived signals control the morphogenesis of epithelial tissues by controlling the collective orientation of epithelial polarization. PMID:25307480

  4. Single-parameter quantification of the sensitivity of a molecular collision to molecular polarization.

    PubMed

    de Miranda, Marcelo P; Kendrick, Brian K

    2009-12-31

    This article introduces the concept of intrinsic entropy, S, of a molecular collision. Defined in rigorously quantum mechanical terms as the von Neumann entropy of the intrinsic density matrices of reagents and products, the intrinsic entropy is a dimensionless number in the 0 < or = S < or = 1 range. Its limits are associated with situations where the collision cross section is due to a single combination of reagent and product polarizations (S = 0) or where there is absolutely no selectivity with respect to the molecular polarizations (S = 1). The usefulness of the intrinsic entropy as a quantifier of the sensitivity of a molecular collision to molecular polarizations is demonstrated with examples for the benchmark H + D(2) reaction. PMID:20028174

  5. Numerical tools for atomistic simulations.

    SciTech Connect

    Fang, H.; Gullett, Philip Michael; Slepoy, Alexander; Horstemeyer, Mark F.; Baskes, Michael I.; Wagner, Gregory John; Li, Mo

    2004-01-01

    The final report for a Laboratory Directed Research and Development project entitled 'Parallel Atomistic Computing for Failure Analysis of Micromachines' is presented. In this project, atomistic algorithms for parallel computers were developed to assist in quantification of microstructure-property relations related to weapon micro-components. With these and other serial computing tools, we are performing atomistic simulations of various sizes, geometries, materials, and boundary conditions. These tools provide the capability to handle the different size-scale effects required to predict failure. Nonlocal continuum models have been proposed to address this problem; however, they are phenomenological in nature and are difficult to validate for micro-scale components. Our goal is to separately quantify damage nucleation, growth, and coalescence mechanisms to provide a basis for macro-scale continuum models that will be used for micromachine design. Because micro-component experiments are difficult, a systematic computational study that employs Monte Carlo methods, molecular statics, and molecular dynamics (EAM and MEAM) simulations to compute continuum quantities will provide mechanism-property relations associated with the following parameters: specimen size, number of grains, crystal orientation, strain rates, temperature, defect nearest neighbor distance, void/crack size, chemical state, and stress state. This study will quantify sizescale effects from nanometers to microns in terms of damage progression and thus potentially allow for optimized micro-machine designs that are more reliable and have higher fidelity in terms of strength. In order to accomplish this task, several atomistic methods needed to be developed and evaluated to cover the range of defects, strain rates, temperatures, and sizes that a material may see in micro-machines. Therefore we are providing a complete set of tools for large scale atomistic simulations that include pre-processing of

  6. Exploring the structure-solubility relationship of asphaltene models in toluene, heptane, and amphiphiles using a molecular dynamic atomistic methodology.

    PubMed

    Aray, Yosslen; Hernández-Bravo, Raiza; Parra, José G; Rodríguez, Jesús; Coll, David S

    2011-10-27

    The solubility parameters, δ, of several asphaltene models were calculated by mean of an atomistic NPT ensemble. Continental and archipelago models were explored. A relationship between the solubility parameter and the molecule structure was determined. In general, increase of the fused-rings number forming the aromatic core and the numbers of heteroatoms such as oxygen, nitrogen, and sulfur produces an increase of the solubility parameter, while increases of the numbers and length of the aliphatic chains yield a systematic decrease of this parameter. Molecules with large total carbon atom number at the tails, n(c), and small aromatic ring number, n(r), exhibit the biggest values of δ, while molecules with small n(c) and large n(r) show the smallest δ values. A good polynomial correlation δ = 5.967(n(r)/n(c)) - 3.062(n(r)/n(c))(2) + 0.507(n(r)/n(c))(3) + 16.593 with R(2) = 0.965 was found. The solubilities of the asphaltene models in toluene, heptane, and amphiphiles were studied using the Scatchard-Hildebrand and the Hansen sphere methodologies. Generally, there is a large affinity between the archipelago model and amphiphiles containing large aliphatic tails and no aromatic rings, while continental models show high affinity for amphiphiles containing an aromatic ring and small aliphatic chains. PMID:21905686

  7. Using Atomistic Molecular Dynamics Simulations to Guide Development of Coarse-Grained Models of Polyethylene glycol (PEG), Elastic-like peptides (ELP) and Collagen-like peptides (CMP) For Biomaterial Design

    NASA Astrophysics Data System (ADS)

    Stanzione, Francesca; Jayaraman, Arthi

    Molecular dynamics (MD) is a well established technique to study the structure and dynamics of biomolecular systems. While atomistic simulations maintain chemical details, they are computationally intensive, thus limiting the accessible time, the length scales and the sampling. To overcome these limitations, coarse-grained (CG) models have proven to be successful in reproducing experimentally relevant length and time scales with reasonable computational expense. CG models can be developed to be phenomenological by effectively reproducing experimental results or can be developed by mapping rigorously to structural information provided by atomistic MD simulations. The latter method is recommended for biomolecules and biomaterials since atomistic simulations capture the detailed effect of the medium on interactions that affect the structure, dynamics and functional properties of the biomolecules, and that can be programmed into the CG models. In this poster we highlight three different cases where atomistic MD simulations provide such essential information to guide CG models: Polyethylene glycol, Elastic-like peptides and Collagen-like peptides based biomaterials.

  8. Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential

    NASA Astrophysics Data System (ADS)

    Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

    2015-12-01

    To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results.To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are

  9. Effect of the barometric phase transition of a DMPA bilayer on the lipid/water interface. An atomistic description by molecular dynamics simulation.

    PubMed

    Casares, J J Giner; Camacho, L; Romero, M T Martín; Cascales, J J López

    2007-12-13

    Understanding the structure and dynamics of phospholipid bilayers is of fundamental relevance in biophysics, biochemistry, and chemical physics. Lipid Langmuir monolayers are used as a model of lipid bilayers, because they are much more easily studied experimentally, although some authors question the validity of this model. With the aim of throwing light on this debate, we used molecular dynamics simulations to obtain an atomistic description of a membrane of dimyristoylphosphatidic acid under different surface pressures. Our results show that at low surface pressure the interdigitation between opposite lipids (that is, back-to-back interactions) controls the system structure. In this setting and due to the absence of this effect in the Langmuir monolayers, the behavior between these two systems differs considerably. However, when the surface pressure increases the lipid interdigitation diminishes and so monolayer and bilayer behavior converges. In this work, four computer simulations were carried out, subjecting the phospholipids to lateral pressures ranging from 0.17 to 40 mN/m. The phospholipids were studied in their charged state because this approach is closer to the experimental situation. Special attention was paid to validating our simulation results by comparison with available experimental data, therebeing in general excellent agreement between experimental and simulation data. In addition, the properties of the lipid/solution interface associated with the lipid barometric phase transition were studied. PMID:18004836

  10. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies.

    PubMed

    Raffaini, Giuseppina; Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  11. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

    PubMed Central

    Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Summary Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  12. Large scale atomistic simulation of single-layer graphene growth on Ni(111) surface: molecular dynamics simulation based on a new generation of carbon-metal potential.

    PubMed

    Xu, Ziwei; Yan, Tianying; Liu, Guiwu; Qiao, Guanjun; Ding, Feng

    2016-01-14

    To explore the mechanism of graphene chemical vapor deposition (CVD) growth on a catalyst surface, a molecular dynamics (MD) simulation of carbon atom self-assembly on a Ni(111) surface based on a well-designed empirical reactive bond order potential was performed. We simulated single layer graphene with recorded size (up to 300 atoms per super-cell) and reasonably good quality by MD trajectories up to 15 ns. Detailed processes of graphene CVD growth, such as carbon atom dissolution and precipitation, formation of carbon chains of various lengths, polygons and small graphene domains were observed during the initial process of the MD simulation. The atomistic processes of typical defect healing, such as the transformation from a pentagon into a hexagon and from a pentagon-heptagon pair (5|7) to two adjacent hexagons (6|6), were revealed as well. The study also showed that higher temperature and longer annealing time are essential to form high quality graphene layers, which is in agreement with experimental reports and previous theoretical results. PMID:26658834

  13. Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

    NASA Astrophysics Data System (ADS)

    Kawakami, Tomonori; Shigemoto, Isamu; Matubayasi, Nobuyuki

    2012-12-01

    Affinity of small molecule to polymer is an essential property for designing polymer materials with tuned permeability. In the present work, we develop a computational approach to the free energy ΔG of binding a small solute molecule into polymer using the atomistic molecular dynamics (MD) simulation combined with the method of energy representation. The binding free energy ΔG is obtained by viewing a single polymer as a collection of fragments and employing an approximate functional constructed from distribution functions of the interaction energy between solute and the fragment obtained from MD simulation. The binding of water is then examined against 9 typical polymers. The relationship is addressed between the fragment size and the calculated ΔG, and a useful fragment size is identified to compromise the performance of the free-energy functional and the sampling efficiency. It is found with the appropriate fragment size that the ΔG convergence at a statistical error of ˜0.2 kcal/mol is reached at ˜4 ns of replica-exchange MD of the water-polymer system and that the mean absolute deviation of the computational ΔG from the experimental is 0.5 kcal/mol. The connection is further discussed between the polymer structure and the thermodynamic ΔG.

  14. Polarization and molecular-orbital dependence of strong-field enhanced ionization

    NASA Astrophysics Data System (ADS)

    Lai, Wei; Guo, Chunlei

    2016-04-01

    In this work we perform a polarization dependence study of enhanced ionization (EI) in diatomic molecules. We find that EI exists when the field polarization is parallel to the molecular axis but disappears when polarization is perpendicular. We further study EI with circular polarization and find that EI exists with circular polarization indicating that rescattering does not play a significant role for EI. Furthermore, we study molecular orbital effect on EI. We find that EI exists in σ type but not π type outmost molecular orbitals.

  15. Atomistic simulation of graphene-based polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

    2016-05-01

    Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

  16. Non-Zeeman circular polarization of molecular maser spectral lines

    SciTech Connect

    Houde, Martin

    2014-11-01

    We apply the anisotropic resonant scattering model developed to explain the presence of non-Zeeman circular polarization signals recently detected in the {sup 12}CO (J = 2 → 1) and (J = 1 → 0) transitions in molecular clouds to Stokes V spectra of SiO v = 1 and v = 2, (J = 1 → 0) masers commonly observed in evolved stars. It is found that the observed antisymmetric 'S'- and symmetric '∪'- or '∩'-shaped spectral profiles naturally arise when the maser radiation scatters off populations of foreground molecules located outside the velocity range covered by the background maser radiation. Using typical values for the relevant physical parameters, it is estimated that magnetic field strengths on the order of a few times 15 mG are sufficient to explain the observational results found in the literature.

  17. Atomistic molecular dynamics simulations of the structure of symmetric Polyelectrolyte block copolymer micelle in salt-free aqueous solution

    NASA Astrophysics Data System (ADS)

    Chockalingam, Rajalakshmi; Natarajan, Upendra

    2014-03-01

    The structure of a symmetric polystyrene- b - poly(acrylic acid) (PS- b - PAA) micelle in salt-free aqueous solution as a function of degree-of-neutralization (or ionization, f) of the PAA is studied via explicit-atom-ion MD simulations, for the first time for a polyelectrolyte block copolymer in a polar solvent. Micelle size increases with fin agreement with experimental observations in literature, due to extension of PAA at higher ionization. Pair RDF's with respect to water oxygens show that corona-water interaction becomes stronger with f due to an increase in number density of carboxylate (COO-) groups on the chain. Water-PAA coordination (carboxylate O's) increases with ionization. H-bonding between PAA and water increases with f due to greater extent of corona-water affinity. With increase in f, atom and counter-ion ρ profiles confirm extension of corona blocks and micelle existing in the ``osmotic regime,'' and a decrease in scattering peak intensity, in agreement with neutron scattering experiments and mean-field theory in literature. Inter-chain distance in PS core is found to decrease with ionization. Macromolecular Simulation and Modeling Laboratory, Dept. of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036.

  18. Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Jana, Chandan; Jayamurugan, G.; Ganapathy, Rajesh; Maiti, Prabal K.; Jayaraman, N.; Sood, A. K.

    2006-05-01

    We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ˜Nx with the number of monomers. We find two distinct exponents depending on the generations, x =0.47 for G1-G3 and x =0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G +1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.

  19. The NorM MATE Transporter from N. gonorrhoeae: Insights into Drug and Ion Binding from Atomistic Molecular Dynamics Simulations

    PubMed Central

    Leung, Yuk Ming; Holdbrook, Daniel A.; Piggot, Thomas J.; Khalid, Syma

    2014-01-01

    The multidrug and toxic compound extrusion transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. The substrates transported by these proteins include toxic metabolites and antimicrobial drugs. These proteins contribute to multidrug resistance in both mammalian and bacterial cells and are therefore extremely important from a biomedical perspective. Although specific residues of the protein are known to be responsible for the extrusion of solutes, mechanistic details and indeed structures of all the conformational states remain elusive. Here, we report the first, to our knowledge, simulation study of the recently resolved x-ray structure of the multidrug and toxic compound extrusion transporter, NorM from Neisseria gonorrhoeae (NorM_NG). Multiple, atomistic simulations of the unbound and bound forms of NorM in a phospholipid lipid bilayer allow us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein. In particular, we identify the molecular rearrangements that occur to enable the Na+ ion to enter the cation-binding cavity even in the presence of a bound drug molecule. These include side chain flipping of a key residue, GLU-261 from pointing toward the central cavity to pointing toward the cation binding side when bound to a Na+ ion. Our simulations also provide support for cation binding in the drug-bound and apo states of NorM_NG. PMID:25028887

  20. Effect of Na+ and Ca2+ ions on a lipid Langmuir monolayer: an atomistic description by molecular dynamics simulations.

    PubMed

    Giner Casares, Juan José; Camacho, Luis; Martín-Romero, Maria Teresa; López Cascales, José Javier

    2008-12-01

    Studying the effect of alkali and alkaline-earth metal cations on Langmuir monolayers is relevant from biophysical and nanotechnological points of view. In this work, the effect of Na(+) and Ca(2+) on a model of an anionic Langmuir lipid monolayer of dimyristoylphosphatidate (DMPA(-)) is studied by molecular dynamics simulations. The influence of the type of cation on lipid structure, lipid-lipid interactions, and lipid ordering is analyzed in terms of electrostatic interactions. It is found that for a lipid monolayer in its solid phase, the effect of the cations on the properties of the lipid monolayer can be neglected. The influence of the cations is enhanced for the lipid monolayer in its gas phase, where sodium ions show a high degree of dehydration compared with calcium ions. This loss of hydration shell is partly compensated by the formation of lipid-ion-lipid bridges. This difference is ascribed to the higher charge-to-radius ratio q/r for Ca(2+), which makes ion dehydration less favorable compared to Na(+). Owing to the different dehydration behavior of sodium and calcium ions, diminished lipid-lipid coordination, lipid-ion coordination, and lipid ordering are observed for Ca(2+) compared to Na(+). Furthermore, for both gas and solid phases of the lipid Langmuir monolayers, lipid conformation and ion dehydration across the lipid/water interface are studied. PMID:19012310

  1. Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations.

    PubMed

    Côté, Sébastien; Wei, Guanghong; Mousseau, Normand

    2014-07-01

    The huntingtin protein is characterized by a segment of consecutive glutamines (Q(N)) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (htt(NT)) positioned just before the Q(N) region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt(NT)Q(N) fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps-approach, reorganization, anchoring, and insertion-that are very diverse at the atomic level. On the membrane, the htt(NT) peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains-mainly Leu-4, Leu-7, Phe-11 and Leu-14-positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the htt(NT) peptide. These observations do not significantly change upon adding the Q(N) region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt(NT) region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q(N) region could also play a key role for the oligomerization of htt(NT)Q(N) on phospholipid membranes. PMID:24415136

  2. Single Circularly Polarized Attosecond Pulse Generation by Intense Few Cycle Elliptically Polarized Laser Pulses and Terahertz Fields from Molecular Media

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2013-01-01

    We present a method for producing a single circularly polarized attosecond pulse by an intense few cycle elliptically polarized laser pulse combined with a terahertz field from numerical solutions of the time-dependent Schrödinger equation for the molecular ion H2+. It is found that in the presence of a 62.5 THz (λ=4800nm) field at an intensity of ˜1014W/cm2, a single circularly polarized 114 as pulse can be generated by an elliptical polarized laser pulse at a wavelength of 400 nm with an ellipticity of ɛ=0.59. The efficiency of circular polarization attosecond pulse generation is interpreted based on a classical model of single electron recollision with the parent ion.

  3. Atomistic Mechanisms of Chemical Mechanical Polishing of a Cu Surface in Aqueous H2O2: Tight-Binding Quantum Chemical Molecular Dynamics Simulations.

    PubMed

    Kawaguchi, Kentaro; Ito, Hiroshi; Kuwahara, Takuya; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2016-05-11

    We applied our original chemical mechanical polishing (CMP) simulator based on the tight-binding quantum chemical molecular dynamics (TB-QCMD) method to clarify the atomistic mechanism of CMP processes on a Cu(111) surface polished with a SiO2 abrasive grain in aqueous H2O2. We reveal that the oxidation of the Cu(111) surface mechanically induced at the friction interface is a key process in CMP. In aqueous H2O2, in the first step, OH groups and O atoms adsorbed on a nascent Cu surface are generated by the chemical reactions of H2O2 molecules. In the second step, at the friction interface between the Cu surface and the abrasive grain, the surface-adsorbed O atom intrudes into the Cu bulk and dissociates the Cu-Cu bonds. The dissociation of the Cu-Cu back-bonds raises a Cu atom from the surface that is mechanically sheared by the abrasive grain. In the third step, the raised Cu atom bound to the surface-adsorbed OH groups is removed from the surface by the generation and desorption of a Cu(OH)2 molecule. In contrast, in pure water, there are no geometrical changes in the Cu surface because the H2O molecules do not react with the Cu surface, and the abrasive grain slides smoothly on the planar Cu surface. The comparison between the CMP simulations in aqueous H2O2 and pure water indicates that the intrusion of a surface-adsorbed O atom into the Cu bulk is the most important process for the efficient polishing of the Cu surface because it induces the dissociation of the Cu-Cu bonds and generates raised Cu atoms that are sheared off by the abrasive grain. Furthermore, density functional theory calculations show that the intrusion of the surface-adsorbed O atoms into the Cu bulk has a high activation energy of 28.2 kcal/mol, which is difficult to overcome at 300 K. Thus, we suggest that the intrusion of surface-adsorbed O atoms into the Cu bulk induced by abrasive grains at the friction interface is a rate-determining step in the Cu CMP process. PMID:27092706

  4. Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas aeruginosa

    PubMed Central

    Parkin, Jamie; Khalid, Syma

    2014-01-01

    Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine. PMID:25418166

  5. Spin-polarized current of a transistor in single Mn12 molecular magnets.

    PubMed

    Park, Joonho; Yang, Heok; Park, K S; Lee, Eok-Kyun

    2007-11-01

    Focusing on the framework of how to realize the molecular spintronics in a single molecular magnet, we present theoretical studies on the spin-polarized quantum transport behavior through a single Mn12 molecular magnet. Our theoretical results were obtained by carrying out density functional theoretical calculation within the Keldysh nonequilibrium Green function formalism. The ultimate goal of the molecular spintronics is to develop single molecule transistors which generate spin-polarized currents through the molecular magnet. We obtained the density of states, the transmission coefficients and the characteristic features of the current-voltage (I-V) on the spin-polarized transport properties of Mn12 by the theoretical calculation. These results show the possibility for the realization of molecular spintroinics using single molecular magnets. PMID:18047130

  6. SHG microscopy excited by polarization controlled beam for three-dimensional molecular orientation measurement

    NASA Astrophysics Data System (ADS)

    Yoshiki, K.; Hashimoto, M.; Araki, T.

    2006-08-01

    We have developed a second-harmonic-generation (SGH) microscope to observe the three-dimensional molecular orientation with three-dimensional high spatial resolution using a polarization mode converter. The mode converter consists of a parallel-aligned nematic-liquid-crystal spatial-light-modulator (PAL-SLM) and quarter-waveplates, and converts a incident linearly polarized beam to orthogonal linearly polarized beams or radially polarized beam. We combined the mode converter with SHG microscope to obtain the local information of the three-dimensional molecular orientation. We demonstrated the detection of three-dimensional molecular orientation of collagen fiber in human Achilles' tendon. For high precision three-dimensional molecular orientation measurement, we propose a technique to calibrate the dependence of SHG detection efficiencies on molecular orientation using a liposome.

  7. Molecular model of self diffusion in polar organic liquids: implications for conductivity and fluidity in polar organic liquids and electrolytes.

    PubMed

    Frech, Roger; Petrowsky, Matt

    2014-03-01

    Decades of studying isothermal and temperature-dependent mass and charge transport in polar organic liquids and electrolytes have resulted in two mutually incompatible models and the failure to develop a general molecular level picture. The hydrodynamic model describes conductivity, diffusion, and dielectric relaxation in terms of viscosity, while the inadequacy of the thermal activation model leads to empirical descriptions and fitting procedures whose adjustable parameters have little or no physical significance. We recently demonstrated that transport data can be characterized with a high degree of accuracy and self-consistency using the compensated Arrhenius formalism (CAF), where the transport property of interest assumes an Arrhenius-like form that also includes a dielectric constant dependence in the exponential prefactor. Here, we provide the molecular-level basis for the CAF by first modifying transition state theory, emphasizing the coupling of the diffusing molecule's motion with the dynamical motion of the surrounding matrix. We then explicitly include the polarization energy contribution from the dipolar medium. The polarization energy is related to molecular and system properties through the dipole moment and dipole density, respectively. The energy barrier for transport is coupled to the polarization energy, and we show that accounting for the role of the polarization energy leads naturally to the dielectric constant dependence in the exponential prefactor. PMID:24559237

  8. Molecular photoelectron momentum distributions by intense orthogonally polarized attosecond ultraviolet laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Chelkowski, Szczepan; Bandrauk, André D.

    2015-10-01

    We study molecular photoelectron momentum distributions (MPMDs) of aligned H2+ by intense orthogonally polarized attosecond ultraviolet laser pulses. Photoionization is simulated by numerically solving corresponding three-dimensional time dependent Schrödinger equations with static nuclei. It is found that altering pulse phases ϕ varies the structure of MPMDs, which is attributed to the interference effect between orthogonal polarization ionizations. The phase ϕ dependent MPMDs are also a function of molecular alignment and pulse wavelengths. Altering the symmetry of initial electronic states offers the possibility of imaging molecular orbitals by orthogonal polarization attosecond MPMDs.

  9. Polar Spinel-Perovskite Interfaces: an atomistic study of Fe3O4(111)/SrTiO3(111) structure and functionality

    PubMed Central

    Gilks, Daniel; McKenna, Keith P.; Nedelkoski, Zlatko; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Lari, Leonardo; Kepaptsoglou, Demie; Ramasse, Quentin; Tear, Steve; Lazarov, Vlado K.

    2016-01-01

    Atomic resolution scanning transmission electron microscopy and electron energy loss spectroscopy combined with ab initio electronic calculations are used to determine the structure and properties of the Fe3O4(111)/SrTiO3(111) polar interface. The interfacial structure and chemical composition are shown to be atomically sharp and of an octahedral Fe/SrO3 nature. Band alignment across the interface pins the Fermi level in the vicinity of the conduction band of SrTiO3. Density functional theory calculations demonstrate very high spin-polarization of Fe3O4 in the interface vicinity which suggests that this system may be an excellent candidate for spintronic applications. PMID:27411576

  10. Polar Spinel-Perovskite Interfaces: an atomistic study of Fe3O4(111)/SrTiO3(111) structure and functionality.

    PubMed

    Gilks, Daniel; McKenna, Keith P; Nedelkoski, Zlatko; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Lari, Leonardo; Kepaptsoglou, Demie; Ramasse, Quentin; Tear, Steve; Lazarov, Vlado K

    2016-01-01

    Atomic resolution scanning transmission electron microscopy and electron energy loss spectroscopy combined with ab initio electronic calculations are used to determine the structure and properties of the Fe3O4(111)/SrTiO3(111) polar interface. The interfacial structure and chemical composition are shown to be atomically sharp and of an octahedral Fe/SrO3 nature. Band alignment across the interface pins the Fermi level in the vicinity of the conduction band of SrTiO3. Density functional theory calculations demonstrate very high spin-polarization of Fe3O4 in the interface vicinity which suggests that this system may be an excellent candidate for spintronic applications. PMID:27411576

  11. Polar Spinel-Perovskite Interfaces: an atomistic study of Fe3O4(111)/SrTiO3(111) structure and functionality

    NASA Astrophysics Data System (ADS)

    Gilks, Daniel; McKenna, Keith P.; Nedelkoski, Zlatko; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Lari, Leonardo; Kepaptsoglou, Demie; Ramasse, Quentin; Tear, Steve; Lazarov, Vlado K.

    2016-07-01

    Atomic resolution scanning transmission electron microscopy and electron energy loss spectroscopy combined with ab initio electronic calculations are used to determine the structure and properties of the Fe3O4(111)/SrTiO3(111) polar interface. The interfacial structure and chemical composition are shown to be atomically sharp and of an octahedral Fe/SrO3 nature. Band alignment across the interface pins the Fermi level in the vicinity of the conduction band of SrTiO3. Density functional theory calculations demonstrate very high spin-polarization of Fe3O4 in the interface vicinity which suggests that this system may be an excellent candidate for spintronic applications.

  12. Atomistic simulations of bulk, surface and interfacial polymer properties

    NASA Astrophysics Data System (ADS)

    Natarajan, Upendra

    In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

  13. Femtosecond Raman induced polarization spectroscopy studies of coherent rotational dynamics in molecular fluids

    SciTech Connect

    Morgen, M M

    1997-05-01

    We develop a polarization-sensitive femtosecond pump probe technique, Raman induced polarization spectroscopy (RIPS), to study coherent rotation in molecular fluids. By observing the collisional dephasing of the coherently prepared rotational states, we are able to extract information concerning the effects of molecular interactions on the rotational motion. The technique is quite sensitive because of the zero background detection method, and is also versatile due to its nonresonant nature.

  14. Visualizing molecular polar order in tissues via electromechanical coupling

    PubMed Central

    Denning, Denise; Alilat, Sofiane; Habelitz, Stefan; Fertala, Andrzej; Rodriguez, Brian J.

    2015-01-01

    Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides. PMID:22985991

  15. Polarization conversion-based molecular sensing using anisotropic plasmonic metasurfaces

    NASA Astrophysics Data System (ADS)

    Verre, R.; Maccaferri, N.; Fleischer, K.; Svedendahl, M.; Odebo Länk, N.; Dmitriev, A.; Vavassori, P.; Shvets, I. V.; Käll, M.

    2016-05-01

    Anisotropic media induce changes in the polarization state of transmitted and reflected light. Here we combine this effect with the refractive index sensitivity typical of plasmonic nanoparticles to experimentally demonstrate self-referenced single wavelength refractometric sensing based on polarization conversion. We fabricated anisotropic plasmonic metasurfaces composed of gold dimers and, as a proof of principle, measured the changes in the rotation of light polarization induced by biomolecular adsorption with a surface sensitivity of 0.2 ng cm-2. We demonstrate the possibility of miniaturized sensing and we show that experimental results can be reproduced by analytical theory. Various ways to increase the sensitivity and applicability of the sensing scheme are discussed.Anisotropic media induce changes in the polarization state of transmitted and reflected light. Here we combine this effect with the refractive index sensitivity typical of plasmonic nanoparticles to experimentally demonstrate self-referenced single wavelength refractometric sensing based on polarization conversion. We fabricated anisotropic plasmonic metasurfaces composed of gold dimers and, as a proof of principle, measured the changes in the rotation of light polarization induced by biomolecular adsorption with a surface sensitivity of 0.2 ng cm-2. We demonstrate the possibility of miniaturized sensing and we show that experimental results can be reproduced by analytical theory. Various ways to increase the sensitivity and applicability of the sensing scheme are discussed. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01336h

  16. Rotations of molecular photoelectron angular distributions with intense ultrashort circularly polarized attosecond laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Chelkowski, Szczepan; Bandrauk, André D.

    2013-04-01

    Molecular photoelectron angular distributions (MPADs) by intense (I0 ⩾ 1014 W/cm2) circularly polarized ultrashort, few cycle (attosecond) ultraviolet laser pulses are presented from numerical solutions of time dependent Schrödinger equations. For the aligned molecular ion H_2^+, the MPADs exhibit rotations with respect to the polarization and molecular symmetry axes which are determined by the symmetry of the initial electronics states. It is also found that the rotation angle of MPADs is insensitive to the pulse intensity. We attribute these effects to the asymmetry between the parallel and perpendicular (to the molecular axis) polarization photoionization. Influence of the molecular alignment and ionizing pulse ellipticity on the rotation of MPADs is also shown to allow control of the nonsymmetric ionization.

  17. Alignment layer-free molecular ordering induced by masked photopolymerization with non-polarized light

    NASA Astrophysics Data System (ADS)

    Hisano, Kyohei; Kurata, Yosuke; Aizawa, Miho; Ishizu, Masaki; Sasaki, Takeo; Shishido, Atsushi

    2016-07-01

    Controlled and uniform molecular alignment can provide and enhance functionality in polymer films. We first report that masked photopolymerization with non-polarized light enables direct and precise control of molecular alignment without using a conventional molecular alignment layer. The photopolymerization of a mixture composed of an optically anisotropic acrylate monomer and an isotropic dimethacrylate crosslinker induces either unidirectional or complex molecular alignment, depending upon the shape of the photomask. Such molecular alignments are successfully achieved by shear stress arising from molecular diffusion, even when the photopolymerization is carried out at isotropic temperatures of both the monomer mixture and the obtained polymers.

  18. Polarization conversion-based molecular sensing using anisotropic plasmonic metasurfaces.

    PubMed

    Verre, R; Maccaferri, N; Fleischer, K; Svedendahl, M; Odebo Länk, N; Dmitriev, A; Vavassori, P; Shvets, I V; Käll, M

    2016-05-19

    Anisotropic media induce changes in the polarization state of transmitted and reflected light. Here we combine this effect with the refractive index sensitivity typical of plasmonic nanoparticles to experimentally demonstrate self-referenced single wavelength refractometric sensing based on polarization conversion. We fabricated anisotropic plasmonic metasurfaces composed of gold dimers and, as a proof of principle, measured the changes in the rotation of light polarization induced by biomolecular adsorption with a surface sensitivity of 0.2 ng cm(-2). We demonstrate the possibility of miniaturized sensing and we show that experimental results can be reproduced by analytical theory. Various ways to increase the sensitivity and applicability of the sensing scheme are discussed. PMID:27153470

  19. Chirp and polarization control of femtosecond molecular fragmentation

    PubMed Central

    Goswami, T; Das, D K; Kumar, S K Karthick; Goswami, D

    2013-01-01

    We explore the simultaneous effect of chirp and polarization as the two control parameters for non-resonant photo-dissociation of n-propyl benzene. Experiments performed over a wide range of laser intensities show that these two control knobs behave mutually exclusively. Specifically, for the coherently enhanced fragments (C3H3+, C5H5+) with negatively chirped pulses and C6H5+ with positively chirped pulses, polarization effect is the same as compared to that in the case of transform-limited pulses. Though a change in polarization affects the overall fragmentation efficiency, the fragmentation pattern of n-propyl benzene molecule remains unaffected in contrast to the chirp case. PMID:24115807

  20. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-08-01

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe2+ molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0×1014 W/cm2, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schrödinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe2+, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  1. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-08-15

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe{sup 2+} molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0x10{sup 14} W/cm{sup 2}, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schroedinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe{sup 2+}, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  2. Comparing submillimeter polarized emission with near-infrared polarization of background stars for the Vela C molecular cloud

    NASA Astrophysics Data System (ADS)

    Santos, Fabio P.; Ade, Peter; Angilè, Francesco E.; Ashton, Peter; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fissel, Laura M.; Fukui, Yasuo; Galitzki, Nicholas; Gandilo, Natalie; Klein, Jeffrey; Li, Zhi-Yun; Korotkov, Andrei; Martin, Peter G.; Matthews, Tristan; Moncelsi, Lorenzo; nakamura, fumitaka; Barth Netterfield, Calvin; Novak, Giles; Pascale, Enzo; Poidevin, Frédérick; Savini, Giorgio; Scott, Douglas; Shariff, Jamil; Soler, Juan D.; Thomas, Nicholas; tucker, carole; Tucker, Gregory S.; Ward-Thompson, Derek; BLASTPOL

    2016-06-01

    We present a large-scale combination of near-infrared (near-IR) interstellar polarization data from background starlight, with polarized emission data at sub-millimetric (sub-mm) bands for the Vela C molecular cloud. The sub-mm data were obtained by the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry (BLASTPol) during the 2012 flight in Antartica. The near-IR data consist of more than 6700 detections in the I-band, covering a wide area around the cloud, mostly in the range of visual extinctions between 2 and 16 mag. The main goal was to determine the polarization efficiency ratio Reff , defined as p500/(pI/τV), where p500 is the polarization fraction at 500 μm and optical depths τV are estimated from cataloged near-IR photometry. To ensure that the same column density of material is producing both polarization from emission and extinction, we introduce a new method to select stars that are located in the near-background, the Gaussian-logistic (GL) technique. The polarization efficiency ratio is critically affected by stellar objects with background contamination from the diffuse Galactic material, emphasizing the need for a careful selection. Accounting for the statistical and systematic uncertainties from the GL method, we estimate an average Reff value of 2.4 ± 0.8, which can be used to test dust grain models designed specifically for molecular clouds. Reff appears to be relatively flat as a function of the cloud depth, suggesting that significant grain modification might occur only at higher densities.

  3. Atomistic bond relaxation, energy entrapment, and electron polarization of the RbN and CsN clusters (N ≤ 58).

    PubMed

    Guo, Yongling; Bo, Maolin; Wang, Yan; Liu, Yonghui; Huang, Yongli; Sun, Chang Q

    2015-11-11

    We systematically examined the effect of atomic undercoordination on the performance of bonds and electrons of Rb and Cs atomic clusters and their solid skins using a combination of photoelectron spectrometric analysis and density functional theory calculations. Results show that atomic coordination number reduction shortens the bonds by up to 30% for the Rb13 and Cs13 clusters, which densifies the local electrons and entraps their binding energies. Consistency between predictions and observations revealed that the Rb 4p level shifts from 13.654 eV for an isolated atom to a bulk value of 14.940 eV and the Cs 5p level shifts from 10.284 to 11.830 eV upon bulk formation. Such core-electron densification and entrapment polarize the valence charge from the inner to the outermost layer of skins, which perturbs the local Hamiltonian and hence dictates the unusual behavior of the Rb and Cs solid skins and nanocrystals. PMID:26507096

  4. Molecular orientation sensitive second harmonic microscopy by radially and azimuthally polarized light

    PubMed Central

    Ehmke, Tobias; Nitzsche, Tim Heiko; Knebl, Andreas; Heisterkamp, Alexander

    2014-01-01

    We demonstrate the possibility to switch the z-polarization component of the illumination in the vicinity of the focus of high-NA objective lenses by applying radially and azimuthally polarized incident light. The influence of the field distribution on nonlinear effects was first investigated by the means of simulations. These were performed for high-NA objective lenses commonly used in nonlinear microscopy. Special attention is paid to the influence of the polarization of the incoming field. For linearly, circularly and radially polarized light a considerable polarization component in z-direction is generated by high NA focusing. Azimuthal polarization is an exceptional case: even for strong focusing no z-component arises. Furthermore, the influence of the input polarization on the intensity contributing to the nonlinear signal generation was computed. No distinct difference between comparable input polarization states was found for chosen thresholds of nonlinear signal generation. Differences in signal generation for radially and azimuthally polarized vortex beams were experimentally evaluated in native collagen tissue (porcine cornea). The findings are in good agreement with the theoretical predictions and display the possibility to probe the molecular orientation along the optical axis of samples with known nonlinear properties. The combination of simulations regarding the nonlinear response of materials and experiments with different sample orientations and present or non present z-polarization could help to increase the understanding of nonlinear signal formation in yet unstudied materials. PMID:25071961

  5. Molecular above-threshold-ionization angular distributions with intense circularly polarized attosecond XUV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2012-05-01

    Photoionization of aligned and fixed nuclei three-dimensional H2+ and two-dimensional H2 by intense circularly polarized attosecond extreme ultraviolet laser pulses is investigated from numerical solutions of the time-dependent Schrödinger equation. Molecular above-threshold-ionization angular distributions are found to be rotated with respect to the two laser perpendicular polarizations or, equivalently the symmetry axes of the molecule. The angle of rotation is critically sensitive to laser wavelength λ, photoelectron energy Een, and molecular internuclear distance R. The correlated interaction of the two electrons in H2 is shown to also influence such angular distribution rotations in different electronic states.

  6. General Reactive Atomistic Simulation Program

    Energy Science and Technology Software Center (ESTSC)

    2004-09-22

    GRASP (General Reactive Atomistic Simulation Program) is primarily intended as a molecular dynamics package for complex force fields, The code is designed to provide good performance for large systems, either in parallel or serial execution mode, The primary purpose of the code is to realistically represent the structural and dynamic properties of large number of atoms on timescales ranging from picoseconds up to a microsecond. Typically the atoms form a representative sample of some material,more » such as an interface between polycrystalline silicon and amorphous silica. GRASP differs from other parallel molecular dynamics codes primarily due to it’s ability to handle relatively complicated interaction potentials and it’s ability to use more than one interaction potential in a single simulation. Most of the computational effort goes into the calculation of interatomic forces, which depend in a complicated way on the positions of all the atoms. The forces are used to integrate the equations of motion forward in time using the so-called velocity Verlet integration scheme. Alternatively, the forces can be used to find a minimum energy configuration, in which case a modified steepest descent algorithm is used.« less

  7. Polarization and molecular information transmission in the cell

    NASA Astrophysics Data System (ADS)

    Valdez-Gomez, Adriano; Ramirez-Santiago, Guillermo

    2012-02-01

    During chemotaxis, pseudopodia are extended at the leading edge and retracted at the back of the cell. Efficient chemotaxis is the result of a refined interplay between signaling modules to transmit and integrate spatial information such as PtdIns(3,4,5)P3. The localization of PtdIns(3,4,5)P3 is expected to depend on the distributions or activities of PI3Ks, PTEN, and 5-phosphatases. The spatial signals spread relatively slowly so that high local concentrations of PIP3 in the plasma membrane appear in patches. These gradients induce localization of PIP3 and PTEN to the front and back of the cell, respectively. To simulate this polarization process that involves the action of seven reaction-channels inside the cell we carried out extensive stochastic simulations using Gilliespie algorithm. The simulations were done on a square cell with ten thousand sites (100x100) emulating a square cell with side 10>μm long. We found that there are localized patches of PIP3 at the active receptors and segregation of PTEN on the opposite side of the cell. When we block the reaction-channel, PTEN + PIP3 ->PIP2 that involves the production of PIP2 we obtained a five-fold increase in the concentration of PIP3. This finding appears to be consistent with the o

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

    PubMed Central

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

    1997-01-01

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

  9. Exploiting the magnetomechanical interaction for cooling magnetic molecular junctions by spin-polarized currents

    NASA Astrophysics Data System (ADS)

    Brüggemann, J.; Weiss, S.; Nalbach, P.; Thorwart, M.

    2016-02-01

    We present a scheme for cooling a vibrational mode of a magnetic molecular nanojunction by a spin-polarized charge current upon exploiting the interaction between its magnetic moment and the vibration. The spin-polarized charge current polarizes the magnetic moment of the nanoisland, thereby lowering its energy. A small but finite coupling between the vibration and the magnetic moment permits a direct exchange of energy such that vibrational energy can be transferred into the magnetic state. For positive bias voltages, this generates an effective cooling of the molecular vibrational mode. We determine parameter regimes for the cooling of the vibration to be optimal. Although the flowing charge current inevitably heats up the vibrational mode via Ohmic energy losses, we show that due to the magnetomechanical coupling, the vibrational energy (i.e, the effective phonon temperature) can be lowered below 50% of its initial value, when the two leads are polarized anti-parallel. In contrast to the cooling effect for positive bias voltages, net heating of the vibrational mode occurs for negative bias voltages. The cooling effect is enhanced for a stronger anti-parallel magnetic polarization of the leads, while the heating is stronger for a larger parallel polarization. Yet, dynamical cooling is also possible with parallel lead alignments when the two tunneling barriers are asymmetric.

  10. Molecular Designs for Enhancement of Polarity in Ferroelectric Soft Materials

    NASA Astrophysics Data System (ADS)

    Ohtani, Ryo; Nakaya, Manabu; Ohmagari, Hitomi; Nakamura, Masaaki; Ohta, Kazuchika; Lindoy, Leonard F.; Hayami, Shinya

    2015-11-01

    The racemic oxovanadium(IV) salmmen complexes, [VO((rac)-(4-X-salmmen))] (X = C12C10C5 (1), C16 (2), and C18 (3); salmmen = N,N‧-monomethylenebis-salicylideneimine) with “banana shaped” molecular structures were synthesized, and their ferroelectric properties were investigated. These complexes exhibit well-defined hysteresis loops in their viscous phases, moreover, 1 also displays liquid crystal behaviour. We observed a synergetic effect influenced by three structural aspects; the methyl substituents on the ethylene backbone, the banana shaped structure and the square pyramidal metal cores all play an important role in generating the observed ferroelectricity, pointing the way to a useful strategy for the creation of advanced ferroelectric soft materials.

  11. Molecular Designs for Enhancement of Polarity in Ferroelectric Soft Materials

    PubMed Central

    Ohtani, Ryo; Nakaya, Manabu; Ohmagari, Hitomi; Nakamura, Masaaki; Ohta, Kazuchika; Lindoy, Leonard F.; Hayami, Shinya

    2015-01-01

    The racemic oxovanadium(IV) salmmen complexes, [VO((rac)-(4-X-salmmen))] (X = C12C10C5 (1), C16 (2), and C18 (3); salmmen = N,N′-monomethylenebis-salicylideneimine) with “banana shaped” molecular structures were synthesized, and their ferroelectric properties were investigated. These complexes exhibit well-defined hysteresis loops in their viscous phases, moreover, 1 also displays liquid crystal behaviour. We observed a synergetic effect influenced by three structural aspects; the methyl substituents on the ethylene backbone, the banana shaped structure and the square pyramidal metal cores all play an important role in generating the observed ferroelectricity, pointing the way to a useful strategy for the creation of advanced ferroelectric soft materials. PMID:26568045

  12. Molecular density functional theory of water including density–polarization coupling

    NASA Astrophysics Data System (ADS)

    Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

    2016-06-01

    We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle’s density and multipolar polarization density and includes the density–polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density–polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

  13. Molecular density functional theory of water including density-polarization coupling.

    PubMed

    Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

    2016-06-22

    We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities. PMID:27116250

  14. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  15. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.

    PubMed

    Duan, Li L; Feng, Guo Q; Zhang, Qing G

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  16. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

    PubMed Central

    Duan, Li L.; Feng, Guo Q.; Zhang, Qing G.

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  17. Atomistic characterisation of Li+ mobility and conductivity in Li(7-x)PS(6-x)Ix argyrodites from molecular dynamics simulations, solid-state NMR, and impedance spectroscopy.

    PubMed

    Pecher, Oliver; Kong, Shiao-Tong; Goebel, Thorsten; Nickel, Vera; Weichert, Katja; Reiner, Christof; Deiseroth, Hans-Jörg; Maier, Joachim; Haarmann, Frank; Zahn, Dirk

    2010-07-26

    The atomistic mechanisms of Li(+) ion mobility/conductivity in Li(7-x)PS(6-x)I(x) argyrodites are explored from both experimental and theoretical viewpoints. Ionic conductivity in the title compound is associated with a solid-solid phase transition, which was characterised by low-temperature differential scanning calorimetry, (7)Li and (127)I NMR investigations, impedance measurements and molecular dynamics simulations. The NMR signals of both isotopes are dominated by anisotropic interactions at low temperatures. A significant narrowing of the NMR signal indicates a motional averaging of the anisotropic interactions above 177+/-2 K. The activation energy to ionic conductivity was assessed from both impedance spectroscopy and molecular dynamics simulations. The latter revealed that a series of interstitial sites become accessible to the Li(+) ions, whilst the remaining ions stay at their respective sites in the argyrodite lattice. The interstitial positions each correspond to the centres of tetrahedra of S/I atoms, and differ only in terms of their common corners, edges, or faces with adjacent PS(4) tetrahedra. From connectivity analyses and free-energy rankings, a specific tetrahedron is identified as the key restriction to ionic conductivity, and is clearly differentiated from local mobility, which follows a different mechanism with much lower activation energy. Interpolation of the lattice parameters as derived from X-ray diffraction experiments indicates a homogeneity range for Li(7-x)PS(6-x)I(x) with 0.97 < or = x < or = 1.00. Within this range, molecular dynamics simulations predict Li(+) conductivity at ambient conditions to vary considerably. PMID:20544750

  18. GJ 841B-THE SECOND DQ WHITE DWARF WITH POLARIZED CH MOLECULAR BANDS

    SciTech Connect

    Vornanen, T.; Berdyugin, A. V.; Piirola, V.; Berdyugina, S. V. E-mail: andber@utu.f E-mail: sveta@kis.uni-freiburg.d

    2010-09-01

    We report a discovery of the circularly polarized CH A {sup 2}{Delta}-X {sup 2}{Pi} and B {sup 2}{Sigma}{sup -}-X {sup 2}{Pi} molecular bands in the spectrum of the DQ white dwarf (WD) GJ 841B. This is only the second such object since the discovery of G99-37 in the 1970s. GJ 841B is also the first WD to unambiguously show polarization in the C{sub 2} Swan bands. By modeling the intensity and circular polarization in the CH bands, we determine the longitudinal magnetic field strength of 1.3 {+-} 0.5 MG and the temperature of 6100 {+-} 200 K in the absorbing region. We also present new observations of G99-37 and obtain estimates of the magnetic field strength 7.3 {+-} 0.3 MG and temperature 6200 {+-} 200 K, in good agreement with previous results.

  19. Field-free molecular alignment of asymmetric top molecules using elliptically polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Rouzée, A.; Guérin, S.; Faucher, O.; Lavorel, B.

    2008-04-01

    We show theoretically that a short specific elliptically polarized laser pulse driving an asymmetric top molecule can induce postpulse revivals of three-dimensional (3D) alignment. By choosing the field ellipticity resulting in the best compromise between the alignment of two molecular axes, we demonstrate that efficient 3D alignment can be achieved at low temperature. In the experiment, the field-free alignment of moderately cool ethylene molecules is probed by using a technique based on the optical Kerr effect. Control of 3D field-free alignment opens the door to a large range of applications in chemistry as well as in molecular optics.

  20. Molecular photoelectron angular distributions with intense attosecond circularly polarized UV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Chelkowski, Szczepan; Bandrauk, André D.

    2014-01-01

    We investigate effects of intermediate resonant electronic states on molecular photoelectron angular distributions (MPADs) by intense circularly polarized attosecond UV laser pulses. Simulations are performed on aligned H2+ by numerically solving the corresponding three dimensional time dependent Schrödinger equations. MPADs exhibit signature of rotations, which is shown to be critically sensitive to the symmetry of the intermediate resonant electronic state and the pulse intensity. This sensitivity is attributed to the coherent population transfer in the initial and intermediate resonant states, thus suggesting a method to control molecular photoionization on attosecond time scale.

  1. Web-based implementation of atomistic visualization

    NASA Astrophysics Data System (ADS)

    Bhattarai, D.; Czech, W.; Karki, B. B.; Yuen, D. A.

    2008-12-01

    Atomistic (molecular) visualization is one of the most widely studied applications of scientific visualization. It deals with time-varying three dimensional positional data representing snapshots of atomic configurations produced by molecular dynamics simulations of a variety of materials including geomaterials. We have recently developed an efficient scheme, which integrates the analysis and rendering tasks together in order to support interactive visualization at space-time multi-resolution of these data. Our scheme allows us to gain better insight into bonding, radial distribution, atomic coordination, clustering, structural stability and distortion, and diffusion. We are currently extending the support for web-based access to atomistic visualization by developing a three-level distributed application with platform independence and portability. The first layer contains off-screen rendering engine whose functionality is exposed using Web Service. This layer supports batch-style rendering that allows remote analysis of data and provides general way to access service from different types of clients. The second layer is a web application that enables user to interact with data using Web Service as entry point to rendering engine. Finally, the front-end of the system is a web browser (e.g. Firefox, Safari, Internet Explorer). We will also take the advantage of relational database to store simulation results and retrieve them from rendering service. We will present the details of the implementation and applications.

  2. Atomistic Monte Carlo Simulation of Lipid Membranes

    PubMed Central

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

  3. Atomistic study on dithiolated oligo-phenylenevinylene gated device

    SciTech Connect

    Mahmoud, Ahmed Lugli, Paolo

    2014-11-28

    Thanks to their semiconducting behavior, conjugated molecules are considered as an attractive candidate for future electronic devices. Understanding the charge transport characteristics through such molecules for different device applications would accelerate the progress in the field of molecular electronics. In addition, it would become more feasible to introduce/enhance specific properties of molecular devices. This theoretical paper focuses on atomistic simulation and characterization of novel molecular FET employing dithiolated oligo-phenylenevinylene molecules. The simulation is validated by its agreement with the experimental measurements conducted on the same molecules. The employed molecule has oxygen linkers, which are responsible for the strongly nonlinear current characteristics on the molecular device. We perform a thorough atomistic device analysis to illustrate the principles behind the nonlinear current characteristics and the gating effect.

  4. Circularly polarized attosecond pulses from molecular high-order harmonic generation by ultrashort intense bichromatic circularly and linearly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2012-04-01

    We describe the generation of high-order elliptically and circularly polarized harmonic spectra in an aligned H+2 molecule ion by a combination of two-colour ultrashort intense laser fields from numerical solutions of the corresponding time-dependent Schrödinger equation (TDSE). In intense bichromatic circularly and linearly or circularly polarized laser pulses with intensity I0 and angular frequencies ω0 and 2ω0, it is found that maximum molecular high-order harmonic generation (MHOHG) energies are functions of the molecular internuclear distance. Based on a classical model of laser-induced electron collisions with neighbouring ions, the optimal values of the pulse relative carrier envelope phase phi, the molecular internuclear distance R and the angle thetav of molecular alignment to the laser polarization axis are obtained for efficiently producing MHOHG spectra with the maximum harmonic energy Ip + 13.5Up, where Ip is the ionization potential of the molecule and Up = I0/4meω20 is the ponderomotive energy of the continuum electron at intensity I0 and frequency ω0 of the laser pulse. The results have been confirmed from corresponding TDSE nonperturbative numerical simulations. The polarization property of the generated harmonics is also presented. The mechanism of MHOHG is further characterized with a Gabor time frequency analysis. It is confirmed that a single collision trajectory of the continuum electron with neighbouring ions dominates in the MHOHG processes. The high efficiency of the proposed MHOHG scheme provides a possible source for production of elliptically and/or circularly polarized attosecond extreme ultraviolet pulses. Circularly polarized attosecond pulses can also be generated by using intense ultrashort circularly polarized laser pulses in combination with static electric fields of comparable intensity for H+2 at equilibrium. A time frequency analysis also confirms the role of single recollisions as the dominant mechanism of the generation

  5. Revealing molecular order inside and between PBTTT nanoribbons through the polarized X-ray scattering

    NASA Astrophysics Data System (ADS)

    Collins, Brian; Delongchamp, Dean

    Electronic and optical properties of conjugated polymers emerge not only through molecular architecture, but also through hierarchical ordering from the molecular to the mesoscale. Characterizing aspects of that ordering critical to properties can be challenging, however. For example, local molecular orientation within and connectivity between ordered structures is considered paramount for charge transport in conjugated polymer films. While some of these aspects can be imaged with state-of-the-art microscopy measurements, true statistical measurements of molecular order and connectivity remain elusive due to the low levels of crystalline packing that limit diffractive and other techniques capable of statistical analysis. Recently, we demonstrated how resonant scattering with polarized soft X-rays (PSoXS) is sensitive to molecular orientation and that such measurements could be used to locate sources and types of ordering within larger nanostructures on a statistical basis. Here we combine forward simulation and measurements of PSoXS on PBTTT nanoribbon films to extract critical information such as the average level of molecular alignment within nanoribbon structures and the level of connectivity between ribbons that promote the dominant charge transport mechanisms in these films. Further development of PSoXS will enable crucial insight into internal molecular order within organic materials tied to optical and electronic properties and how to control these properties for use in novel devices.

  6. In silico affinity profiling of neuroactive polyphenols for post-traumatic calpain inactivation: a molecular docking and atomistic simulation sensitivity analysis.

    PubMed

    Kumar, Pradeep; Choonara, Yahya E; Pillay, Viness

    2015-01-01

    Calcium-activated nonlysosomal neutral proteases, calpains, are believed to be early mediators of neuronal damage associated with neuron death and axonal degeneration after traumatic neural injuries. In this study, a library of biologically active small molecular weight calpain inhibitors was used for model validation and inhibition site recognition. Subsequently, two natural neuroactive polyphenols, curcumin and quercetin, were tested for their sensitivity and activity towards calpain's proteolytic sequence and compared with the known calpain inhibitors via detailed molecular mechanics (MM), molecular dynamics (MD), and docking simulations. The MM and MD energy profiles (SJA6017 < AK275 < AK295 < PD151746 < quercetin < leupeptin < PD150606 < curcumin < ALLN < ALLM < MDL-28170 < calpeptin) and the docking analysis (AK275 < AK295 < PD151746 < ALLN < PD150606 < curcumin < leupeptin < quercetin < calpeptin < SJA6017 < MDL-28170 < ALLM) demonstrated that polyphenols conferred comparable calpain inhibition profiling. The modeling paradigm used in this study provides the first detailed account of corroboration of enzyme inhibition efficacy of calpain inhibitors and the respective calpain-calpain inhibitor molecular complexes' energetic landscape and in addition stimulates the polyphenol bioactive paradigm for post-SCI intervention with implications reaching to experimental in vitro, in cyto, and in vivo studies. PMID:25546626

  7. Molecular Order of Arterial Collagen Using Circular Polarization Second-Harmonic Generation Imaging.

    PubMed

    Turcotte, Raphaël; Mattson, Jeffrey M; Wu, Juwell W; Zhang, Yanhang; Lin, Charles P

    2016-02-01

    Second-harmonic generation (SHG) originates from the interaction between upconverted fields from individual scatterers. This renders SHG microscopy highly sensitive to molecular distribution. Here, we aim to take advantage of the difference in SHG between aligned and partially aligned molecules to probe the degree of molecular order during biomechanical testing, independently of the absolute orientation of the scattering molecules. Toward this goal, we implemented a circular polarization SHG imaging approach and used it to quantify the intensity change associated with collagen fibers straightening in the arterial wall during mechanical stretching. We were able to observe the delayed alignment of collagen fibers during mechanical loading, thus demonstrating a simple method to characterize molecular distribution using intensity information alone. PMID:26806883

  8. NGC 7538 IRS. 1. Interaction of a polarized dust spiral and a molecular outflow

    SciTech Connect

    Wright, M. C. H.; Hull, Charles L. H.; Pillai, Thushara; Zhao, Jun-Hui; Sandell, Göran

    2014-12-01

    We present dust polarization and CO molecular line images of NGC 7538 IRS 1. We combined data from the Submillimeter Array, the Combined Array for Research in Millimeter-wave Astronomy, and the James Clerk Maxwell Telescope to make images with ∼2.''5 resolution at 230 and 345 GHz. The images show a remarkable spiral pattern in both the dust polarization and molecular outflow. These data dramatically illustrate the interplay between a high infall rate onto IRS 1 and a powerful outflow disrupting the dense, clumpy medium surrounding the star. The images of the dust polarization and the CO outflow presented here provide observational evidence for the exchange of energy and angular momentum between the infall and the outflow. The spiral dust pattern, which rotates through over 180° from IRS 1, may be a clumpy filament wound up by conservation of angular momentum in the infalling material. The redshifted CO emission ridge traces the dust spiral closely through the MM dust cores, several of which may contain protostars. We propose that the CO maps the boundary layer where the outflow is ablating gas from the dense gas in the spiral.

  9. NGC 7538 IRS. 1. Interaction of a Polarized Dust Spiral and a Molecular Outflow

    NASA Astrophysics Data System (ADS)

    Wright, M. C. H.; Hull, Charles L. H.; Pillai, Thushara; Zhao, Jun-Hui; Sandell, Göran

    2014-12-01

    We present dust polarization and CO molecular line images of NGC 7538 IRS 1. We combined data from the Submillimeter Array, the Combined Array for Research in Millimeter-wave Astronomy, and the James Clerk Maxwell Telescope to make images with ~2.''5 resolution at 230 and 345 GHz. The images show a remarkable spiral pattern in both the dust polarization and molecular outflow. These data dramatically illustrate the interplay between a high infall rate onto IRS 1 and a powerful outflow disrupting the dense, clumpy medium surrounding the star. The images of the dust polarization and the CO outflow presented here provide observational evidence for the exchange of energy and angular momentum between the infall and the outflow. The spiral dust pattern, which rotates through over 180° from IRS 1, may be a clumpy filament wound up by conservation of angular momentum in the infalling material. The redshifted CO emission ridge traces the dust spiral closely through the MM dust cores, several of which may contain protostars. We propose that the CO maps the boundary layer where the outflow is ablating gas from the dense gas in the spiral.

  10. Broad-band polarization in molecular spectra. [Zeeman effect in magnetic stars

    NASA Technical Reports Server (NTRS)

    Illing, R. M. E.

    1981-01-01

    The rotational lines of the CN(0,0) red system have been observed to show a strongly asymmetric Zeeman profile. Certain molecules are very susceptible to magnetic perturbation because of the weakness of their spin-rotation coupling; a fairly weak magnetic field can cause a complete Paschen-Back effect. The calculation of transition probabilities incorporating this effect into the Hamiltonian is discussed, and the detailed calculation is then given. The resulting transition probabilities are transformed into synthetic line profiles by using the Unno (1956) model of polarized radiation transfer. The dependence of the net polarized flux on magnetic field and equivalent width is investigated. It is shown that entire band systems may be significantly polarized. Broad-band circular polarization of sunspots may be due, in part, to molecular bands. Analysis of the CH G band indicates a magnetic field of 0.25-0.50 x 10 to the 6th gauss in the white dwarf G99-37, an order of magnitude lower than previous estimates.

  11. Molecular Mechanisms That Influence the Macrophage M1–M2 Polarization Balance

    PubMed Central

    Wang, Nan; Liang, Hongwei; Zen, Ke

    2014-01-01

    As an essential component of innate immunity, macrophages have multiple functions in both inhibiting or promoting cell proliferation and tissue repair. Diversity and plasticity are hallmarks of macrophages. Classical M1 and alternative M2 activation of macrophages, mirroring the Th1–Th2 polarization of T cells, represent two extremes of a dynamic changing state of macrophage activation. M1-type macrophages release cytokines that inhibit the proliferation of surrounding cells and damage contiguous tissue, and M2-type macrophages release cytokines that promote the proliferation of contiguous cells and tissue repair. M1–M2 polarization of macrophage is a tightly controlled process entailing a set of signaling pathways, transcriptional and posttranscriptional regulatory networks. An imbalance of macrophage M1–M2 polarization is often associated with various diseases or inflammatory conditions. Therefore, identification of the molecules associated with the dynamic changes of macrophage polarization and understanding their interactions is crucial for elucidating the molecular basis of disease progression and designing novel macrophage-mediated therapeutic strategies. PMID:25506346

  12. Flexoelectricity and the polarity of complex ferroelastic twin patterns

    NASA Astrophysics Data System (ADS)

    Salje, Ekhard K. H.; Li, Suzhi; Stengel, Massimiliano; Gumbsch, Peter; Ding, Xiangdong

    2016-07-01

    We study, by means of an atomistic toy model, the interplay of ferroelastic twin patterns and electrical polarization. Our molecular dynamics simulations reproduce polarity in straight twin walls as observed experimentally. We show, by making contact with continuum theory, that the effect is governed by linear flexoelectricity. Complex twin patterns, with very high densities of kinks and/or junctions, produce winding structures in the dipolar field, which are reminiscent of polarization vortices. By means of a "cold shearing" technique, we produce patches with high vortex densities; these unexpectedly show a net macroscopic polarization even if neither the original sample nor the applied mechanical perturbation breaks inversion symmetry by itself. These results may explain some puzzling experimental observations of "parasitic" polarity in the paraelectric phase of BaTi O3 and LaAl O3 .

  13. Exchange and polarization effect in high-order harmonic imaging of molecular structures

    SciTech Connect

    Sukiasyan, Suren; Ivanov, Misha Yu.; Patchkovskii, Serguei; Smirnova, Olga; Brabec, Thomas

    2010-10-15

    We analyze the importance of exchange, polarization, and electron-electron correlation in high-order harmonic generation in molecules interacting with intense laser fields. We find that electron exchange can become particularly important for harmonic emission associated with intermediate excitations in the molecular ion. In particular, for orbitals associated with two-hole one-particle excitations, exchange effects can eliminate structure-related minima and maxima in the harmonic spectra. Laser-induced polarization of the neutral molecule may also have major effects on orbital structure-related minima and maxima in the harmonic spectra. Finally, we show how exchange terms in recombination can be viewed as a shakedownlike process induced by sudden electronic excitation in the ion.

  14. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step.

    PubMed

    Schwierz, Nadine; Frost, Christina V; Geissler, Phillip L; Zacharias, Martin

    2016-01-20

    Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient. PMID:26694883

  15. Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer.

    PubMed

    Berhanu, Workalemahu M; Masunov, Artëm E

    2015-01-01

    Amyloid fibrils are highly ordered protein aggregates associated with many diseases affecting millions of people worldwide. Polyphenols such as Curcumin, Exifone, and Myricetin exhibit modest inhibition toward fibril formation of tau peptide which is associated with Alzheimer's disease. However, the molecular mechanisms of this inhibition remain elusive. We investigated the binding of three polyphenol molecules to the protofibrils of an amyloidogenic fragment VQIVYK of tau peptide by molecular dynamics simulations in explicit solvent. We find that polyphenols induce conformational changes in the oligomer aggregate. These changes disrupt the amyloid H bonding, perturbing the aggregate. While the structural evolution of the control oligomer with no ligand is limited to the twisting of the β-sheets without their disassembly, the presence of polyphenol molecule pushes the β-sheets apart, and leads to a loosely packed structure where two of four β-sheets dissociate in each of the three cases considered here. The H-bonding capacity of polyphenols is responsible for the observed behavior. The calculated binding free energies and its individual components enabled better understanding of the binding. Results indicated that the contribution from Van der Waals interactions is more significant than electrostatic contribution to the binding. The findings from this study are expected to assist in the development of aggregation inhibitors. Significant binding between polyphenols and aggregate oligomer identified in our simulations confirms the previous experimental observations in which polyphenols refold the tau peptide without forming covalent bonds. PMID:25093402

  16. Information processing in parallel through directionally resolved molecular polarization components in coherent multidimensional spectroscopy

    NASA Astrophysics Data System (ADS)

    Yan, Tian-Min; Fresch, Barbara; Levine, R. D.; Remacle, F.

    2015-08-01

    We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, kl, k l = ∑ i l i k i where ki is the propagation direction of the ith pulse and {li} is a set of integers that encodes the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, which are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by nonlinear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible.

  17. Control of density fluctuations in atomistic-continuum simulations of dense liquids.

    PubMed

    Kotsalis, E M; Walther, J H; Koumoutsakos, P

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids. PMID:17677596

  18. Dynamics of dilute solutions of poly(aspartic acid) and its sodium salt elucidated from atomistic molecular dynamics simulations with explicit water.

    PubMed

    Ramachandran, Sanoop; Katha, Anki Reddy; Kolake, Subramanya Mayya; Jung, Bokyung; Han, Sungsoo

    2013-11-01

    The use of forward osmosis (FO) process for seawater desalination has attracted tremendous interest in recent years. Besides the manufacture of suitable membranes, the major technical challenge in the efficient deployment of the FO technology lies in the development of a suitable "draw solute". Owing to its inherent advantages, poly(aspartic acid) has arisen to be an attractive candidate for this purpose. However, an investigation of its molecular level properties has not been studied in detail. In this paper, the dynamics of poly(aspartic acid) and its sodium salt in the dilute concentration regime have been reported. The quantification of the polymer conformational properties, its solvation behavior, and the counterion dynamics are studied. The neutral polymer shows a preferentially coiled structure whereas the fully ionized polymer has an extended structure. Upon comparing with poly(acrylic acid) polymer, another polymer which has been used as a draw solute, poly(aspartic acid) forms more number of hydrogen bonds as well as fewer ion pairs. PMID:24099271

  19. Effect of molecular anisotropy on the intensity and degree of polarization of light scattered from model atmospheres

    NASA Technical Reports Server (NTRS)

    Bahethi, O. P.; Fraser, R. S.

    1980-01-01

    Computations of the properties of sunlight scattered from models of the earth-atmosphere system are presented to show the effect of molecular anisotropy on the intensity, flux, and degree of polarization of the scattered light. The values of these parameters change significantly when the anisotropy factor is neglected in the molecular optical thickness and scattering phase matrix. However, if the Rayleigh scattering optical thickness is kept constant and the molecular anisotropy factor is included only in the Rayleigh phase matrix, the flux does not change, the intensity changes by a small amount, but the changes in the degree of polarization are still significant.

  20. Polarization Sensitive Measurements of Molecular Reorientation in a Glass Capacitor Cell

    NASA Astrophysics Data System (ADS)

    Cooper, Nathan; Lawhead, Carlos; Anderson, Josiah; Shiver, Tegan; Prayaga, Chandra; Ujj, Laszlo

    2014-03-01

    It is well known that molecules having a permanent dipole moment tend to orient in the direction of the electric field at room temperature. The reorientation can be probed with the help of linear spectroscopy methods such as fluorescence anisotropy measurements. We have used nonlinear polarization sensitive Raman scattering spectroscopy to quantify the orientation effect of the dipoles. Vibrational spectra of the molecules has been recorded as a function of the external electric field. The polarization changes observed during the measurement are directly linked to the molecular reorientation rearrangement. Spectra has been recorded with a laser spectrometer comprised of a Nd:YAG laser and an optical parametric oscillator and an imaging spectrometer with a CCD detector. In order to make this measurement we have constructed a glass capacitor cell coated in TiO and applied a significant electric field (0-3 kV/mm) to the sample. Our measurements showed that the orientation effect is most significant for liquid crystals as observed previously with non-polarization sensitive CARS spectroscopy.

  1. Large molecular weight nitroxide biradicals providing efficient dynamic nuclear polarization at temperatures up to 200 K.

    PubMed

    Zagdoun, Alexandre; Casano, Gilles; Ouari, Olivier; Schwarzwälder, Martin; Rossini, Aaron J; Aussenac, Fabien; Yulikov, Maxim; Jeschke, Gunnar; Copéret, Christophe; Lesage, Anne; Tordo, Paul; Emsley, Lyndon

    2013-08-28

    A series of seven functionalized nitroxide biradicals (the bTbK biradical and six derivatives) are investigated as exogenous polarization sources for dynamic nuclear polarization (DNP) solid-state NMR at 9.4 T and with ca. 100 K sample temperatures. The impact of electron relaxation times on the DNP enhancement (ε) is examined, and we observe that longer inversion recovery and phase memory relaxation times provide larger ε. All radicals are tested in both bulk 1,1,2,2-tetrachloroethane solutions and in mesoporous materials, and the difference in ε between the two cases is discussed. The impact of the sample temperature and magic angle spinning frequency on ε is investigated for several radicals each characterized by a range of electron relaxation times. In particular, TEKPol, a bulky derivative of bTbK with a molecular weight of 905 g·mol(-1), is presented. Its high-saturation factor makes it a very efficient polarizing agent for DNP, yielding unprecedented proton enhancements of over 200 in both bulk and materials samples at 9.4 T and 100 K. TEKPol also yields encouraging enhancements of 33 at 180 K and 12 at 200 K, suggesting that with the continued improvement of radicals large ε may be obtained at higher temperatures. PMID:23961876

  2. Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics.

    PubMed

    Amani, Ehsan; Movahed, Saeid

    2016-06-01

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. PMID:27155300

  3. Cascade defect evolution processes: Comparison of atomistic methods

    NASA Astrophysics Data System (ADS)

    Xu, Haixuan; Stoller, Roger E.; Osetsky, Yury N.

    2013-11-01

    Determining defect evolution beyond the molecular dynamics (MD) time scale is critical to bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity to the atomistic processes involved. To demonstrate this capability, three examples are presented in which SEAKMC has been used to investigate the evolution of typical radiation-induced defects in bcc iron. Depending on the particular example, SEAKMC results are compared with those obtained using two other on-the-fly KMC techniques, object KMC, and MD. The three examples are: (1) evolution of a vacancy-rich region similar to the core of a displacement cascade, (2) the stability of recently reported interstitial clusters with a structure similar to the C15 Laves phase, and (3) long-term aging of atomic displacement cascade debris. In the various examples, the SEAKMC approach provides better agreement with MD simulations, highlights the importance of the underlying atomistic processes, and provides new information on long-term defect evolution in iron.

  4. Atomistic Simulation of the Transition from Atomistic to Macroscopic Cratering

    SciTech Connect

    Samela, Juha; Nordlund, Kai

    2008-07-11

    Using large-scale atomistic simulations, we show that the macroscopic cratering behavior emerges for projectile impacts on Au at projectile sizes between 1000 and 10 000 Au atoms at impact velocities comparable to typical meteoroid velocities. In this size regime, we detect a compression of material in Au nanoparticle impacts similar to that observed for hypervelocity macroscopic impacts. The simulated crater volumes agree with the values calculated using the macroscopic crater size scaling law, in spite of a downwards extrapolation over more than 15 orders of magnitude in terms of the impactor volume. The result demonstrates that atomistic simulations can be used as a tool to understand the strength properties of materials in cases where only continuum models have been possible before.

  5. Terazulene Isomers: Polarity Change of OFETs through Molecular Orbital Distribution Contrast.

    PubMed

    Yamaguchi, Yuji; Takubo, Maki; Ogawa, Keisuke; Nakayama, Ken-Ichi; Koganezawa, Tomoyuki; Katagiri, Hiroshi

    2016-09-01

    Intermolecular orbital coupling is fundamentally important to organic semiconductor performance. Recently, we reported that 2,6':2',6″-terazulene (TAz1) exhibited excellent performance as an n-type organic field-effect transistor (OFET) via molecular orbital distribution control. To validate and develop this concept, here we present three other terazulene regioisomers, which have three azulene molecules connected at the 2- or 6-position along the long axis of the azulene, thus constructing a linear expanded π-conjugation system: 2,2':6',2″-terazulene (TAz2), 2,2':6',6″-terazulene (TAz3), and 6,2':6',6″-terazulene (TAz4). TAz2 and TAz3 exhibit ambipolar characteristics; TAz4 exhibits clear n-type transistor behavior as an OFET. The lowest unoccupied molecular orbitals (LUMOs) of all terazulenes are fully delocalized over the entire molecule. In contrast, the highest occupied molecular orbitals (HOMOs) of TAz2 and TAz3 are delocalized over the 2,2'-biazulene units; the HOMOs of TAz4 are localized at one end of the azulene unit. These findings confirm that terazulene isomers which are simple hydrocarbon compounds are versatile materials with a tunable-polarity FET characteristic that depends on the direction of the azulene unit and the related contrast of the molecular orbital distribution in the terazulene backbone. PMID:27511286

  6. Molecular level all-optical logic with chlorophyll absorption spectrum and polarization sensitivity

    NASA Astrophysics Data System (ADS)

    Raychaudhuri, B.; Bhattacharyya (Bhaumik), S.

    2008-06-01

    Chlorophyll is suggested as a suitable medium for realizing optical Boolean logic at the molecular level in view of its wavelength-selective property and polarization sensitivity in the visible region. Spectrophotometric studies are made with solutions of total chlorophyll and chromatographically isolated components, viz. chlorophyll a and b and carotenoids extracted from pumpkin leaves of different maturity stages. The absorption features of matured chlorophyll with two characteristic absorption peaks and one transmission band are molecular properties and independent of concentration. A qualitative explanation of such an absorption property is presented in terms of a ‘particle in a box’ model and the property is employed to simulate two-input optical logic operations. If both of the inputs are either red or blue, absorption is high. If either one is absent and replaced by a wavelength of the transmission band, e.g. green, absorption is low. Assigning these values as 0 s or 1 s, AND and OR operations can be performed. A NOT operation can be simulated with the transmittance instead of the absorbance. Also, the shift in absorbance values for two different polarizations of the same monochromatic light can simulate two logical states with a single wavelength. Cyclic change in absorbance is noted over a rotation of 360° for both red and blue peaks, although the difference is not very large. Red monochromatic light with polarizations apart by 90°, corresponding to maximum and minimum absorption, respectively, may be assigned as the two logical states. The fluorescence emissions for different pigment components are measured at different excitation wavelengths and the effect of fluorescence on the red absorbance is concluded to be negligible.

  7. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  8. Induction of molecular chirality by circularly polarized light in cyclic azobenzene with a photoswitchable benzene rotor.

    PubMed

    Hashim, P K; Thomas, Reji; Tamaoki, Nobuyuki

    2011-06-20

    New phototriggered molecular machines based on cyclic azobenzene were synthesized in which a 2,5-dimethoxy, 2,5-dimethyl, 2,5-difluorine or unsubstituted-1,4-dioxybenzene rotating unit and a photoisomerizable 3,3'-dioxyazobenzene moiety are bridged together by fixed bismethylene spacers. Depending upon substitution on the benzene moiety and on the E/Z conformation of the azobenzene unit, these molecules suffer various degrees of restriction on the free rotation of the benzene rotor. The rotation of the substituted benzene rotor within the cyclic azobenzene cavity imparts planar chirality to the molecules. Cyclic azobenzene 1, with methoxy groups at both the 2- and 5-positions of the benzene rotor, was so conformationally restricted that free rotation of the rotor was prevented in both the E and Z isomers and the respective planar chiral enantiomers were resolved. In contrast, compound 2, with 2,5-dimethylbenzene as the rotor, demonstrated the property of a light-controlled molecular brake, whereby rotation of the 2,5-dimethylbenzene moiety is completely stopped in the E isomer (brake ON, rotation OFF), while the rotation is allowed in the Z isomer (brake OFF, rotation ON). The cyclic azobenzene 3, with fluorine substitution on the benzene rotor, was in the brake OFF state regardless of E/Z photoisomerization of the azobenzene moiety. More interestingly, for the first time, we demonstrated the induction of molecular chirality in a simple monocyclic azobenzene by circular-polarized light. The key characteristics of cyclic azobenzene 2, that is, stability of the chiral structure in the E isomer, fast racemization in the Z isomer, and the circular dichroism of enantiomers of both E and Z isomers, resulted in a simple reversible enantio-differentiating photoisomerization directly between the E enantiomers. Upon exposure to r- or l-circularly polarized light at 488 nm, partial enrichment of the (S)- or (R)-enantiomers of 2 was observed. PMID:21567494

  9. Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation

    PubMed Central

    Hughes, Daniel ST; Keynes, Roger J; Tannahill, David

    2009-01-01

    Background The polarization of somite-derived sclerotomes into anterior and posterior halves underlies vertebral morphogenesis and spinal nerve segmentation. To characterize the full extent of molecular differences that underlie this polarity, we have undertaken a systematic comparison of gene expression between the two sclerotome halves in the mouse embryo. Results Several hundred genes are differentially-expressed between the two sclerotome halves, showing that a marked degree of molecular heterogeneity underpins the development of somite polarity. Conclusion We have identified a set of genes that warrant further investigation as regulators of somite polarity and vertebral morphogenesis, as well as repellents of spinal axon growth. Moreover the results indicate that, unlike the posterior half-sclerotome, the central region of the anterior-half-sclerotome does not contribute bone and cartilage to the vertebral column, being associated instead with the development of the segmented spinal nerves. PMID:19463158

  10. Balloon-Borne Submillimeter Polarimetry of the Vela C Molecular Cloud: Systematic Dependence of Polarization Fraction on Column Density and Local Polarization-Angle Dispersion

    NASA Astrophysics Data System (ADS)

    Fissel, Laura M.; Ade, Peter A. R.; Angilè, Francesco E.; Ashton, Peter; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fukui, Yasuo; Galitzki, Nicholas; Gandilo, Natalie N.; Klein, Jeffrey; Korotkov, Andrei L.; Li, Zhi-Yun; Martin, Peter G.; Matthews, Tristan G.; Moncelsi, Lorenzo; Nakamura, Fumitaka; Netterfield, Calvin B.; Novak, Giles; Pascale, Enzo; Poidevin, Frédérick; Santos, Fabio P.; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Diego Soler, Juan; Thomas, Nicholas E.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

    2016-06-01

    We present results for Vela C obtained during the 2012 flight of the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry. We mapped polarized intensity across almost the entire extent of this giant molecular cloud, in bands centered at 250, 350, and 500 μm. In this initial paper, we show our 500 μm data smoothed to a resolution of 2.‧5 (approximately 0.5 pc). We show that the mean level of the fractional polarization p and most of its spatial variations can be accounted for using an empirical three-parameter power-law fit, p \\propto {{\\boldsymbol{N}}}-0.45 {{\\boldsymbol{S}}}-0.60, where N is the hydrogen column density and S is the polarization-angle dispersion on 0.5 pc scales. The decrease of p with increasing S is expected because changes in the magnetic field direction within the cloud volume sampled by each measurement will lead to cancellation of polarization signals. The decrease of p with increasing N might be caused by the same effect, if magnetic field disorder increases for high column density sightlines. Alternatively, the intrinsic polarization efficiency of the dust grain population might be lower for material along higher density sightlines. We find no significant correlation between N and S. Comparison of observed submillimeter polarization maps with synthetic polarization maps derived from numerical simulations provides a promising method for testing star formation theories. Realistic simulations should allow for the possibility of variable intrinsic polarization efficiency. The measured levels of correlation among p, N, and S provide points of comparison between observations and simulations.

  11. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    SciTech Connect

    Habasaki, Junko; Ngai, K. L.

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO{sub 3}), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, T{sub B} (or T{sub c}) and the glass transition temperature T{sub g}, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, N{sub B}, within the first minimum of the pair correlation function, g(r){sub min}, increases. On crossing T{sub B} (>T{sub g}), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at T{sub g}. The glass transition temperature, T{sub g}, is characterized by the saturation of the total number of “bonds,” N{sub B} and the corresponding decrease in degree of freedom, F = [(3N − 6) − N{sub B}], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at T{sub g}, the number of bonds shows a remarkable change at around T{sub B}. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, f{sub g}, of each coordination polyhedron, which can be defined by f{sub g} = [(3N{sub V} − 6) − N{sub b}]. Here, 3N{sub v} is the degree of freedom of N{sub V} vertices of the polyhedron, and N{sub b} is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion

  12. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    NASA Astrophysics Data System (ADS)

    Habasaki, Junko; Ngai, K. L.

    2015-04-01

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO3), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, TB (or Tc) and the glass transition temperature Tg, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, NB, within the first minimum of the pair correlation function, g(r)min, increases. On crossing TB (>Tg), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at Tg. The glass transition temperature, Tg, is characterized by the saturation of the total number of "bonds," NB and the corresponding decrease in degree of freedom, F = [(3N - 6) - NB], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at Tg, the number of bonds shows a remarkable change at around TB. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, fg, of each coordination polyhedron, which can be defined by fg = [(3NV - 6) - Nb]. Here, 3Nv is the degree of freedom of NV vertices of the polyhedron, and Nb is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of Nb of cation-cation (or anion-anion) pairs in the polyhedron, although the

  13. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations--Existence of infinite overlapping networks in a fragile ionic liquid.

    PubMed

    Habasaki, Junko; Ngai, K L

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO3), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, TB (or Tc) and the glass transition temperature Tg, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, NB, within the first minimum of the pair correlation function, g(r)min, increases. On crossing TB (>Tg), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at Tg. The glass transition temperature, Tg, is characterized by the saturation of the total number of "bonds," NB and the corresponding decrease in degree of freedom, F = [(3N - 6) - NB], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at Tg, the number of bonds shows a remarkable change at around TB. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, fg, of each coordination polyhedron, which can be defined by fg = [(3NV - 6) - Nb]. Here, 3Nv is the degree of freedom of NV vertices of the polyhedron, and Nb is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of Nb of cation-cation (or anion-anion) pairs in the polyhedron, although the

  14. p/n-Polarity of thiophene oligomers in photovoltaic cells: role of molecular vs. supramolecular properties.

    PubMed

    Ghosh, Tanwistha; Gopal, Anesh; Saeki, Akinori; Seki, Shu; Nair, Vijayakumar C

    2015-04-28

    Molecular and supramolecular properties play key roles in the optoelectronic properties and photovoltaic performances of organic materials. In the present work, we show how small changes in the molecular structure affect such properties, which in turn control the intrinsic and fundamental properties such as the p/n-polarity of organic semiconductors in bulk-heterojunction solar cells. Herein, we designed and synthesized two acceptor-donor-acceptor type semiconducting thiophene oligomers end-functionalized with oxazolone/isoxazolone derivatives (OT1 and OT2 respectively). The HOMO-LUMO energy levels of both derivatives were found to be positioned in such a way that they can act as electron acceptors to P3HT and electron donors to PCBM. However, OT1 functions as a donor (with PCBM) and OT2 as an acceptor (with P3HT) in BHJ photovoltaic cells, and their reverse roles results in either no or poor performance of the cells. Detailed studies using UV-vis absorption and fluorescence spectroscopy, time-correlated single photon counting, UV-photoelectron spectroscopy, density functional theory calculations, X-ray diffraction, and thermal gravimetric analysis proved that both molecular and supramolecular properties contributed equally but in a contrasting manner to the abovementioned observation. The obtained results were further validated by flash-photolysis time-resolved microwave conductivity studies which showed an excellent correlation between the structure, property, and device performances of the materials. PMID:25805168

  15. Effect of molecular anisotropy on the intensity and degree of polarization of light scattered from model atmospheres

    NASA Technical Reports Server (NTRS)

    Bahethi, O. P.; Fraser, R. S.

    1975-01-01

    Computations of the intensity, flux, degree of polarization, and the positions of neutral points are presented for models of the terrestrial gaseous and hazy atmospheres by incorporating the molecular anisotropy due to air in the Rayleigh scattering optical thickness and phase matrix. Molecular anisotropy causes significant changes in the intensity, flux and the degree of polarization of the scattered light. The positions of neutral points do not change significantly. When the Rayleigh scattering optical thickness is kept constant and the molecular anisotropy factor is included only in the Rayleigh phase matrix, the flux does not change and the intensity and positions of neutron points change by a small amount. The changes in the degree of polarization are still significant.

  16. Anisotropic Molecular Orientation of Poly [4, 4'-oxydiphenylene- 1, 2, 3, 4-cyclobutanetetracarboximide] Films Irradiated by Linearly Polarized UV Light

    NASA Astrophysics Data System (ADS)

    Sakamoto, Kenji; Usami, Kiyoaki; Araya, Takeshi; Ushioda, Sukekatsu

    1999-12-01

    We have investigated the anisotropic molecular orientation of poly [4, 4'-oxydiphenylene-1, 2, 3, 4-cyclobutanetetracarboximide] (CBDA-ODA) films induced by irradiation with linearly polarized ultraviolet light (LPUVL). The molecular orientation was monitored by measuring the polarized infrared (IR) absorption spectra of a 10-nm-thick film. The anisotropy of the molecular orientation exceeded that of a rubbed film with the same film thickness. From the LPUVL exposure dependence of IR absorption we found that preferential cleavage occurs to the cyclobutane ring in the polyimide backbone structure oriented parallel to the polarization direction of LPUVL. Then the orientation of the cleaved polyimide molecule is randomized. We conclude that the large anisotropy of the LPUVL-exposed film is caused by the anisotropic cleavage of the cyclobutane rings and the orientational randomization of the cleaved polyimide molecules.

  17. Investigation of the local structure of mixtures of an ionic liquid with polar molecular species through molecular dynamics: cluster formation and angular distributions.

    PubMed

    Carrete, Jesús; Méndez-Morales, Trinidad; Cabeza, Óscar; Lynden-Bell, Ruth M; Gallego, Luis J; Varela, Luis M

    2012-05-24

    In this work, we used molecular dynamics simulations to analyze in detail the spatial distributions of the different constituents in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with three polar molecular species: water and two alcohols of different chain lengths (methanol and ethanol). In particular, we report results regarding the influence of the chosen species and its concentration on the formation of ionic and molecular clusters over the whole miscibility range, as well as on the angular distribution of polar molecules around the anion and the cation in these systems. Both analyses showed that addition of a molecular species breaks down the polar network of the pure ionic liquid in clusters whose mean size decreases progressively as more molecules are added. At very high concentrations of the molecular species, the ions are found to be isolated in mixtures with water and methanol, but they tend to form pairs in ethanol. In mixtures with water we identified large clusters that form a water network at very high water concentrations, while at low water concentrations polar molecules tend to form smaller aggregates. In contrast, in mixtures with alkanols there is no evidence of the formation of large alcohol clusters at any concentration. Spatial order in alcohol was also studied by means of the Kirkwood G factor, reaching the conclusion that the angular correlations which appear in pure alcohols due to dipole interactions are destroyed by the ionic liquid, even when present only in tiny amounts. PMID:22587330

  18. Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    SciTech Connect

    Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N

    2004-04-15

    We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.

  19. A Molecular Probe for the Detection of Polar Lipids in Live Cells.

    PubMed

    Bader, Christie A; Shandala, Tetyana; Carter, Elizabeth A; Ivask, Angela; Guinan, Taryn; Hickey, Shane M; Werrett, Melissa V; Wright, Phillip J; Simpson, Peter V; Stagni, Stefano; Voelcker, Nicolas H; Lay, Peter A; Massi, Massimiliano; Plush, Sally E; Brooks, Douglas A

    2016-01-01

    Lipids have an important role in many aspects of cell biology, including membrane architecture/compartment formation, intracellular traffic, signalling, hormone regulation, inflammation, energy storage and metabolism. Lipid biology is therefore integrally involved in major human diseases, including metabolic disorders, neurodegenerative diseases, obesity, heart disease, immune disorders and cancers, which commonly display altered lipid transport and metabolism. However, the investigation of these important cellular processes has been limited by the availability of specific tools to visualise lipids in live cells. Here we describe the potential for ReZolve-L1™ to localise to intracellular compartments containing polar lipids, such as for example sphingomyelin and phosphatidylethanolamine. In live Drosophila fat body tissue from third instar larvae, ReZolve-L1™ interacted mainly with lipid droplets, including the core region of these organelles. The presence of polar lipids in the core of these lipid droplets was confirmed by Raman mapping and while this was consistent with the distribution of ReZolve-L1™ it did not exclude that the molecular probe might be detecting other lipid species. In response to complete starvation conditions, ReZolve-L1™ was detected mainly in Atg8-GFP autophagic compartments, and showed reduced staining in the lipid droplets of fat body cells. The induction of autophagy by Tor inhibition also increased ReZolve-L1™ detection in autophagic compartments, whereas Atg9 knock down impaired autophagosome formation and altered the distribution of ReZolve-L1™. Finally, during Drosophila metamorphosis fat body tissues showed increased ReZolve-L1™ staining in autophagic compartments at two hours post puparium formation, when compared to earlier developmental time points. We concluded that ReZolve-L1™ is a new live cell imaging tool, which can be used as an imaging reagent for the detection of polar lipids in different intracellular

  20. A Molecular Probe for the Detection of Polar Lipids in Live Cells

    PubMed Central

    Bader, Christie A.; Shandala, Tetyana; Carter, Elizabeth A.; Ivask, Angela; Guinan, Taryn; Hickey, Shane M.; Werrett, Melissa V.; Wright, Phillip J.; Simpson, Peter V.; Stagni, Stefano; Voelcker, Nicolas H.; Lay, Peter A.; Massi, Massimiliano; Brooks, Douglas A.

    2016-01-01

    Lipids have an important role in many aspects of cell biology, including membrane architecture/compartment formation, intracellular traffic, signalling, hormone regulation, inflammation, energy storage and metabolism. Lipid biology is therefore integrally involved in major human diseases, including metabolic disorders, neurodegenerative diseases, obesity, heart disease, immune disorders and cancers, which commonly display altered lipid transport and metabolism. However, the investigation of these important cellular processes has been limited by the availability of specific tools to visualise lipids in live cells. Here we describe the potential for ReZolve-L1™ to localise to intracellular compartments containing polar lipids, such as for example sphingomyelin and phosphatidylethanolamine. In live Drosophila fat body tissue from third instar larvae, ReZolve-L1™ interacted mainly with lipid droplets, including the core region of these organelles. The presence of polar lipids in the core of these lipid droplets was confirmed by Raman mapping and while this was consistent with the distribution of ReZolve-L1™ it did not exclude that the molecular probe might be detecting other lipid species. In response to complete starvation conditions, ReZolve-L1™ was detected mainly in Atg8-GFP autophagic compartments, and showed reduced staining in the lipid droplets of fat body cells. The induction of autophagy by Tor inhibition also increased ReZolve-L1™ detection in autophagic compartments, whereas Atg9 knock down impaired autophagosome formation and altered the distribution of ReZolve-L1™. Finally, during Drosophila metamorphosis fat body tissues showed increased ReZolve-L1™ staining in autophagic compartments at two hours post puparium formation, when compared to earlier developmental time points. We concluded that ReZolve-L1™ is a new live cell imaging tool, which can be used as an imaging reagent for the detection of polar lipids in different intracellular

  1. Quantum Monte Carlo study of molecular polarization and antiferroelectric ordering in squaric acid crystals

    NASA Astrophysics Data System (ADS)

    Ishizuka, Hiroaki; Motome, Yukitoshi; Furukawa, Nobuo; Suzuki, Sei

    2011-08-01

    Effects of geometrical frustration and quantum fluctuation are theoretically investigated for the proton ordering in a quasi-two-dimensional hydrogen-bonded system, namely a squaric acid crystal. We elucidate the phase diagram for an effective model, the transverse-field Ising model on a frustrated checkerboard lattice, by using quantum Monte Carlo simulation. A crossover to a liquidlike paraelectric state with well-developed molecular polarizations is identified, distinguishably from long-range ordering. The emergence of long-range order from the liquidlike state exhibits peculiar aspects originating from the lifting of quasimacroscopic degeneracy, such as colossal enhancement of the transition temperature and a vanishingly small anomaly in the specific heat.

  2. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

  3. Polarity inversion of N-face GaN by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Wong, M.H.; Mishra, Umesh K.; Wu Feng; Mates, Thomas E.; Speck, James S.

    2008-11-01

    The polarity of GaN grown by plasma-assisted molecular beam epitaxy was inverted from N-face to Ga-face by simultaneously exposing the surface to Mg and activated N fluxes during a growth interruption at a reduced substrate temperature. Growth studies suggested that a Mg{sub x}N{sub y} compound was responsible for inverting the crystal. The change in polarity was verified in situ by reflection high energy electron diffraction via GaN surface reconstructions, and ex situ by convergent beam electron diffraction and KOH etch studies. The surface of the inverted material showed smooth step flow features. Ga-face high electron mobility transistors with good dc and small signal performance were fabricated on the inverted epilayers. A drain-source current of 0.84 A/mm was measured at a gate-source voltage of +1 V. Current-gain cutoff and maximum oscillation frequencies of 22 and 53 GHz, respectively, were measured in these devices. The device performance is similar to that of Ga-face transistors with comparable dimensions.

  4. Atomistic aspects of crack propagation along high angle grain boundaries

    SciTech Connect

    Farkas, D.

    1997-12-31

    The author presents atomistic simulations of the crack tip configuration near a high angle {Sigma} = 5 [001](210) symmetrical tilt grain boundary in NiAl. The simulations were carried out using molecular statics and embedded atom (EAM) potentials. The cracks are stabilized near a Griffith condition involving the cohesive energy of the grain boundary. The atomistic configurations of the tip region are different in the presence of the high angle grain boundary than in the bulk. Three different configurations of the grain boundary were studied corresponding to different local compositions. It was found that in ordered NiAl, cracks along symmetrical tilt boundaries show a more brittle behavior for Al rich boundaries than for Ni-rich boundaries. Lattice trapping effects in grain boundary fracture were found to be more significant than in the bulk.

  5. Propagation of intense and short circularly polarized pulses in a molecular gas: From multiphoton ionization to nonlinear macroscopic effects

    NASA Astrophysics Data System (ADS)

    Lytova, M.; Lorin, E.; Bandrauk, A. D.

    2016-07-01

    We present a detailed analysis of the propagation dynamics of short and intense circularly polarized pulses in an aligned diatomic gas. Compared to linearly polarized intense pulses, high harmonic generation (HHG) and the coherent generation of attosecond pulses in the intense-circular-polarization case are a new research area. More specifically, we numerically study the propagation of intense and short circularly polarized pulses in the one-electron H2+ molecular gas, using a micro-macro Maxwell-Schrödinger model. In this model, the macroscopic polarization is computed from the solution of a large number of time-dependent Schrödinger equations, the source of dipole moments, and using a trace operator. We focus on the intensity and the phase of harmonics generated in the H2+ gas as a function of the pulse-propagation distance. We show that short coherent circularly polarized pulses of same helicity can be generated in the molecular gas as a result of cooperative phase-matching effects.

  6. Circularly polarized molecular high-order harmonic generation in H2+ with intense laser pulses and static fields

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-06-01

    Molecular high-order harmonic generation (MHOHG) by a combined intense circularly polarized laser pulse and static electric field has been studied from the appropriate time-dependent Schrödinger equation (TDSE) for the H2+ molecular ion. It is found that for a particular static field strength derived from a classical model, efficient MHOHG spectra are obtained with maximum energy Ip + 9.05Up, where Ip is the ionization potential and Up=E02/4meω02 is the ponderomotive energy at amplitude E0 and frequency ω0 of the circularly polarized laser pulse. The static field controls recollision of the electron with parent ions and is confirmed by numerical solutions of the H2+ TDSE at equilibrium. To produce circularly polarized MHOHG spectra, a combination of an elliptically polarized pulse and a static electric field is found to be most efficient. A time-frequency analysis obtained via Gabor transforms is employed to identify electron recollision times responsible for the generation of these high-order harmonics. It is found that only single recollision trajectories contribute to the circularly polarized harmonics, thus generating new sources for high-frequency circularly polarized attosecond pulses.

  7. Molecular Dynamics of Flexible Polar Cations in a Variable Confined Space: Toward Exceptional Two-Step Nonlinear Optical Switches.

    PubMed

    Xu, Wei-Jian; He, Chun-Ting; Ji, Cheng-Min; Chen, Shao-Li; Huang, Rui-Kang; Lin, Rui-Biao; Xue, Wei; Luo, Jun-Hua; Zhang, Wei-Xiong; Chen, Xiao-Ming

    2016-07-01

    The changeable molecular dynamics of flexible polar cations in the variable confined space between inorganic chains brings about a new type of two-step nonlinear optical (NLO) switch with genuine "off-on-off" second harmonic generation (SHG) conversion between one NLO-active state and two NLO-inactive states. PMID:27159779

  8. Atomistic Simulation of Initiation in Hexanitrostilbene

    NASA Astrophysics Data System (ADS)

    Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

    2015-06-01

    We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  9. Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

    DOE PAGESBeta

    Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.; Najm, Habib N.; Debusschere, Bert

    2015-08-11

    We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We alsomore » consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.« less

  10. Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

    SciTech Connect

    Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.; Najm, Habib N.; Debusschere, Bert

    2015-08-11

    We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We also consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.

  11. Atomistic Properties of Y Uranium

    SciTech Connect

    Benjamin Beeler; Chaitanya Deo; Mmichael Baskes; Maria Okuniewski

    2012-02-01

    The properties of the body-centered cubic y phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (y) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of y U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic y calculation of U properties above 0 K with interatomic potentials.

  12. Two-center interference in molecular photoelectron energy spectra with intense attosecond circularly polarized XUV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bian, Xue-Bin; Bandrauk, André D.

    2014-08-01

    We study two-center electron interference in molecular photoionization processes by intense attosecond circularly polarized extreme ultraviolet (XUV) laser pulses in both symmetric H2+ and nonsymmetric HHe2+ one-electron diatomic systems. Simulations from numerical solutions of time-dependent Schrödinger equations for the oriented symmetric molecular ion H2+ exhibit a signature of interference with double peaks (minima) in molecular attosecond photoelectron energy spectra (MAPES) at critical angles ϑc between the continuum electron momentum pe and the molecular internuclear R axis. The interference patterns are shown to be influenced by the molecular Coulomb potential, leading to a shift of the critical angle ϑc. Dependence of the two-center interference on the pulse ellipticity is also investigated. Furthermore, it is found that the interference phenomena are critically sensitive to the molecular orbital symmetry. For the nonsymmetric molecular ion HHe2+, such double peaks in MAPES also occur, thus suggesting a method for imaging orbitals in molecules by intense ultrashort circularly polarized XUV pulses on the attosecond time scale.

  13. On the valve nature of a monolayer of aligned molecular magnets in tunneling spin-polarized electrons: Towards organic molecular spintronics

    SciTech Connect

    Chakrabarti, Sudipto; Pal, Amlan J.

    2014-01-06

    We form a monolayer of magnetic organic molecules and immobilize their moments pointing either upwards or downwards with respect to the substrate through an electrostatic-binding process. Such a monolayer is probed with a scanning tunneling microscope tip, which is also magnetized with the magnetization vector pointing towards (or away from) apex of the tip. From spin-polarized tunneling current, we show that the current was higher when magnetization vectors of the tip and molecules were parallel as compared to that when they were anti-parallel. We show that for tunneling of spin-polarized electrons, aligned organic molecular magnets can act as a valve.

  14. Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene.

    PubMed

    Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

    2014-04-30

    Polarization energy corresponds to the stabilization of the cation or anion state of an atom or molecule when going from the gas phase to the solid state. The decrease in ionization energy and increase in electron affinity in the solid state are related to the (electronic and nuclear) polarization of the surrounding atoms and molecules in the presence of a charged entity. Here, through a combination of molecular mechanics and quantum mechanics calculations, we evaluate the polarization energies in two prototypical organic semiconductors, pentacene and 6,13-bis(2-(tri-isopropylsilyl)ethynyl)pentacene (TIPS-pentacene). Comparison of the results for the two systems reveals the critical role played by the molecular packing configurations in the determination of the polarization energies and provides physical insight into the experimental data reported by Lichtenberger and co-workers (J. Amer. Chem. Soc. 2010, 132, 580; J. Phys. Chem. C 2010, 114, 13838). Our results underline that the impact of packing configurations, well established in the case of the charge-transport properties, also extends to the polarization properties of π-conjugated materials. PMID:24725006

  15. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

    PubMed Central

    Mitchell, J. S.; Laughton, C. A.; Harris, Sarah A.

    2011-01-01

    Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA. PMID:21247872

  16. An Examination of the Deflection Method for the Study of Molecular Polarity

    ERIC Educational Resources Information Center

    Kempa, R. F.; Auld, J.

    1974-01-01

    Describes and discusses the procedure for a demonstration, found in the CHEMStudy film "Shapes and Polarities of Molecules" and in the Nuffield Advanced Chemistry and Physical Science materials, to qualitatively illustrate the differences between polar and non-polar liquids. (PEB)

  17. High-order-harmonic generation in molecular sequential double ionization by intense circularly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Lu, Huizhong; Bandrauk, André D.

    2015-08-01

    We present effects of electron energy transfer by electron collisions on high-order-harmonic generation (HHG) in molecular sequential double ionization by intense circularly polarized laser pulses. Results from numerical solutions of time-dependent Schrödinger equations for extended (large internuclear distance) H2 where electrons are entangled and hence delocalized by exchange show that HHG with cutoff energy up to Ip+24 Up can be obtained, where Ip is the molecule ionization potential and Up=I0/4 ω02 (in atomic units) is the ponderomotive energy for pulse intensity I0 and frequency ω0. A time-frequency analysis is employed to identify electron collisions for the generation of harmonics. Extended HHG arises from electron energy exchange, which agrees well with the prediction of a classical two electron collision model. Results for nonsymmetric HHe+ where initially electrons are localized on He are also compared and confirm the role of initial electron delocalization via entanglement for obtaining extended HHG plateaus.

  18. Molecular Dynamics Modeling of Dielectric Polarization and Ferroelectricity in Poly(vinylidene fluoride) and Related Polymers

    NASA Astrophysics Data System (ADS)

    Calame, Jeffrey

    Molecular dynamics studies of the dielectric polarization response of a constrained bond length and bond angle, united-atom-based model of lamellar crystals of poly(vinylidene fluoride) (PVDF) are reported. Classical ferroelectricity is observed in PVDF, and when variations in the basic PVDF-like interaction parameters are allowed, a transition between classical and relaxor ferroelectricity is found to depend systematically on the polymer repeat unit dipole moment and on the united atom radius of the non-CH2 functional group. The effects of step and ramp electric field reversal are studied. A complicated sequence of reorientation processes occurs over a wide range of time scales, including a weak, temperature-independent response of 1-2 ps duration associated with local torsional motion, followed by a slow-rising delay regime lasting 10s of ns or longer that involves trans-gauche (TG) transitions in the amorphous phase. After the delay, a large-amplitude primary reorientation occurs over a relatively short additional duration (0.1 to 2 ns), which is due to rotation of large sub-segments in the crystalline phase with few TG transitions. The overall sequence concludes with a slow terminal rise lasting several 100s of ns involving an improvement in crystalline order. Work supported by the U.S. Office of Naval Research.

  19. Identification of the molecular mechanisms contributing to polarized trafficking in osteoblasts.

    PubMed

    Prêle, Cecilia M; Horton, Michael A; Caterina, Paul; Stenbeck, Gudrun

    2003-01-01

    The directionality of matrix deposition in vivo is governed by the ability of a cell to direct vesicularflow to a specific target site. Osteoblastic cells direct newly synthesized bone matrix proteins toward the bone surface. In this study, we dissect the molecular mechanisms underlying the polarized trafficking of matrix protein in osteoblasts. We demonstrate using TEM, immunocytochemistry, and cDNA analysis, the ability of osteoblastic cells in culture to form tight junction-like structures and report the expression of the tight junction associated proteins occludin and claudins 1-3 in these cells. We identify intercellular contact sites and the leading edge of migratory osteoblasts as major target sites of vesicular trafficking in osteoblasts. Proteins required for this process, rsec6, NSF, VAMP1, and syntaxin 4, as well as the bone matrix protein, osteopontin, localize to these sites. We demonstrate that osteoblasts in vivo possess VAMP1 and, furthermore, report the expression of two VAMP1 splice variants in these cells. In addition, osteoblasts express the NSF attachment protein alpha-SNAP and the t-SNARE SNAP23. Thus, cell-to-cell contact sites and the leading edge of migratory osteoblasts contain a unique complement of proteins required for SNARE mediated membrane fusion. PMID:12490191

  20. Atomistic modeling and simulation of nanopolycrystalline solids

    NASA Astrophysics Data System (ADS)

    Yang, Zidong

    In the past decades, nanostructured materials have opened new and fascinating avenues for research. Nanopolycrystalline solids, which consist of nano-sized crystalline grains and significant volume fractions of amorphous grain boundaries, are believed to have substantially different response to the thermal-mechanical-electric-magnetic loads, as compared to the response of single-crystalline materials. Nanopolycrystalline materials are expected to play a key role in the next generation of smart materials. This research presents a framework (1) to generate full atomistic models, (2) to perform non-equilibrium molecular dynamics simulations, and (3) to study multi-physics phenomena of nanopolycrystalline solids. This work starts the physical model and mathematical representation with the framework of molecular dynamics. In addition to the latest theories and techniques of molecular dynamics simulations, this work implemented principle of objectivity and incorporates multi-physics features. Further, a database of empirical interatomic potentials is established and the combination scheme for potentials is revisited, which enables investigation of a broad spectrum of chemical elements (as in periodic table) and compounds (such as rocksalt, perovskite, wurtzite, diamond, etc.). The configurational model of nanopolycrystalline solids consists of two spatial components: (1) crystalline grains, which can be obtained through crystal structure optimization, and (2) amorphous grain boundaries, which can be obtained through amorphization process. Therefore, multi-grain multi-phase nanopolycrystalline material system can be constructed by partitioning the space for grains, followed by filling the inter-grain space with amorphous grain boundaries. Computational simulations are performed on several representative crystalline materials and their mixture, such as rocksalt, perovskite and diamond. Problems of relaxation, mechanical loading, thermal stability, heat conduction

  1. Atomistic simulations of langmuir monolayer collapse.

    PubMed

    Lorenz, Christian D; Travesset, Alex

    2006-11-21

    Monolayers at the vapor/water interface collapse by exploring the third dimension at sufficient lateral compression, either by forming three-dimensional structures or by solubilization into the aqueous solution. In this paper, we provide an atomistic description of collapse from molecular dynamics (MD) simulations. More specifically, we investigate monolayers of arachidic acids spread on pure water and in an aqueous solution with Ca2+ ions in the subphase. In both cases, it is found that the collapsed systems generally lead to the formation of multilayer structures, which in the system with Ca2+ ions, proceeds by an intermediate regime where the monolayer exhibits significant roughness (of the order of 4 A). If no roughness is present, the system forms collapsed structures into the aqueous solution. The computational cost of atomic MD limits our simulations to relatively small system sizes, fast compression rates, and temporal scales on the order of a nanosecond. We discuss the issues caused by these limitations and present a detailed discussion of how the collapse regime proceeds at long time scales. We conclude with a summary of the implications of our results for further theoretical and experimental studies. PMID:17106994

  2. Atomistic theory of amyloid fibril nucleation

    NASA Astrophysics Data System (ADS)

    Cabriolu, Raffaela; Kashchiev, Dimo; Auer, Stefan

    2010-12-01

    We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution. Our analysis illustrates the unique feature of ANT that the size of the fibril nucleus is a constant integer in a given supersaturation range. We obtain the ANT nucleation rate and compare it with the rates determined previously in the scope of the classical nucleation theory (CNT) and the corrected classical nucleation theory (CCNT). We find that while the CNT nucleation rate is orders of magnitude greater than the ANT one, the CCNT and ANT nucleation rates are in very good quantitative agreement. The results obtained are applicable to homogeneous nucleation, which occurs when the protein solution is sufficiently pure and/or strongly supersaturated.

  3. Polarization of molecular angular momentum in the chemical reactions Li + HF and F + HD

    NASA Astrophysics Data System (ADS)

    Krasilnikov, Mikhail B.; Popov, Ruslan S.; Roncero, Octavio; De Fazio, Dario; Cavalli, Simonetta; Aquilanti, Vincenzo; Vasyutinskii, Oleg S.

    2013-06-01

    The quantum mechanical approach to vector correlation of angular momentum orientation and alignment in chemical reactions [G. Balint-Kurti and O. S. Vasyutinskii, J. Phys. Chem. A 113, 14281 (2009)], 10.1021/jp902796v is applied to the molecular reagents and products of the Li + HF [L. Gonzalez-Sanchez, O. S. Vasyutinskii, A. Zanchet, C. Sanz-Sanz, and O. Roncero, Phys. Chem. Chem. Phys. 13, 13656 (2011)], 10.1039/c0cp02452j and F + HD [D. De Fazio, J. Lucas, V. Aquilanti, and S. Cavalli, Phys. Chem. Chem. Phys. 13, 8571 (2011)], 10.1039/c0cp02738c reactions for which accurate scattering information has become recently available through time-dependent and time-independent approaches. Application of the theory to two important particular cases of the reactive collisions has been considered: (i) the influence of the angular momentum polarization of reactants in the entrance channel on the spatial distribution of the products in the exit channel and (ii) angular momentum polarization of the products of the reaction between unpolarized reactants. In the former case, the role of the angular momentum alignment of the reactants is shown to be large, particularly when the angular momentum is perpendicular to the reaction scattering plane. In the latter case, the orientation and alignment of the product angular momentum was found to be significant and strongly dependent on the scattering angle. The calculation also reveals significant differences between the vector correlation properties of the two reactions under study which are due to difference in the reaction mechanisms. In the case of F + HD reaction, the branching ratio between HF and DF production points out interest in the insight gained into the detailed dynamics, when information is available either from exact quantum mechanical calculations or from especially designed experiments. Also, the geometrical arrangement for the experimental determination of the product angular momentum orientation and alignment based

  4. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.

    SciTech Connect

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-09-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  5. Petroleum alteration by thermochemical sulfate reduction - A comprehensive molecular study of aromatic hydrocarbons and polar compounds

    NASA Astrophysics Data System (ADS)

    Walters, Clifford C.; Wang, Frank C.; Qian, Kuangnan; Wu, Chunping; Mennito, Anthony S.; Wei, Zhibin

    2015-03-01

    Thermochemical sulfate reduction (TSR) alters petroleum composition as it proceeds towards the complete oxidation of hydrocarbons to CO2. The effects of TSR on the molecular and isotopic composition of volatile species are well known; however, the non-volatile higher molecular weight aromatic and polar species have not been well documented. To address this deficiency, a suite of onshore Gulf coast oils and condensates generated from and accumulating in Smackover carbonates was assembled to include samples that experienced varying levels of TSR alteration and in reservoir thermal cracking. The entire molecular composition of aromatic hydrocarbons and NSO species were characterized and semi-quantified using comprehensive GC × GC (FID and CSD) and APPI-FTICR-MS. The concentration of thiadiamondoids is a reliable indicator of the extent of TSR alteration. Once generated by TSR, thiadiamondoids remain thermally stable in all but the most extreme reservoir temperatures (>180 °C). Hydrocarbon concentrations and distributions are influenced by thermal cracking and TSR. With increasing TSR alteration, oils become enriched in monoaromatic hydrocarbons and the distribution of high molecular weight aromatic hydrocarbons shifts towards more condensed species with a decrease in the number of alkyl carbons. Organosulfur compounds are created by the TSR process. In addition to the increase in benzothiophenes and dibenzothiophenes noted in previous studies, TSR generates condensed species containing one or more sulfur atoms that likely are composed of a single or multiple thiophenic cores. We hypothesize that these species are generated from the partial oxidation of PAHs and dealkylation reactions, followed by sulfur incorporation and condensation reactions. The organosulfur species remaining in the TSR altered oils are "proto-solid bitumen" moieties that upon further condensation, oxidation or sulfur incorporation result in highly sulfur enriched solid bitumen, which is

  6. Molecularly imprinted polymers for the pre-concentration of polar organic micropollutants for compound-specific isotope analysis

    NASA Astrophysics Data System (ADS)

    Bakkour, Rani; Hofstetter, Thomas B.

    2014-05-01

    Compound-specific isotope analysis (CSIA) is a promising tool for assessing transformations of polar organic micropollutants such as pesticides, pharmaceuticals and consumer chemicals in aquatic systems. There are, however, two major challenges: (1) Polar organic micropollutants occur at very low levels and, as a consequence, large amounts of water are required to achieve analyte enrichment with factors of 50'000 and more, inevitably leading to large interferences from the aqueous matrix. (2) The polarity of these micropollutants impedes the use of typical non-polar sorbates for solid-phase enrichment. In view of these challenges, the use of molecularly imprinted polymers (MIP) is a promising approach to produce tailor-made materials for highly selective enrichment of polar organic micropollutants with reduced matrix interferences. In this work, we explore the use of MIP to selectively enrich benzotriazoles, an important class of polar aquatic micropollutants. Polymers were synthesized in the presence of 5,6-dimethyl-1H-benzotriazole as a template, which leaves cavities in the polymer matrix with a very high affinity to the template and closely related structures including our main target analyte, 1H-benzotrizole. After extraction of the template, specific recognition of substituted benzotriazoles is expected by the synthesized MIPs. As the MIP has no specific affinity to the matrix, there is also expected to be negligible enrichment of the matrix. Retention factors of the MIP are compared for different synthetic procedures and to non-imprinted polymers where no specific intermolecular interactions with benzotriazoles are expected. Optimum performance of the MIP is demonstrated in this study in terms of the selectivity of enrichment, recoveries of analytes and the goodness of carbon and nitrogen isotope ratios measured by gas chromatography isotopic ratio mass spectrometry (GC/IRMS). This approach will enable us to enrich large amounts of aqueous samples while

  7. Biomembranes in atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Pluhackova, Kristyna; Böckmann, Rainer A.

    2015-08-01

    The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.

  8. Atomistic k ⋅ p theory

    SciTech Connect

    Pryor, Craig E.; Pistol, M.-E.

    2015-12-14

    Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system.

  9. Growth of polar and non-polar nitride semiconductor quasi-substrates by hydride vapor phase epitaxy for the development of optoelectronic devices by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Moldawer, Adam Lyle

    The family of nitride semiconductors has had a profound influence on the development of optoelectronics for a large variety of applications. However, as of yet there are no native substrates commercially available that are grown by liquid phase methods as with Si and GaAs. As a result, the majority of electronic and optoelectronic devices are grown heteroepitaxially on sapphire and SiC. This PhD research addresses both the development of polar and non-polar GaN and AIN templates by Hydride Vapor Phase Epitaxy (HVPE) on sapphire and SiC substrates, as well as the growth and characterization of optoelectronic devices on these templates by molecular beam epitaxy (MBE). Polar and non-polar GaN templates have been grown in a vertical HVPE reactor on the C- and R-planes of sapphire respectively. The growth conditions have been optimized to allow the formation for thick (50um) GaN templates without cracks. These templates were characterized structurally by studying their surface morphologies by SEM and AFM, and their structure through XRD and TEM. The polar C-plane GaN templates were found to be atomically smooth. However, the surface morphology of the non-polar GaN films grown on the R-plane of sapphire were found to have a facetted surface morphology, with the facets intersecting at 120° angles. This surface morphology reflects an equilibrium growth, since the A-plane of GaN grows faster than the M-planes of GaN due to the lower atomic density of the plane. For the development of deep-UV optoelectronics, it is required to grow AIGaN quantum wells on AIN templates. However, since AIN is a high melting point material, such templates have to be grown at higher temperatures, close to half the melting point of the material (1500 °C). As these temperatures cannot be easily obtained by traditional furnace heating, an HVPE reactor has been designed to heat the substrate inductively to these temperatures. This apparatus has been used to grow high-quality, transparent AIN films

  10. Analysis of Pigment Orientation in Photosystem II at Different Temperatures by Polarization Fluorescence and Molecular Exciton Theory

    NASA Astrophysics Data System (ADS)

    Lu, L.; Wei, L.; Luo, X.; Ni, X.; Lu, J.

    2014-05-01

    The effect of temperature on pigment orientation in photosystem II (PSII) was studied by fl uorescence excitation and polarization fl uorescence spectra of spinach thylakoid solution and molecular exciton theory. Experimental results showed that at 15 to 45 °C, the absorption band of chlorophyll a at 436 nm at room tempe rature red-shifted with increased temperature. The excitation spectra intensity reached the maximum at 35 °C but signifi cantly dropped at 65 and 78 °C. The polarization fl uorescence spectra revealed that the fl uorescence peak of PSII did not change at 15 and 45 °C, and the calculated degree of fl uorescence polarization increased with increased temperature. Spectral and molecular exciton theory analyses indicated that temperature affected pigment orientation in PSII, as well as the coupling strength between pigments or pigment and protein, thereby changing photosynthetic effi ciency. These results can serve as a reference for studies on energy absorption, energy transmission, regulation mechanism, and prospective applications in solar cell materials.

  11. Atomistic simulations of surfactant adsorption kinetics at interfaces

    NASA Astrophysics Data System (ADS)

    Iskrenova, Eugeniya; Patnaik, Soumya

    2014-03-01

    Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

  12. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

    PubMed Central

    Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

    2014-01-01

    Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

  13. The effects of polar excipients transcutol and dexpanthenol on molecular mobility, permeability, and electrical impedance of the skin barrier.

    PubMed

    Björklund, Sebastian; Pham, Quoc Dat; Jensen, Louise Bastholm; Knudsen, Nina Østergaard; Nielsen, Lars Dencker; Ekelund, Katarina; Ruzgas, Tautgirdas; Engblom, Johan; Sparr, Emma

    2016-10-01

    In the development of transdermal and topical products it is important to understand how formulation ingredients interact with the molecular components of the upper layer of the skin, the stratum corneum (SC), and thereby influence its macroscopic barrier properties. The aim here was to investigate the effect of two commonly used excipients, transcutol and dexpanthenol, on the molecular as well as the macroscopic properties of the skin membrane. Polarization transfer solid-state NMR methods were combined with steady-state flux and impedance spectroscopy measurements to investigate how these common excipients influence the molecular components of SC and its barrier function at strictly controlled hydration conditions in vitro with excised porcine skin. The NMR results provide completely new molecular insight into how transcutol and dexpanthenol affect specific molecular segments of both SC lipids and proteins. The presence of transcutol or dexpanthenol in the formulation at fixed water activity results in increased effective skin permeability of the model drug metronidazole. Finally, impedance spectroscopy data show clear changes of the effective skin capacitance after treatment with transcutol or dexpanthenol. Based on the complementary data, we are able to draw direct links between effects on the molecular properties and on the macroscopic barrier function of the skin barrier under treatment with formulations containing transcutol or dexpanthenol. PMID:27388135

  14. Strong interfacial polarization in ZnO decorated reduced-graphene oxide synthesized by molecular level mixing.

    PubMed

    Jammula, Rama Krishna; Pittala, Suresh; Srinath, Sanyadhanam; Srikanth, Vadali V S S

    2015-07-14

    Globally, there is a great demand for energy storage materials and devices. In this context, charge storage capacitors are of great prominence. Metal oxide-graphene composites are excellent candidates for charge storage materials. This is because the dielectric properties of these composites can be controlled by the nature, dimensions and spatial distribution of the conductive components in these composites. ZnO decorated reduced-graphene oxide (r-GO) is synthesized and studied in this context. ZnO-r-GO composites are synthesized using molecular-level mixing. The composites are named as ZnO-0.1G, ZnO-0.2G and ZnO-0.3G in the order of increasing r-GO content. At 1 kHz, the dielectric permittivity (ε') values of ZnO-0.1G, ZnO-0.2G and ZnO-0.3G are nearly 11 (ε' = 114), 15 (ε' = 153) and 40 (ε' = 400) times greater than that of ZnO (ε' = 10). The strong interfacial polarization (Maxwell-Wagner polarization) in these composites is attributed to the presence of functional groups (which are polar in nature) on the r-GO sheets and also to the presence of lattice and/or topological defects in the r-GO. Temperature dependent electric modulus (M'') studies further confirm the observed interfacial polarization. PMID:26073161

  15. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

    PubMed Central

    2015-01-01

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

  16. Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

    SciTech Connect

    Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

    2014-10-21

    We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example.

  17. Atomistic modeling of dropwise condensation

    NASA Astrophysics Data System (ADS)

    Sikarwar, B. S.; Singh, P. L.; Muralidhar, K.; Khandekar, S.

    2016-05-01

    The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

  18. Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.

    NASA Astrophysics Data System (ADS)

    Debolt, Stephen Edward

    Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

  19. A systematic procedure to build a relaxed dense-phase atomistic representation of a complex amorphous polymer using a coarse-grained modeling approach

    PubMed Central

    Li, Xianfeng; Latour, Robert A.

    2009-01-01

    A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 102, thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications. PMID:20161121

  20. Atomistic mechanisms of rapid energy transport in light-harvesting molecules

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2011-03-01

    Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

  1. Cascade Defect Evolution Processes: Comparison of Atomistic Methods

    SciTech Connect

    Xu, Haixuan; Stoller, Roger E; Osetskiy, Yury N

    2013-11-01

    Determining the defect evolution beyond the molecular dynamics (MD) time scale is critical in bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity. In this study, SEAKMC is applied to investigate the cascade defect evolution in bcc iron. First, the evolution of a vacancy rich region is simulated and compared with results obtained using autonomous basin climbing (ABC) +KMC and kinetic activation-relaxation technique (kART) simulations. Previously, it is found the results from kART are orders of magnitude faster than ABC+KMC. The results obtained from SEAKMC are similar to kART but the time predicted is about one order of magnitude faster than kART. The fidelity of SEAKMC is confirmed by statistically relevant MD simulations at multiple higher temperatures, which proves that the saddle point sampling is close to complete in SEAKMC. The second is the irradiation-induced formation of C15 Laves phase nano-size defect clusters. In contrast to previous studies, which claim the defects can grow by capturing self-interstitials, we found these highly stable clusters can transform to <111> glissile configuration on a much longer time scale. Finally, cascade-annealing simulations using SEAKMC is compared with traditional object KMC (OKMC) method. SEAKMC predicts substantially fewer surviving defects compared with OKMC. The possible origin of this difference is discussed and a possible way to improve the accuracy of OKMC based on SEAKMC results is outlined. These studies demonstrate the atomistic fidelity of SEAKMC in comparison with other on-the-fly KMC methods and provide new information on long-term defect evolution in iron.

  2. Using elaborative interrogation to induce characteristics of polar and nonpolar solvents from animations of their molecular structures

    NASA Astrophysics Data System (ADS)

    Ems-Wilson, Janice

    This study concerned (a) how general chemistry students learn to classify solvent polarity from animated molecules, (b) whether peer interaction increases the number of correct classifications, and (c) whether language, academic ability, logical thinking ability, or prior knowledge interact with rate of learning or posttest performance. Two types of interaction were compared, group discussion and elaborative interrogation. The study rested on three assumptions: (a) animated molecules are appropriate for learning the concept of solvent polarity, (b) question stems and a guided interrogation enhance learning of a visual concept, (c) general chemistry students can induce the concept of solvent polarity from animated molecules when no guiding cues, either visual or verbal, are given. After a review of molecular geometry and bonding theories, students were presented with four trials of ten animated molecular structures. Ten three-to-five minute discussions were distributed among the four trials. Prior to the trials the experimental group received a 45-minute training session on elaborative interrogation; the topic was what happens on the molecular level when a carbonated beverage is opened. The control group received a 45-minute expository lecture on the same carbonated beverage topic. Participants were given a four-part posttest immediately following the trials. Results of the study suggest that most students tend to classify the solvent polarity of animated molecules based on certain structural features using a prototype or feature-frequency categorization strategy. Elaborative interrogation did not show a significant effect on the rate of learning or on the performance of learners on posttest measures of recall and comprehension. The experimental group noted a significantly greater number and range of types of features, and offered higher quality generalizations and explanations of their polarity classification procedure. Finally, the results implied that learning

  3. Ab initio molecular dynamics study of polarization effects on ionic hydration in aqueous AlCl3 solution

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2003-12-01

    The solvation shell structure and dynamics of Al3+ and Cl- in an aqueous solution of 0.8 M AlCl3 are studied under ambient conditions by using an ab initio molecular dynamics method. The solvation structures obtained from our ab initio simulations are in good agreement with the experimental ones for both Al3+ and Cl-. A detailed analysis of intramolecular geometry of hydration waters and dipole moments of the ingredients shows that the polarization has substantial effects on the structures and dynamics of both the cation and anion hydration shells. Implications for metal hydrolysis of Al3+ will also be given.

  4. Atomistic Simulations of a Thermotropic Biaxial Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Peláez, Jorge; Wilson, Mark R.

    2006-12-01

    We have performed molecular dynamics simulations of a 2,5-bis-(p-hydroxyphenyl)-1,3,4-oxadiazole mesogen (ODBP-Ph-C7) at a fully atomistic level for a range of temperatures within the region that has experimentally been assigned to a biaxial nematic phase. Analysis of the data shows that the simulated nematic phase is biaxial but that the degree of biaxiality is small. The simulations show also the formation of ferroelectric domains in the nematic where the molecular short axis is aligned with the oxadiazole dipoles parallel to each other. Removal of electrostatic interactions leads to destabilization of ferroelectric domains and destabilization of the biaxiality. An additional simulation shows the slow growth of a mesophase directly from the isotropic fluid over a period of approximately 50 ns. This is the first time this has been achieved within the framework of an all-atom model.

  5. Tailoring of polar and nonpolar ZnO planes on MgO (001) substrates through molecular beam epitaxy

    PubMed Central

    2012-01-01

    Polar and nonpolar ZnO thin films were deposited on MgO (001) substrates under different deposition parameters using oxygen plasma-assisted molecular beam epitaxy (MBE). The orientations of ZnO thin films were investigated by in situ reflection high-energy electron diffraction and ex situ X-ray diffraction (XRD). The film roughness measured by atomic force microscopy evolved as a function of substrate temperature and was correlated with the grain sizes determined by XRD. Synchrotron-based X-ray absorption spectroscopy (XAS) was performed to study the conduction band structures of the ZnO films. The fine structures of the XAS spectra, which were consistent with the results of density functional theory calculation, indicated that the polar and nonpolar ZnO films had different electronic structures. Our work suggests that it is possible to vary ZnO film structures from polar to nonpolar using the MBE growth technique and hence tailoring the electronic structures of the ZnO films. PACS: 81; 81.05.Dz; 81.15.Hi. PMID:22405056

  6. A Comparative Study of Molecular Structure, pKa, Lipophilicity, Solubility, Absorption and Polar Surface Area of Some Antiplatelet Drugs

    PubMed Central

    Remko, Milan; Remková, Anna; Broer, Ria

    2016-01-01

    Theoretical chemistry methods have been used to study the molecular properties of antiplatelet agents (ticlopidine, clopidogrel, prasugrel, elinogrel, ticagrelor and cangrelor) and several thiol-containing active metabolites. The geometries and energies of most stable conformers of these drugs have been computed at the Becke3LYP/6-311++G(d,p) level of density functional theory. Computed dissociation constants show that the active metabolites of prodrugs (ticlopidine, clopidogrel and prasugrel) and drugs elinogrel and cangrelor are completely ionized at pH 7.4. Both ticagrelor and its active metabolite are present at pH = 7.4 in neutral undissociated form. The thienopyridine prodrugs ticlopidine, clopidogrel and prasugrel are lipophilic and insoluble in water. Their lipophilicity is very high (about 2.5–3.5 logP values). The polar surface area, with regard to the structurally-heterogeneous character of these antiplatelet drugs, is from very large interval of values of 3–255 Å2. Thienopyridine prodrugs, like ticlopidine, clopidogrel and prasugrel, with the lowest polar surface area (PSA) values, exhibit the largest absorption. A high value of polar surface area (PSA) of cangrelor (255 Å2) results in substantial worsening of the absorption in comparison with thienopyridine drugs. PMID:27007371

  7. Modeling the atomistic growth behavior of gold nanoparticles in solution

    NASA Astrophysics Data System (ADS)

    Turner, C. Heath; Lei, Yu; Bao, Yuping

    2016-04-01

    The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

  8. Modeling the atomistic growth behavior of gold nanoparticles in solution.

    PubMed

    Turner, C Heath; Lei, Yu; Bao, Yuping

    2016-04-28

    The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions. PMID:27091290

  9. Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

    NASA Astrophysics Data System (ADS)

    Xu, Haixuan; Osetsky, Yuri N.; Stoller, Roger E.

    2012-09-01

    The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

  10. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    SciTech Connect

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2005-12-31

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process.

  11. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    SciTech Connect

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2007-01-12

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process. We also discuss a technique for optimizing the calculation of fine-scale information on the fly for use in a coarse-scale simulation, and discuss the specific case of a fine-scale model that calculates void growth explicitly feeding into a coarse-scale mechanics model to study damage localization.

  12. Atomistic simulations to micro-mechanisms of adhesion in automotive applications

    NASA Astrophysics Data System (ADS)

    Sen, Fatih Gurcag

    This study aimed at depicting atomistic and microstructural aspects of adhesion and friction that appear in different automotive applications and manufacturing processes using atomistic simulations coupled with tribological tests and surface characterization experiments. Thin films that form at the contact interfaces due to chemical reactions and coatings that are developed to mitigate or enhance adhesion were studied in detail. The adhesion and friction experiments conducted on diamond-like carbon (DLC) coatings against Al indicated that F incorporation into DLC decreased the coefficient of friction (COF) by 30% -with respect to H-DLC that is known to have low COF and anti-adhesion properties against Al- to 0.14 owing to formation of repulsive F-F interactions at the sliding interface as shown by density functional theory (DFT) calculations. F atoms transferred to the Al surface with an increase in the contact pressure, and this F transfer led to the formation of a stable AlF3 compound at the Al surface as confirmed by XPS and cross-sectional FIB-TEM. The incorporation of Si and O in a F-containing DLC resulted in humidity independent low COF of 0.08 due to the hydration effect of the Si-O-Si chains in the carbonaceous tribolayers that resulted in repulsive OH-OH interactions at the contact interface. At high temperatures, adhesion of Al was found to be enhanced as a result of superplastic oxide fibers on the Al surface. Molecular dynamics (MD) simulations of tensile deformation of Al nanowires in oxygen carried out with ReaxFF showed that native oxide of Al has an oxygen deficient, low density structure and in O2, the oxygen diffusion in amorphous oxide healed the broken Al-O bonds during applied strain and resulted in the superplasticity. The oxide shell also provided nucleation sites for dislocations in Al crystal. In fuel cell applications, where low Pt/carbon adhesion is causing durability problems, spin-polarized DFT showed that metals with unfilled d

  13. Epitaxial growth and optical properties of Al- and N-polar AlN films by laser molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Chen, X. W.; Jia, C. H.; Chen, Y. H.; Wang, H. T.; Zhang, W. F.

    2014-03-01

    Epitaxial aluminum nitride (AlN) films with c-axis orientation were grown on both (1 1 1) MgO and c-sapphire substrates by laser molecular beam epitaxy. The in-plane epitaxial relationships were determined to be [1 1 \\bar{{2}} 0]AlN‖[0 \\bar{{1}} 1]MgO and [1 \\bar{{1}} 0 0]AlN‖[1 1 \\bar{{2}} 0]sapphire, and the lattice mismatch was 4.2% and 13.2% for AlN films on MgO and sapphire, respectively. The AlN films were shown to be Al- and N-polar on MgO and sapphire, respectively. The former is assumed to be caused by the centre of inversion symmetry of (1 1 1) MgO substrate, while the latter is due to the O polarity of sapphire. The full-width at half-maximum of the ω-scanning spectrum for AlN film on (1 1 1) MgO substrate is smaller than that on the c-sapphire substrate. The optical band-gap energies for AlN films grown on MgO and sapphire were found to be 5.93 and 5.84 eV, close to the standard band gap of 6.2 eV, and the calculated Urbach energies were 0.27 eV and 0.53 eV, respectively. These results indicate a lower amorphous content and/or less defects/impurities in Al-polar than N-polar AlN.

  14. Electron dynamics of molecular double ionization by circularly polarized laser pulses

    SciTech Connect

    Tong, Aihong; Zhou, Yueming; Huang, Cheng; Lu, Peixiang

    2013-08-21

    Using the classical ensemble method, we have investigated double ionization (DI) of diatomic molecules driven by circularly polarized laser pulses with different internuclear distances (R). The results show that the DI mechanism changes from sequential double ionization (SDI) to nonsequential double ionization (NSDI) as the internuclear distance increases. In SDI range, the structure of the electron momentum distribution changes seriously as R increases, which indicates the sensitive dependence of the release times of the two electrons on R. For NSDI, because of the circular polarization, the ionization of the second electron is not through the well-known recollision process but through a process where the first electron ionizes over the inner potential barrier of the molecule, moves directly towards the other nucleus, and kicks out the second electron.

  15. Equation of state for mixtures of non-polar molecular fluids

    NASA Astrophysics Data System (ADS)

    Ihm, G.; Song, Yuhua; Mason, E. A.

    We present a new analytical equation of state for mixtures of non-polar fluids by a generalization of the Ihm-Song-Mason corresponding-states equation for non-polar fluids. It has a sound statistical-mechanical basis and is both simple and accurate enough to describe the thermodynamic properties of mixtures at all fluid densities, temperatures, and compositions. The temperature-dependent parameters in the equation are fundamentally related to the intermolecular forces, but can be calculated with reasonable accuracy for most practical purposes just from experimental second virial coefficients. The remaining constant parameters are best found empirically from p-ν-T data on pure dense fluids (one constant parameter for each pure fluid). No 'mixing rules' are needed. We test the equation of state on three systems with quite different available input information -Ar + Kr, CH4 + CF4, and CO2 + C2H6. Agreement with experiment is good for all three systems.

  16. Differential study on molecular suppressed ionization in intense linearly and circularly polarized laser fields

    NASA Astrophysics Data System (ADS)

    Deng, Yongkai; Liu, Yunquan; Liu, Xianrong; Liu, Hong; Yang, Yudong; Wu, Chengyin; Gong, Qihuang

    2011-12-01

    We present a differential study on above-threshold ionization of the O2 (N2) molecule as well as the companion atom Xe (Ar) (with close ionization potential) produced by linearly and circularly polarized laser fields (25 fs, 795 nm). The photoelectron angular distributions of the companion target are similar at the same laser condition. In both linearly and circularly polarized fields, we observe that the photoelectron yields of O2 are suppressed in the entire energy spectral range as compared with Xe with fully differential measurements, but not for the N2-Ar pair. This is different from the prediction of photoelectron energy spectra by the model including the interference terms [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.85.2280 85, 2280 (2000)], from which the low-energy photoelectrons of O2 were expected to be strongly suppressed in both linearly and circularly polarized laser fields. Resorting to the basic strong-field ionization picture, we believe that the lower orbital-dependent multiphoton excitation or tunneling possibility of O2 as compared with Xe is responsible for this effect. High-resolution fully differential data pose a stringent test on the current strong-field calculations on molecules.

  17. Ultrastructure and molecular phylogenetics of Helmichia lacustris, a microsporidium with an uncoiled isofilar polar filament.

    PubMed

    Tokarev, Yuri S; Voronin, Vladimir N; Seliverstova, Elena V; Grushetskaya, Tatiana A; Issi, Irma V

    2012-03-01

    The description of Helmichia lacustris Voronin (Parazitologiya 34:327-331 1998) is supplemented with morphogenesis and ultrastructure of the extrusion apparatus. Formation of the anterior (made up by rare short lamellae) and posterior (made up by spongy matter or small vesicles) regions of the polaroplast is preceded by granulated spheres and agglomerations of bean-like bodies, respectively. The anchoring disc is formed by an oval structure of moderate electron density, sometimes possessing a granular texture. The parasite development occurs within the cisterns of granular endoplasmatic reticulum (ER) of the host cell. Each group of spores is enclosed within a two-layered sheath, including the smooth inner membrane of the sporophorous vesicle and the outer ribosome-encrusted membrane (which originates from the host cell ER) of the parasitophorous vacuole. Two microsporidia, H. lacustris (GenBank accession number GU130406) and Euplotespora binucleata (GenBank accession number DQ675604) share 78.1% of 16S rRNA gene sequence similarity. Both parasites are characterized by an uncoiled isofilar polar filament. They form a cluster nested among terrestrial and aquatic microsporidia with well-developed coiled polar filaments, suggesting that an uncoiled polar filament in this species is a result of reduction, rather than a "primitive" character. PMID:21863399

  18. Electron dynamics of molecular double ionization by elliptically polarized few-cycle laser pulses

    NASA Astrophysics Data System (ADS)

    Ai-Hong, Tong; Guo-Qiang, Feng; Dan, Liu

    2015-03-01

    Using the classical ensemble method, we have investigated double ionization (DI) of diatomic molecules driven by elliptically polarized few-cycle laser pulses. The results show that DI channel depends strongly on internuclear distances (R), which is dominated by nonsequential double ionization (NSDI) for small and large R, while sequential double ionization (SDI) for mediate R. By tracing NSDI trajectories, we find that NSDI mainly originates from recollision process for small R and collision process for large R. Moreover, the correlated momentum distributions along the long axis strongly depend on the carrier-envelope-phase (CEP), and this phase dependence is affected by R.

  19. Effect of AlN buffer layer properties on the morphology and polarity of GaN nanowires grown by molecular beam epitaxy

    SciTech Connect

    Brubaker, Matt D.; Rourke, Devin M.; Sanford, Norman A.; Bertness, Kris A.; Bright, Victor M.

    2011-09-01

    Low-temperature AlN buffer layers grown via plasma-assisted molecular beam epitaxy on Si (111) were found to significantly affect the subsequent growth morphology of GaN nanowires. The AlN buffer layers exhibited nanowire-like columnar protrusions, with their size, shape, and tilt determined by the AlN V/III flux ratio. GaN nanowires were frequently observed to adopt the structural characteristics of the underlying AlN columns, including the size and the degree of tilt. Piezoresponse force microscopy and polarity-sensitive etching indicate that the AlN films and the protruding columns have a mixed crystallographic polarity. Convergent beam electron diffraction indicates that GaN nanowires are Ga-polar, suggesting that Al-polar columns are nanowire nucleation sites for Ga-polar nanowires. GaN nanowires of low density could be grown on AlN buffers that were predominantly N-polar with isolated Al-polar columns, indicating a high growth rate for Ga-polar nanowires and suppressed growth of N-polar nanowires under typical growth conditions. AlN buffer layers grown under slightly N-rich conditions (V/III flux ratio = 1.0 to 1.3) were found to provide a favorable growth surface for low-density, coalescence-free nanowires.

  20. Cavity partition and functionalization of a [2+3] organic molecular cage by inserting polar P[double bond, length as m-dash]O bonds.

    PubMed

    Feng, Genfeng; Liu, Wei; Peng, Yuxin; Zhao, Bo; Huang, Wei; Dai, Yafei

    2016-07-28

    The cavity of a [2+3] organic molecular cage was partitioned and functionalized by inserting inner-directed P[double bond, length as m-dash]O bonds, which shows CO2 capture and CH4 exclusion due to the size-matching and polarity effects. Computational results demonstrate that the successful segmentation via polar P[double bond, length as m-dash]O bonds facilitates the CO2 molecules to reside selectively inside the cavity. PMID:27356151

  1. Molecular-scale remnants of the liquid-gas transition in supercritical polar fluids.

    PubMed

    Sokhan, V P; Jones, A; Cipcigan, F S; Crain, J; Martyna, G J

    2015-09-11

    An electronically coarse-grained model for water reveals a persistent vestige of the liquid-gas transition deep into the supercritical region. A crossover in the density dependence of the molecular dipole arises from the onset of nonpercolating hydrogen bonds. The crossover points coincide with the Widom line in the scaling region but extend farther, tracking the heat capacity maxima, offering evidence for liquidlike and gaslike state points in a "one-phase" fluid. The effect is present even in dipole-limit models, suggesting that it is common for all molecular liquids exhibiting dipole enhancement in the liquid phase. PMID:26406855

  2. Molecular-Scale Remnants of the Liquid-Gas Transition in Supercritical Polar Fluids

    NASA Astrophysics Data System (ADS)

    Sokhan, V. P.; Jones, A.; Cipcigan, F. S.; Crain, J.; Martyna, G. J.

    2015-09-01

    An electronically coarse-grained model for water reveals a persistent vestige of the liquid-gas transition deep into the supercritical region. A crossover in the density dependence of the molecular dipole arises from the onset of nonpercolating hydrogen bonds. The crossover points coincide with the Widom line in the scaling region but extend farther, tracking the heat capacity maxima, offering evidence for liquidlike and gaslike state points in a "one-phase" fluid. The effect is present even in dipole-limit models, suggesting that it is common for all molecular liquids exhibiting dipole enhancement in the liquid phase.

  3. An atomistically validated continuum model for strain relaxation and misfit dislocation formation

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Ward, D. K.; Zimmerman, J. A.; Cruz-Campa, J. L.; Zubia, D.; Martin, J. E.; van Swol, F.

    2016-06-01

    In this paper, molecular dynamics (MD) calculations have been used to examine the physics behind continuum models of misfit dislocation formation and to assess the limitations and consequences of approximations made within these models. Without compromising the physics of misfit dislocations below a surface, our MD calculations consider arrays of dislocation dipoles constituting a mirror imaged "surface". This allows use of periodic boundary conditions to create a direct correspondence between atomistic and continuum representations of dislocations, which would be difficult to achieve with free surfaces. Additionally, by using long-time averages of system properties, we have essentially reduced the errors of atomistic simulations of large systems to "zero". This enables us to deterministically compare atomistic and continuum calculations. Our work results in a robust approach that uses atomistic simulation to accurately calculate dislocation core radius and energy without the continuum boundary conditions typically assumed in the past, and the novel insight that continuum misfit dislocation models can be inaccurate when incorrect definitions of dislocation spacing and Burgers vector in lattice-mismatched systems are used. We show that when these insights are properly incorporated into the continuum model, the resulting energy density expression of the lattice-mismatched systems is essentially indistinguishable from the MD results.

  4. Atomistic simulations of material damping in amorphous silicon nanoresonators

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sankha; Song, Jun; Vengallatore, Srikar

    2016-06-01

    Atomistic simulations using molecular dynamics (MD) are emerging as a valuable tool for exploring dissipation and material damping in nanomechanical resonators. In this study, we used isothermal MD to simulate the dynamics of the longitudinal-mode oscillations of an amorphous silicon nanoresonator as a function of frequency (2 GHz–50 GHz) and temperature (15 K–300 K). Damping was characterized by computing the loss tangent with an estimated uncertainty of 7%. The dissipation spectrum displays a sharp peak at 50 K and a broad peak at around 160 K. Damping is a weak function of frequency at room temperature, and the loss tangent has a remarkably high value of ~0.01. In contrast, at low temperatures (15 K), the loss tangent increases monotonically from 4× {{10}-4} to 4× {{10}-3} as the frequency increases from 2 GHz to 50 GHz. The mechanisms of dissipation are discussed.

  5. Atomistic Simulation of Dislocation-Defect Interactions in Cu

    SciTech Connect

    Wirth, B D; Bulatov, V V; Diaz de la Rubia, T

    2001-01-01

    The mechanisms of dislocation-defect interactions are of practical importance for developing quantitative structure-property relationships, mechanistic understanding of plastic flow localization and predictive models of mechanical behavior in metals under irradiation. In copper and other face centered cubic metals, high-energy particle irradiation produces hardening and shear localization. Post-irradiation microstructural examination in Cu reveals that irradiation has produced a high number density of nanometer sized stacking fault tetrahedra. Thus, the resultant irradiation hardening and shear localization is commonly attributed to the interaction between stacking fault tetrahedra and mobile dislocations, although the mechanism of this interaction is unknown. In this work, we present a comprehensive molecular dynamics simulation study that characterizes the interaction and fate of moving dislocations with stacking fault tetrahedra in Cu using an EAM interatomic potential. This work is intended to produce atomistic input into dislocation dynamics simulations of plastic flow localization in irradiated materials.

  6. Atomistic Simulation of Polymer Crystallization at Realistic Length Scales

    SciTech Connect

    Gee, R H; Fried, L E

    2005-01-28

    Understanding the dynamics of polymer crystallization during the induction period prior to crystal growth is a key goal in polymer physics. Here we present the first study of primary crystallization of polymer melts via molecular dynamics simulations at physically realistic (about 46 nm) length scales. Our results show that the crystallization mechanism involves a spinodal decomposition microphase separation caused by an increase in the average length of rigid trans segments along the polymer backbone during the induction period. Further, the characteristic length of the growing dense domains during the induction period is longer than predicted by classical nucleation theory. These results indicate a new 'coexistence period' in the crystallization, where nucleation and growth mechanisms coexist with a phase separation mechanism. Our results provide an atomistic verification of the fringed micelle model.

  7. Atomistic pathways of the pressure-induced densification of quartz

    NASA Astrophysics Data System (ADS)

    Liang, Yunfeng; Miranda, Caetano R.; Scandolo, Sandro

    2015-10-01

    When quartz is compressed at room temperature it retains its crystal structure at pressures well above its stability domain (0-2 GPa), and collapses into denser structures only when pressure reaches 20 GPa. Depending on the experimental conditions, pressure-induced densification can be accompanied by amorphization; by the formation of crystalline, metastable polymorphs; and can be preceded by the appearance of an intermediate phase, quartz II, with unknown structure. Based on molecular dynamic simulations, we show that this rich phenomenology can be rationalized through a unified theoretical framework of the atomistic pathways leading to densification. The model emphasizes the role played by the oxygen sublattice, which transforms from a bcc-like order in quartz into close-packed arrangements in the denser structures, through a ferroelastic instability of martensitic nature.

  8. First principles molecular dynamics of molten NaI: Structure, self-diffusion, polarization effects, and charge transfer

    NASA Astrophysics Data System (ADS)

    Galamba, N.; Costa Cabral, B. J.

    2007-09-01

    The structure and self-diffusion of NaI and NaCl at temperatures close to their melting points are studied by first principles Hellmann-Feynman molecular dynamics (HFMD). The results are compared with classical MD using rigid-ion (RI) and shell-model (ShM) interionic potentials. HFMD for NaCl was reported before at a higher temperature [N. Galamba and B. J. Costa Cabral, J. Chem. Phys. 126, 124502 (2007)]. The main differences between the structures predicted by HFMD and RI MD for NaI concern the cation-cation and the anion-cation pair correlation functions. A ShM which allows only for the polarization of I- reproduces the main features of the HFMD structure of NaI. The inclusion of polarization effects for both ionic species leads to a more structured ionic liquid, although a good agreement with HFMD is also observed. HFMD Green-Kubo self-diffusion coefficients are larger than those obtained from RI and ShM simulations. A qualitative study of charge transfer in molten NaI and NaCl was also carried out with the Hirshfeld charge partitioning method. Charge transfer in molten NaI is comparable to that in NaCl, and results for NaCl at two temperatures support the view that the magnitude of charge transfer is weakly state dependent for ionic systems. Finally, Hirshfeld charge distributions indicate that differences between RI and HFMD results are mainly related to polarization effects, while the influence of charge transfer fluctuations is minimal for these systems.

  9. Stability of the β-structure in prion protein: A molecular dynamics study based on polarized force field

    NASA Astrophysics Data System (ADS)

    Xu, Zhijun; Lazim, Raudah; Mei, Ye; Zhang, Dawei

    2012-06-01

    Conformational changes of the antiparallel β-sheet in normal cellular prion protein (PrPC) of rat, bovine, and human are investigated by molecular dynamics simulations in both neutral and acidic environment. Using a recently developed simulation method based on an on-the-fly polarized protein-specific charge (PPC) update scheme during the simulation process, we evaluate and compare the cross-species performances of the β-sheet during the early stage transition from the PrPC to its mutant configuration. Through this study, we observe the growth of the β-sheet structure in all species studied with the extent of elongation in β-sheet being different across the three species.

  10. Polarity control and transport properties of Mg-doped (0001) InN by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Choi, Soojeong; Wu Feng; Bierwagen, Oliver; Speck, James S.

    2013-05-15

    The authors report on the plasma-assisted molecular beam epitaxy growth and carrier transport of Mg-doped In-face (0001) InN. The 1.2 {mu}m thick InN films were grown on GaN:Fe templates under metal rich conditions with Mg concentration from 1 Multiplication-Sign 10{sup 17}/cm{sup 3} to 3 Multiplication-Sign 10{sup 20}/cm{sup 3}. A morphological transition, associated with the formation of V-shape polarity inversion domains, was observed at Mg concentration over 7 Multiplication-Sign 10{sup 19}/cm{sup 3} by atomic force microscopy and transmission electron microscopy. Seebeck measurements indicated p-type conductivity for Mg-concentrations from 9 Multiplication-Sign 10{sup 17}/cm{sup 3} to 7 Multiplication-Sign 10{sup 19}/cm{sup 3}, i.e., as it exceeded the compensating (unintentional) donor concentration.

  11. The electron and spin polarized transport in wide-voltage-ranges through colbaltporphyrin-based molecular junctions

    NASA Astrophysics Data System (ADS)

    Cheng, Jue-Fei; Yan, Qiang; Zhou, Liping; Han, Qin; Gao, Lei

    2016-02-01

    The electron and spin polarized transport properties of Co benzene-porphyrin-benzene (BPB) molecule coupled to gold (Au) nanowires in a wide voltage range (0-3.0 V) are investigated. By successively removing the front-end Au atoms, we construct Au nanowires with different molecule-electrode contact symmetries. Multiple negative differential resistance (NDR) peaks emerge at different bias voltage regions. It is found that the low-voltage NDR effect at 0.4 V can only be found in the junctions with S-Au top bindings. High-bias NDR effects intrinsic to central molecule at 2.8 V are observed in all the six structures. In particular, both the electron and spin polarized current-voltage (I-V) curves depend strongly on the contact configurations between Co-BPB molecule and the Au electrodes. And the top-binding may result in spin dependent transport properties and will be the priority selection in the design of molecular devices.

  12. The electron and spin polarized transport in wide-voltage-ranges through colbaltporphyrin-based molecular junctions.

    PubMed

    Cheng, Jue-Fei; Yan, Qiang; Zhou, Liping; Han, Qin; Gao, Lei

    2016-02-28

    The electron and spin polarized transport properties of Co benzene-porphyrin-benzene (BPB) molecule coupled to gold (Au) nanowires in a wide voltage range (0-3.0 V) are investigated. By successively removing the front-end Au atoms, we construct Au nanowires with different molecule-electrode contact symmetries. Multiple negative differential resistance (NDR) peaks emerge at different bias voltage regions. It is found that the low-voltage NDR effect at 0.4 V can only be found in the junctions with S-Au top bindings. High-bias NDR effects intrinsic to central molecule at 2.8 V are observed in all the six structures. In particular, both the electron and spin polarized current-voltage (I-V) curves depend strongly on the contact configurations between Co-BPB molecule and the Au electrodes. And the top-binding may result in spin dependent transport properties and will be the priority selection in the design of molecular devices. PMID:26931718

  13. Rotating-polarization CARS microscopy: combining chemical and molecular orientation sensitivity.

    PubMed

    de Vito, Giuseppe; Bifone, Angelo; Piazza, Vincenzo

    2012-12-31

    Coherent Anti-Stokes Raman Spectroscopy (CARS) is a non-linear process in which the energy difference of a pair of incoming photons matches the energy of the vibrational mode of a molecular bond of interest. This phonon population is coherently probed by a third photon and anti-Stokes radiation is emitted. Here a novel approach to CARS microscopy is presented yielding the intensity of the anti-Stokes emission, the directionality the molecular bonds of interest, and their average orientation. Myelinated axons in fixed mouse-brain slices have been imaged by RP-CARS. We were able to detect the local average direction of the acylic chains of membrane phospholipids and their spatial anisotropy. This novel method may impact the study of healthy brain circuitry as well as demyelinating diseases or other pathological states associated with altered neural connectivity. PMID:23388764

  14. Molecular and system parameters governing mass and charge transport in polar liquids and electrolytes.

    PubMed

    Petrowsky, Matt; Fleshman, Allison; Ismail, Mohd; Glatzhofer, Daniel T; Bopege, Dharshani N; Frech, Roger

    2012-08-23

    Onsager's model of the dielectric constant is used to provide a molecular-level picture of how the dielectric constant affects mass and charge transport in organic liquids and organic liquid electrolytes. Specifically, the molecular and system parameters governing transport are the molecular dipole moment μ and the solvent dipole density N. The compensated Arrhenius formalism (CAF) writes the temperature-dependent ionic conductivity or diffusion coefficient as an Arrhenius-like expression that also includes a static dielectric constant (ε(s)) dependence in the exponential prefactor. The temperature dependence of ε(s) and therefore the temperature dependence of the exponential prefactor is due to the quantity N/T, where T is the temperature. Using the procedure described in the CAF, values of the activation energy can be obtained by scaling out the N/T dependence instead of the ε(s) dependence. It has been previously shown that a plot of the prefactors versus ε(s) results in a master curve, and here it is shown that a master curve also results by plotting the prefactors against N/T. Therefore, the CAF can be applied by using temperature-dependent density data instead of temperature-dependent dielectric constant data. This application is demonstrated for diffusion data of n-nitriles, n-thiols, n-acetates, and 2-ketones, as well as conductivity data for dilute tetrabutylammonium triflate-nitrile electrolytes. PMID:22838847

  15. Atomistic spin dynamics and surface magnons.

    PubMed

    Etz, Corina; Bergqvist, Lars; Bergman, Anders; Taroni, Andrea; Eriksson, Olle

    2015-06-24

    Atomistic spin dynamics simulations have evolved to become a powerful and versatile tool for simulating dynamic properties of magnetic materials. It has a wide range of applications, for instance switching of magnetic states in bulk and nano-magnets, dynamics of topological magnets, such as skyrmions and vortices and domain wall motion. In this review, after a brief summary of the existing investigation tools for the study of magnons, we focus on calculations of spin-wave excitations in low-dimensional magnets and the effect of relativistic and temperature effects in such structures. In general, we find a good agreement between our results and the experimental values. For material specific studies, the atomistic spin dynamics is combined with electronic structure calculations within the density functional theory from which the required parameters are calculated, such as magnetic exchange interactions, magnetocrystalline anisotropy, and Dzyaloshinskii-Moriya vectors. PMID:26030259

  16. Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

    DOE PAGESBeta

    Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; Osetskiy, Yury N.

    2015-01-29

    The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

  17. Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

    SciTech Connect

    Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; Osetskiy, Yury N.

    2015-01-29

    The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies is illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.

  18. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    PubMed

    Petrov, Drazen; Zagrovic, Bojan

    2014-05-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the

  19. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

    PubMed Central

    Petrov, Drazen; Zagrovic, Bojan

    2014-01-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the

  20. Beyond Ribosomal Binding: The Increased Polarity and Aberrant Molecular Interactions of 3-epi-deoxynivalenol.

    PubMed

    Hassan, Yousef I; Zhu, Honghui; Zhu, Yan; Zhou, Ting

    2016-01-01

    Deoxynivalenol (DON) is a secondary fungal metabolite and contaminant mycotoxin that is widely detected in wheat and corn products cultivated around the world. Bio-remediation methods have been extensively studied in the past two decades and promising ways to reduce DON-associated toxicities have been reported. Bacterial epimerization of DON at the C3 carbon was recently reported to induce a significant loss in the bio-toxicity of the resulting stereoisomer (3-epi-DON) in comparison to the parental compound, DON. In an earlier study, we confirmed the diminished bio-potency of 3-epi-DON using different mammalian cell lines and mouse models and mechanistically attributed it to the reduced binding of 3-epi-DON within the ribosomal peptidyl transferase center (PTC). In the current study and by inspecting the chromatographic behavior of 3-epi-DON and its molecular interactions with a well-characterized enzyme, Fusarium graminearum Tri101 acetyltransferase, we provide the evidence that the C3 carbon epimerization of DON influences its molecular interactions beyond the abrogated PTC binding. PMID:27618101

  1. Atomistic Simulation of Electronic and Optical Properties of (100), (110) and (111) Oriented InAs/GaAs Quantum Dots

    NASA Astrophysics Data System (ADS)

    Chimalgi, Vinay; Ahmed, Shaikh

    2014-03-01

    Recent advances in growth techniques and increasing number of experimental studies have made semiconducting InAs/GaAs quantum dots (QDs) grown along different crystallographic directions a reality and promising systems for applications in infrared detection, optical memories, laser, and in quantum cryptography as single photon sources and quantum computation. However, only few theoretical investigations have been performed on these QDs due to the complex nature of the coupling of atomicity, structural fields, polarization, and quantum size-quantization, all strong function of the crystallographic direction. The objective of this paper is to integrate a computational framework employing a combination of fully atomistic valence force-field molecular mechanics and 20-band sp3 s *d5 -SO tight-binding based electronic bandstructure models, and numerically investigate the effects of internal fields on the electronic and optical properties of InAs/GaAs quantum dots grown on (100), (110), and (111) orientated substrates. It is found that, while piezoelectricity has largest effects on lowering the symmetry of (100) oriented QDs, its effect is minimum in (111) orientated QDs. Supported by the U.S. National Science Foundation Grant No. 1102192.

  2. Ambient gas/particle partitioning. 3. Estimating partition coefficients of apolar, polar, and ionizable organic compounds by their molecular structure.

    PubMed

    Arp, Hans Peter H; Gosses, Kai-Uwe

    2009-03-15

    Equilibrium gas/particle partitioning coefficients of terrestrial aerosols, Kip, are dependent on various intermolecular interactions that can be quantified by experimentally determined compound-specific descriptors. For many compounds of environmental interest, such as emerging contaminants and atmospheric phototransformation products, these compound-specific descriptors are unknown or immeasurable. Often, only the molecular structure is known. Here we present the ability of two computer programs to predict equilibrium partitioning to terrestrial aerosols solely on the basis of molecular structure: COSMOtherm and SPARC. The greatest hurdle with designing such an approach is to identify suitable molecular surrogates to represent the dominating sorbing phases, which for ambient terrestrial aerosols are the water insoluble organic matter (WIOM) phase and the mixed-aqueous phase. For the WI0M phase, hypothetical urban secondary organic aerosol structural units from Kalberer et al. Science 2004, 303, 1659-1662 were investigated as input surrogates, and for the mixed-aqueous phase mildly acidic water was used as a surrogate. Using a validation data set of more than 1400 experimentally determined Kip values for polar, apolar, and ionic compounds ranging over 9 orders of magnitude (including semivolatile compounds such as PCDD/Fs, pesticides, and PBDEs), SPARC and COSMOtherm were generally able to predict Kip values well within an order of magnitude over an ambient range of temperature and relative humidity. This is remarkable as these two models were not fitted or calibrated to any experimental data. As these models can be used for potentially any organic molecule, they are particularly recommended for environmental screening purposes and for use when experimental compound descriptor data are not available. PMID:19368193

  3. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    PubMed

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https

  4. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https

  5. EVALUATION OF THE ADSORPTION PROPERTIES OF SILICALITE FOR POTENTIAL APPLICATION TO ISOLATING POLAR LOW-MOLECULAR-WEIGHT ORGANICS FROM DRINKING WATER

    EPA Science Inventory

    Because of their high affinity for water, low-molecular weight polar organic compounds are difficult to isolate from drinking water as a prelude to their identification and determination. Conventional isolation techniques such as solvent extraction, adsorption, gas purging and re...

  6. Force Generation by Molecular-Motor-Powered Microtubule Bundles; Implications for Neuronal Polarization and Growth

    PubMed Central

    Jakobs, Maximilian; Franze, Kristian; Zemel, Assaf

    2015-01-01

    The heavily cross-linked microtubule (MT) bundles found in neuronal processes play a central role in the initiation, growth and maturation of axons and dendrites; however, a quantitative understanding of their mechanical function is still lacking. We here developed computer simulations to investigate the dynamics of force generation in 1D bundles of MTs that are cross-linked and powered by molecular motors. The motion of filaments and the forces they exert are investigated as a function of the motor type (unipolar or bipolar), MT density and length, applied load, and motor connectivity. We demonstrate that only unipolar motors (e.g., kinesin-1) can provide the driving force for bundle expansion, while bipolar motors (e.g., kinesin-5) oppose it. The force generation capacity of the bundles is shown to depend sharply on the fraction of unipolar motors due to a percolation transition that must occur in the bundle. Scaling laws between bundle length, force, MT length and motor fraction are presented. In addition, we investigate the dynamics of growth in the presence of a constant influx of MTs. Beyond a short equilibration period, the bundles grow linearly in time. In this growth regime, the bundle extends as one mass forward with most filaments sliding with the growth velocity. The growth velocity is shown to be dictated by the inward flux of MTs, to inversely scale with the load and to be independent of the free velocity of the motors. These findings provide important molecular-level insights into the mechanical function of the MT cytoskeleton in normal axon growth and regeneration after injury. PMID:26617489

  7. Effect of GaN interlayer on polarity control of epitaxial ZnO thin films grown by molecular beam epitaxy

    SciTech Connect

    Wang, X. Q.; Sun, H. P.; Pan, X. Q.

    2010-10-11

    Epitaxial ZnO thin films were grown on nitrided (0001) sapphire substrates with an intervening GaN layer by rf-plasma-assisted molecular beam epitaxy. It was found that polarity of the ZnO epilayer could be controlled by modifying the GaN interlayer. ZnO grown on a distorted 3-nm-thick GaN interlayer has Zn-polarity while ZnO on a 20-nm-thick GaN interlayer with a high structural quality has O-polarity. High resolution transmission electron microscopy analysis indicates that the polarity of ZnO epilayer is controlled by the atomic structure of the interface between the ZnO buffer layer and the intervening GaN layer.

  8. Polar Order and Symmetry Breaking at the Boundary between Bent-Core and Rodlike Molecular Forms: When 4-Cyanoresorcinol Meets the Carbosilane End Group.

    PubMed

    Westphal, Eduard; Gallardo, Hugo; Caramori, Giovanni Finoto; Sebastián, Nerea; Tamba, Maria-Gabriela; Eremin, Alexey; Kawauchi, Susumu; Prehm, Marko; Tschierske, Carsten

    2016-06-01

    Two isomeric achiral bent-core liquid crystals involving a 4-cyanoresorcinol core and containing a carbosilane unit as nanosegregating segment were synthesized and were shown to form ferroelectric liquid-crystalline phases. Inversion of the direction of one of the COO groups in these molecules leads to a distinct distribution of the electrostatic potential along the surface of the molecule and to a strong change of the molecular dipole moments. Thus, a distinct degree of segregation of the carbosilane units and consequent modification of the phase structure and coherence length of polar order result. For the compound with larger dipole moment (CN1) segregation of the carbosilane units is suppressed, and this compound forms paraelectric SmA and SmC phases; polar order is only achieved after transition to a new LC phase, namely, the ferroelectric leaning phase (SmCLs PS ) with the unique feature that tilt direction and polar direction coincide. The isomeric compound CN2 with a smaller dipole moment forms separate layers of the carbosilane groups and shows a randomized polar SmA phase (SmAPAR ) and ferroelectric polydomain SmCs PS phases with orthogonal combination of tilt and polar direction and much higher polarizations. Thus, surprisingly, the compound with the smaller molecular dipole moment shows increased polar order in the LC phases. Besides ferroelectricity, mirror-symmetry breaking with formation of a conglomerate of macroscopic chiral domains was observed in one of the SmC phases of CN1. These investigations contribute to the general understanding of the development of polar order and chirality in soft matter. PMID:27143620

  9. Grain boundary migration: Atomistic simulation studies

    NASA Astrophysics Data System (ADS)

    Upmanyu, Moneesh

    Control of microstructural evolution is the goal of much of materials processing. Properties of grain boundaries and associated higher order defects determine fundamental microstructural parameters such as grain size/shape and texture, which in turn control an amalgam of material properties and applications. Microstructural evolution theories are based on certain assumptions, and attempts to experimentally validate them have not been promising, predominantly due to the presence of impurities. In this thesis, classical molecular dynamics simulation techniques are used to investigate boundary kinetics. Validity of the assumptions inherent in the theory of grain boundary migration is first ascertained. The U-shaped half-loop geometry is employed in a two-dimensional (triangular lattice) Lennard-Jones system to observe steady-state, curvature driven boundary migration. The classical linear relation between the migration rate and the driving force is recovered at low driving forces. Three-dimensional, highly parallelized simulations of <111> tilt grain boundaries in aluminum (EAM potentials) also confirm this result. The boundary mobility is found to have an Arrhenius dependence on temperature. However, the extracted activation energies of migration are significantly lower than those extracted in experiments, confirming the presence of impurities in the latter. Structurally similar boundaries are found to exhibit the compensation effect. Both boundary mobility and energy vary non-monotonically with the boundary misorientation, exhibiting maxima and minima for high symmetry (low Sigma) special misorientations, respectively. Using these anisotropic boundary properties in a Potts model reveals that the evolution of two-dimensional random textures is mostly controlled by boundary energy anisotropy, not the mobility anisotropy. Atomistic migration mechanism studies suggest that while single hops across the boundary are frequent, migration occurs primarily due to correlated

  10. Binding of polarity-sensitive hydrophobic ligands to erythroid and nonerythroid spectrin: fluorescence and molecular modeling studies.

    PubMed

    Patra, Malay; Mitra, Madhurima; Chakrabarti, Abhijit; Mukhopadhyay, Chaitali

    2014-01-01

    We have used three polarity-sensitive fluorescence probes, 6-propionyl 2-(N,N-dimethyl-amino) naphthalene (Prodan), pyrene and 8-anilino 1-naphthalene sulphonic acid, to study their binding with erythroid and nonerythroid spectrin, using fluorescence spectroscopy. We have found that both bind to prodan and pyrene with high affinities with apparent dissociation constants (Kd) of .50 and .17 μM, for prodan, and .04 and .02 μM, for pyrene, respectively. The most striking aspect of these bindings have been that the binding stoichiometry have been equal to 1 in erythroid spectrin, both in dimeric and tetrameric form, and in tetrameric nonerythroid spectrin. From an estimate of apparent dielectric constants, the polarity of the binding site in both erythroid and nonerythroid forms have been found to be extremely hydrophobic. Thermodynamic parameters associated with such binding revealed that the binding is favored by positive change in entropy. Molecular docking studies alone indicate that both prodan and pyrene bind to the four major structural domains, following the order in the strength of binding to the Ankyrin binding domain > SH3 domain > Self-association domain > N-terminal domain of α-spectrin of both forms of spectrin. The binding experiments, particularly with the tetrameric nonerythroid spectrin, however, indicate more toward the self association domain in offering the unique binding site, since the binding stoichiometry have been 1 in all forms of dimeric and tetrameric spectrin, so far studied by us. Further studies are needed to characterize the hydrophobic binding sites in both forms of spectrin. PMID:24404769

  11. A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions.

    PubMed

    McLaughlin, Keith; Cioce, Christian R; Belof, Jonathan L; Space, Brian; Space, Brian B

    2012-05-21

    A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods. PMID:22612090

  12. Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

    PubMed

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

    2015-03-01

    The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid

  13. Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

    NASA Technical Reports Server (NTRS)

    Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

    2016-01-01

    Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

  14. Atomistic Conversion Reaction Mechanism of WO3 in Secondary Ion Batteries of Li, Na, and Ca.

    PubMed

    He, Yang; Gu, Meng; Xiao, Haiyan; Luo, Langli; Shao, Yuyan; Gao, Fei; Du, Yingge; Mao, Scott X; Wang, Chongmin

    2016-05-17

    Intercalation and conversion are two fundamental chemical processes for battery materials in response to ion insertion. The interplay between these two chemical processes has never been directly seen and understood at atomic scale. Here, using in situ HRTEM, we captured the atomistic conversion reaction processes during Li, Na, Ca insertion into a WO3 single crystal model electrode. An intercalation step prior to conversion is explicitly revealed at atomic scale for the first time for Li, Na, Ca. Nanoscale diffraction and ab initio molecular dynamic simulations revealed that after intercalation, the inserted ion-oxygen bond formation destabilizes the transition-metal framework which gradually shrinks, distorts and finally collapses to an amorphous W and Mx O (M=Li, Na, Ca) composite structure. This study provides a full atomistic picture of the transition from intercalation to conversion, which is of essential importance for both secondary ion batteries and electrochromic devices. PMID:27071488

  15. Atomistically informed solute drag in Al Mg

    NASA Astrophysics Data System (ADS)

    Zhang, F.; Curtin, W. A.

    2008-07-01

    Solute drag in solute-strengthened alloys, caused by diffusion of solute atoms around moving dislocations, controls the stress at deformation rates and temperatures useful for plastic forming processes. In the technologically important Al-Mg alloys, the solute drag stresses predicted by classical theories are much larger than experiments, which is resolved in general by eliminating the singularity of the dislocation core via Peierls-Nabarro-type models. Here, the drag stress versus dislocation velocity is computed numerically using a realistic dislocation core structure obtained from an atomistic model to investigate the role of the core and obtain quantitative stresses for comparison with experiment. The model solves a discrete diffusion equation in a reference frame moving with the dislocation, with input solute enthalpies and diffusion activation barriers in the core computed by or estimated from atomistic studies. At low dislocation velocities, the solute drag stress is controlled by bulk solute diffusion because the core diffusion occurs too quickly. In this regime, the drag stress can be obtained using a Peierls-Nabarro model with a core spreading parameter tuned to best match the atomistic models. At intermediate velocities, both bulk and core diffusion can contribute to the drag, leading to a complex stress-velocity relationship showing two peaks in stress. At high velocities, the drag stress is controlled solely by diffusion within and across the core. Like the continuum models, the drag stress is nearly linear in solute concentration. The Orowan relationship is used to connect dislocation velocity to deformation strain rate. Accounting for the dependence of mobile dislocation density on stress, the simulations are in good agreement with experiments on Al-Mg alloys over a range of concentrations and temperatures.

  16. Development and evaluation of supercritical fluid chromatography/mass spectrometry for polar and high-molecular-weight coal components. Technical progress report

    SciTech Connect

    Chess, E.K.; Smith, R.D.

    1986-01-01

    This Technical Progress Report reviews the technical progress made over the first 18 months of the program. Our goals include the design, development, and evaluation of a combined capillary column supercritical fluid chromatograph/high-performance mass spectrometer capable of analyzing high-molecular-weight polar materials and evaluating the system's potential for application in coal conversion process monitoring. The program includes not only the development and evaluation of the required instrumentation, but the development of polar fluids and compatible chromatographic stationary phases needed for efficient separation and analysis of polar and high-molecular-weight compounds. A new chromatograph/mass spectrometer interface and new mass spectrometer ion source have been designed, constructed, and evaluated using low-polarity supercritical fluids such as pentane. Results from the evaluations have been used to modify the instrumentation to improve performance. The design and fabrication of capillary flow restrictors from fused silica tubing has been explored. Research has also been conducted toward advancing the technology of fabricating high-performance chromatographic columns suitable for use with polar supercritical fluids. Results to date support our initial belief that high-resolution supercritical fluid chromatography (SFC)/high-performance mass spectrometry (MS) will provide a significantly enhanced analytical capability for broad classes of previously intractable fuel components. 10 refs., 13 figs.

  17. Thermodynamic Properties of Asphaltenes: A Predictive Approach Based On Computer Assisted Structure Elucidation and Atomistic Simulations

    SciTech Connect

    Diallo, Mamadou S.; Cagin, Tahir; Faulon, Jean Loup; Goddard, William A.

    2000-08-01

    The authors describe a new methodology for predicting the thermodynamic properties of petroleum geomacromolecules (asphaltenes and resins). This methodology combines computer assisted structure elucidation (CASE) with atomistic simulations (molecular mechanics and molecular dynamics and statistical mechanics). They use quantitative and qualitative structural data as input to a CASE program (SIGNATURE) to generate a sample of ten asphaltene model structures for a Saudi crude oil (Arab Berri). MM calculations and MD simulations are used to estimate selected volumetric and thermal properties of the model structures.

  18. Polarization Behavior of Water in Extreme Aqueous Environments: A molecular dynamics study based on the Gaussian Charge Polarizable Water Model.

    SciTech Connect

    Chialvo, Ariel A; Horita, Juske

    2010-01-01

    We study the polarization behavior of water under geologically-relevant extreme aqueous environments along four equidistant supercritical isotherms, 773 ! T (K) ! 1373, and over a wide pressure range, 0 < P(GPa) ! 30 , by isobaric-isothermal molecular dynamics simulations of the Gaussian Charge Polarizable (GCP ) water model, to unravel and discuss the underlying link between two precisely defined orientational order parameters and the magnitude of the average induced dipole moment of water. The predicted behavior indicates an isothermal linear dependence (a) between the magnitude of the average induced dipole moment ind and the average system density ! , (b) between the magnitude of the average induced dipole ind and that of the total dipole tot , resulting from (c) a compensating (inverse) dependence between the permanent-to-induced dipolar angle ! and the magnitude of the average induced dipole moment ind . Moreover, we interpret this behavior in terms of the evolution of the state dependent tetrahedral order parameter qT and the corresponding bond-order parameter Q6 , supplemented by the microstructural analysis based on the three site-site radial distribution functions of water and the distance-ranked nearest-neighbors distributions. Finally, we show that while water exhibits a dramatic microstructural transformation from an open four-coordinated hydrogen-bonded network at normal conditions to a quasi close-packed coordination, it still preserves a significant degree of hydrogen bonding.

  19. Molecular cloning and characterization of human WINS1 and mouse Wins2, homologous to Drosophila segment polarity gene Lines (Lin).

    PubMed

    Katoh, Masaru

    2002-08-01

    WNT signaling molecules play key roles in carcinogenesis and embryogenesis. Drosophila segment polarity gene Lines (Lin) is essential for Wnt/Wingless-dependent patterning in dorsal epidermis and also for hindgut development. With Wnt signaling, Lin accumulates in the nucleus to modulate transcription of Wnt target genes through association with beta-catenin/Armadillo and TCF/Pangolin. Here, human WINS1 and mouse Wins2, encoding proteins with Drosophila Lin homologous domain, were isolated using bioinformatics and cDNA-PCR. Human WINS1 encoded 757-amino-acid protein, and mouse Wins2 encoded 498-amino-acid protein. Human WINS1 and mouse Wins2 showed 60.0% total-amino-acid identity. Lin homologous domain of WINS1 and Wins2 showed 29.4% and 27.2% amino-acid identity with that of Drosphila Lin, respectively. In the human chromosome 15q26 region, WINS1 gene was clustered with ASB7 gene encoding ankyrin repeat and SOCS box-containing protein 7. Human WINS1 mRNA of 2.8-kb in size was expressed in adult testis, prostate, spleen, thymus, skeletal muscle, fetal kidney and brain. This is the first report on molecular cloning and initial characterization of human WINS1 and mouse Wins2 PMID:12119551

  20. Spitzer And Near-infrared Observations Of A Bi-polar Outflow In The Rosette Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Ybarra, Jason E.; Lada, E. A.; Balog, Z.; Fleming, S. W.; Phelps, R. L.

    2010-01-01

    We present and discuss Spitzer and near-infrared H2 observations of a bi-polar protostellar outflow in the Rosette Molecular Cloud. The outflow is seen in all four IRAC bands and partially in the MIP 24 micron band. A dark cloud seen in absorption in the 8 micron image bisects the outflow and contains an embedded Class 0 object that appears to be the outflow source. Near-infrared narrow-band H2 observations were obtained using the Infrared Side Port Imager (ISPI) on the CTIO 4 meter telescope. Spitzer IRAC color analysis of the shocked emission was performed from which thermal and density maps of the outflow were constructed. We use these data and maps to probe the physical conditions and structure of the flow. This work is based in part on archival data obtained with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA. Support for this work was provided by an award issued by JPL/Caltech, NASA LTSA Grant NNG05GD66G, and the Florida Space Grant Consortium

  1. A robust, coupled approach for atomistic-continuum simulation.

    SciTech Connect

    Aubry, Sylvie; Webb, Edmund Blackburn, III; Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John; Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  2. An Optimization-based Atomistic-to-Continuum Coupling Method

    DOE PAGESBeta

    Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell; Shapeev, Alexander V.

    2014-08-21

    In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally,more » we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.« less

  3. An Optimization-based Atomistic-to-Continuum Coupling Method

    SciTech Connect

    Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell; Shapeev, Alexander V.

    2014-08-21

    In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally, we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.

  4. Progress Towards Atomistic Simulations that Reach Anthropological Timescale and Beyond

    NASA Astrophysics Data System (ADS)

    Li, Ju

    2012-02-01

    Atomistic and first-principles modeling, which describe the world as assembly of atoms and electrons, provide the most fundamental answer to problems of materials. However, they also suffer the most severe timescale limitations. For instance, in molecular dynamics (MD) simulations, in order to resolve atomic vibrations, the integration time step is limited to hundredth of a picosecond, and therefore the simulation duration is limited to sub-microsecond due to computational cost. Although a nanosecond simulation is often enough (surprisingly) for many physical and chemical properties, it is usually insufficient for predicting microstructural evolution and thermo-mechanical properties of materials. In this invited talk I will discuss recent attempts at overcoming the timescale challenges of atomic-resolution simulations: (a) strain-boost hyperdynamics [Phys. Rev. B 82 (2010) 184114] for simulating primarily displacive events and associated issues of activation entropy and the Meyer-Neldel compensation rule, (b) diffusive molecular dynamics (DMD) [Phys. Rev. B 84 (2011) 054103] for microstructural evolution driven by repetitive diffusion events and coupled displacive-diffusive processes, and (c) a Markovian network statistical mechanical treatment of the energy-landscape basin connectivity and a formula for the viscosity of supercooled liquid and glass [PLoS ONE 6 (2011) e17909]. Challenges and future directions are discussed.

  5. Atomistic Hydrodynamics and the Dynamical Hydrophobic Effect in Porous Graphene.

    PubMed

    Strong, Steven E; Eaves, Joel D

    2016-05-19

    Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method for simulating steady-state mass flow of a fluid moving through the nanoscopic spaces of a porous solid. After validating our method on a model system, we use it to study the hydrophobic effect of water moving through pores of electrically doped single-layer graphene. The trend in permeability that we calculate does not follow the hydrophobicity of the membrane but is instead governed by a crossover between two competing molecular transport mechanisms. PMID:27139634

  6. Complete description of ionization energy and electron affinity in organic solids: Determining contributions from electronic polarization, energy band dispersion, and molecular orientation

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroyuki; Yamada, Kazuto; Tsutsumi, Jun'ya; Sato, Naoki

    2015-08-01

    Ionization energy and electron affinity in organic solids are understood in terms of a single molecule perturbed by solid-state effects such as polarization energy, band dispersion, and molecular orientation as primary factors. However, no work has been done to determine the individual contributions experimentally. In this work, the electron affinities of thin films of pentacene and perfluoropentacene with different molecular orientations are determined to a precision of 0.1 eV using low-energy inverse photoemission spectroscopy. Based on the precisely determined electron affinities in the solid state together with the corresponding data of the ionization energies and other energy parameters, we quantitatively evaluate the contribution of these effects. It turns out that the bandwidth as well as the polarization energy contributes to the ionization energy and electron affinity in the solid state while the effect of the surface dipole is at most a few eV and does not vary with the molecular orientation. As a result, we conclude that the molecular orientation dependence of the ionization energy and electron affinity of organic solids originates from the orientation-dependent polarization energy in the film.

  7. Rotations of molecular photoelectron angular distributions in above threshold ionization of H2+ by intense circularly polarized attosecond UV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Chelkowski, Szczepan; Bandrauk, André D.

    2014-10-01

    We present molecular photoelectron angular distributions (MPADs) in multi-photon ionization processes by circularly polarized attosecond UV laser pulses. Simulations are performed on the single electron aligned molecular ion H_2^+ by solving corresponding 3D time-dependent Schrödinger equations. Numerical results of molecular above threshold ionization (MATI) show that rotations of MPADs with respect to the molecular and polarization axes depend on pulse intensities and photoelectron kinetic energies. We attribute the rotation to Γ, the difference between parallel and perpendicular ionization probabilities. It is found that in a resonant ionization process, the rotation angle is also a function of the symmetry of intermediate electronic states. The coherent population transfer between the initial and the resonant electronic states is controlled by pulse intensities. Such dependence of rotations on the pulse intensity is absent in Rydberg resonant ionizations as well as in MATI at large energy photons ℏω > Ip, where ω is angular frequency of photons and Ip is the molecular ionization potential. We describe these processes by a multi-photon perturbation theory model. Effects of molecular alignment and pulse ellipticities on rotations are investigated, confirming the essence of the ionization parameter Γ in rotations of MPADs.

  8. Physically representative atomistic modeling of atomic-scale friction

    NASA Astrophysics Data System (ADS)

    Dong, Yalin

    interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

  9. Atomistic to continuum modeling of solidification microstructures

    SciTech Connect

    Karma, Alain; Tourret, Damien

    2015-09-26

    We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked to experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.

  10. Atomistic to continuum modeling of solidification microstructures

    DOE PAGESBeta

    Karma, Alain; Tourret, Damien

    2015-09-26

    We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

  11. Molecular characterization of polar organosulfates in secondary organic aerosol from the green leaf volatile 3-Z-hexenal

    NASA Astrophysics Data System (ADS)

    Safi Shalamzari, Mohammad; Kahnt, Ariane; Wang, Wu; Vermeylen, Reinhilde; Kleindienst, Tadeusz; Lewandovski, Michael; Maenhaut, Willy; Claeys, Magda

    2014-05-01

    Much information is available about secondary organic aerosol (SOA) formation from terpenes, including mono- and sesquiterpenes, and isoprene. However, information about SOA formation from green leaf volatiles (GLVs), an important class of biogenic volatile organic compounds, which are emitted when plants are wounded or attacked by insects, is very scarce. In the present study, we provide evidence that 3-Z-hexenal is a potential precursor for SOA through formation of organosulfates. Organosulfate formation from 3-Z-hexenal was studied by conducting smog chamber photooxidation experiments in the presence of NO and acidic ammonium seed aerosol, where OH radicals were generated from the NOx mediated photochemical chain reactions. The focus of the study was on the structural characterization of products, i.e., organosulfates (OSs) with a molecular weight (MW) of 226, which are also present in ambient fine aerosol from a forested site (K puszta, Hungary) at a substantial relative abundance that is comparable to that of the MW 216 isoprene-related OSs. Polar OSs are of climatic relevance because of their capacity to increase the hydrophilic properties of aerosols and as such their cloud-condensation nuclei effects. Two different liquid chromatography (LC) techniques were employed to separate the polar OSs: the first technique uses a reversed-phase trifunctionally bonded C18 stationary phase, whereas the second one is based on ion-pairing C18 LC using dibutylammonium acetate as ion-pairing reagent. With regard to mass spectrometry (MS) techniques, use was made of high-resolution MS to determine the accurate mass (measured mass, 225.00809; elemental composition, C6H9O7S) as well as linear ion trap MS to obtain detailed structural information. The MW 226 OSs were structurally characterized as sulfated derivatives of 3,4-dihydroxyhex-2-enoic acid with the sulfate group positioned at C-3 or C-4. The formation of these OSs is explained through photooxidation in the gas phase

  12. [Graviresponse in higher plants and its regulation in molecular bases: relevance to growth and development, and auxin polar transport in etiolated pea seedlings].

    PubMed

    Ueda, Junichi; Miyamoto, Kensuke

    2003-08-01

    We review the graviresponse under true and simulated microgravity conditions on a clinostat in higher plants, and its regulation in molecular bases, especially on the aspect of auxin polar transport in etiolated pea (Pisum sativum L. cv. Alaska) seedlings which were the plant materials subjected to STS-95 space experiments. True and simulated microgravity conditions substantially affected growth and development in etiolated pea seedlings, especially the direction of growth of stems and roots, resulting in automorphosis. In etiolated pea seedlings grown in space, epicotyls were the most oriented toward the direction far from the cotyledons, and roots grew toward the aerial space of Plant Growth Chamber. Automorphosis observed in space were well simulated by a clinorotation on a 3-dimensional clinostat and also phenocopied by the application of auxin polar transport inhibitors of 2,3,5-triiodobenzoic acid, N-(1-naphtyl)phthalamic acid and 9-hydroxyfluorene-9-carboxylic acid. Judging from the results described above together with the fact that activities of auxin polar transport in epicotyls of etiolated pea seedlings grown in space substantially were reduced, auxin polar transport seems to be closely related to automorphosis. Strenuous efforts to learn in molecular levels how gravity contributes to the auxin polar transport in etiolated pea epicotyls resulted in successful identification of PsPIN2 and PsAUX1 genes located in plasma membrane which products are considered to be putative efflux and influx carriers of auxin, respectively. Based on the results of expression of PsPIN2 and PsAUX1 genes under various gravistimulations, a possible role of PsPIN2 and PsAUX1 genes for auxin polar transport in etiolated pea seedlings will be discussed. PMID:14555809

  13. Atomistic modeling of the dislocation dynamics and evaluation of static yield stress

    NASA Astrophysics Data System (ADS)

    Karavaev, A. V.; Dremov, V. V.; Ionov, G. V.

    2015-09-01

    Static strength characteristics of structural materials are of great importance for the analysis of the materials behaviour under mechanical loadings. Mechanical characteristics of structural materials such as elastic limit, strength limit, ultimate tensile strength, plasticity are, unlike elastic moduli, very sensitive to the presence of impurities and defects of crystal structure. Direct atomistic modeling of the static mechanical strength characteristics of real materials is an extremely difficult task since the typical time scales available for the direct modeling in the frames of classical molecular dynamics do not exceed a hundred of nanoseconds. This means that the direct atomistic modeling of the material deformation can be done for the regimes with rather high strain rates at which the yield stress and other mechanical strength characteristics are controlled by microscopic mechanisms different from those at low (quasi-static) strain rates. In essence, the plastic properties of structural materials are determined by the dynamics of the extended defects of crystal structure (edge and screw dislocations) and by interactions between them and with the other defects in the crystal. In the present work we propose a method that is capable to model the dynamics of edge dislocations in the fcc and hcp materials at dynamic deformations and to estimate the material static yield stress in the states of interest in the frames of the atomistic approach. The method is based on the numerical characterization of the stress relaxation processes in specially generated samples containing solitary edge dislocations.

  14. Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal

    NASA Astrophysics Data System (ADS)

    Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J.; van Duin, Adri C. T.; Lu, Xiaohua; Gubbins, Keith E.

    2013-11-01

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O/H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O/H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

  15. Moisture-assisted cracking and atomistic crack path meandering in oxidized hydrogenated amorphous silicon carbide films

    NASA Astrophysics Data System (ADS)

    Matsuda, Yusuke; King, Sean W.; Oliver, Mark; Dauskardt, Reinhold H.

    2013-02-01

    Moisture-assisted cracking of silica-derived materials results from a stress-enhanced reaction between water molecules and moisture-sensitive SiOSi bonds at the crack tip. We report the moisture-assisted cracking of oxidized hydrogenated amorphous silicon carbide films (a-SiCO:H) consisting of both moisture-sensitive SiOSi bonds and moisture-insensitive bonds. The sensitivity of the films to moisture-assisted cracking was observed to increase with the SiOSi bond density, ρSiOSi. This sensitivity was correlated with the number of SiOSi bonds ruptured, NSiOSi, through an atomistic kinetic fracture model. By comparing these correlated NSiOSi values with those estimated by a planar crack model, we demonstrated that at the atomistic scale the crack path meanders three-dimensionally so as to intercept the most SiOSi bonds. This atomistic crack path meandering was verified by a computational method based on graph theory and molecular dynamics. Our findings could provide a basis for better understanding of moisture-assisted cracking in materials consisting of other types of moisture-sensitive and moisture-insensitive bonds.

  16. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

    PubMed

    Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

    2013-01-01

    A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

  17. Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal

    SciTech Connect

    Huang, Liangliang; Gubbins, Keith E.; Seredych, Mykola; Bandosz, Teresa J.; Duin, Adri C. T. van; Lu, Xiaohua

    2013-11-21

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H{sub 2}S and H{sub 2}O/H{sub 2}S mixtures on GO materials and compare the results with experiment. We find that H{sub 2}S molecules dissociate on the carbonyl functional groups, and H{sub 2}O, CO{sub 2}, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H{sub 2}O/H{sub 2}S mixtures, H{sub 2}O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H{sub 2}S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

  18. Development and evaluation of supercritical fluid chromatography/mass spectrometry for polar and high-molecular-weight coal components: Technical progress report, October 1, 1986-September 30, 1987

    SciTech Connect

    Chess, E.K.; Kalinoski, H.T.; Smith, R.D.

    1988-02-01

    This program, Development and Evaluation of Supercritical Fluid Chromatography/Mass Spectrometry for Polar and High-Molecular-Weight Coal Components, is aimed at the development of new analytical technologies for the characterization of previously intractable complex mixtures. The specific goals of this program are twofold: (1) to develop and evaluate a combined high-resolution, capillary column, supercritical fluid chromatograph/high-performance mass spectrometer (SFC/MS) that is capable of analyzing high-molecular-weight materials, such as polar and heavy-end components found in coal conversion processes; and (2) to use this system to develop and evaluate analytical technology applicable to coal process development technology. Studies have been conducted to characterize the performance of the supercritical fluid chromatograph-mass spectrometer interface, and several modifications have been made to the probe, ion source, and associated hardware to improve performance and operator safety. Methods have been developed that allow the mass calibration of the magnetic sector mass spectrometer to 1400 daltons using desorption chemical ionization. Methodologies have been improved for fabricating capillary columns with bonded, crosslinked stationary phases suitable for use with polar fluids. Coal-derived materials and fossil-fuel-derived sediments have been investigated with supercritical fluid chromatograph/mass spectrometry and supercritical fluid extraction/mass spectrometry. Microbore packed columns coupled to a modified mass spectrometer interface allowed the chemical class fractionation of relatively polar complex mixtures derived from coal liquefaction. 6 refs., 12 figs.

  19. Laser polarization fluorescence of optically anisotropic crystals molecular imaging in the differentiation of biological benign and malignant tumors

    NASA Astrophysics Data System (ADS)

    Ushenko, Yu. A.; Dubolazov, A. V.; Karachevtsev, A. O.; Motrich, A. V.; Sidor, M. I.

    2013-09-01

    The model of laser polarization fluorescence of biological tissues considering the mechanisms of optically anisotropic absorption - linear and circular dichroism of protein networks was suggested.Muellermatrix rotation invariants characterizing polarization manifestations of laser fluorescence are determined.The interconnections between the statistical, correlation and fractal parameters characterizing the Mueller-matrix images of laser polarization fluorescence and the peculiarities of the mechanisms of optically anisotropic absorption of histological sections of uterus wall biopsy were found. Effectiveness of the method of azimuthinvariant Mueller-matrix mapping of laser polarization fluorescence of protein networks in the task of differentiation of benign and malignant tumors of uterus wall was demonstrated.

  20. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    PubMed

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26809025

  1. Polarization effects in molecular dynamics simulations of glass-formers Ca(NO3)2.nH2O, n=4, 6, and 8

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.

    2010-04-01

    Thermodynamics, equilibrium structure, and dynamics of glass-forming liquids Ca(NO3)2ṡnH2O, n =4, 6, and 8, have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H2O and NO3- on the basis of previous fluctuating charge models for pure water and the molten salt 2Ca(NO3)2ṡ3KNO3. Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature, Tg, estimated from MD simulations was dependent on polarization, in particular the dependence of Tg with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation, cation-anion, and water-water structures. Polarization increases the diffusion coefficient of H2O, but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization, but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

  2. An atomistic model of slip formation

    NASA Technical Reports Server (NTRS)

    Halicioglu, T.; Cooper, D. M.

    1984-01-01

    The results of an atomistic model for the simulation of the early stages of crack initiation in a two-dimensional triangular lattice are presented. In the current model, each particle in the system is treated discretely and assumed to be interacting with the surrounding particles via Lennard-Jones potentials. A uniaxial load (in incremental elongations) is applied to the rectangular two-dimensional slab in either the x or the y direction. After each incremental elongation the system is equilibrated using a static method. Initially, elastic behavior in the x and y directions is observed. Continued elongation results in plastic deformation. In lattices with point defects, the defects first move to the surface, creating vacancies which trigger plastic deformation.

  3. Quantum Corrections to the 'Atomistic' MOSFET Simulations

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

    2000-01-01

    We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

  4. Atomistic modeling of metallic nanowires in silicon.

    PubMed

    Ryu, Hoon; Lee, Sunhee; Weber, Bent; Mahapatra, Suddhasatta; Hollenberg, Lloyd C L; Simmons, Michelle Y; Klimeck, Gerhard

    2013-09-21

    Scanning tunneling microscope (STM) lithography has recently demonstrated the ultimate in device scaling with buried, conducting nanowires just a few atoms wide and the realization of single atom transistors, where a single P atom has been placed inside a transistor architecture with atomic precision accuracy. Despite the dimensions of the critical parts of these devices being defined by a small number of P atoms, the device electronic properties are influenced by the surrounding 10(4) to 10(6) Si atoms. Such effects are hard to capture with most modeling approaches, and prior to this work no theory existed that could explore the realistic size of the complete device in which both dopant disorder and placement are important. This work presents a comprehensive study of the electronic and transport properties of ultra-thin (<10 nm wide) monolayer highly P δ-doped Si (Si:P) nanowires in a fully atomistic self-consistent tight-binding approach. This atomistic approach covering large device volumes allows for a systematic study of disorder on the physical properties of the nanowires. Excellent quantitative agreement is observed with recent resistance measurements of STM-patterned nanowires [Weber et al., Science, 2012, 335, 64], confirming the presence of metallic behavior at the scaling limit. At high doping densities the channel resistance is shown to be insensitive to the exact channel dopant placement highlighting their future use as metallic interconnects. This work presents the first theoretical study of Si:P nanowires that are realistically extended and disordered, providing a strong theoretical foundation for the design and understanding of atomic-scale electronics. PMID:23897026

  5. Crystallized Silicon Nanostructures - Experimental Characterization and Atomistic Simulations

    SciTech Connect

    Agbo, Solomon; Sutta, Pavol; Calta, Pavel; Biswas, Rana; Pan, Bicai

    2014-07-01

    We have synthesized silicon nanocrystalline structures from thermal annealing of thin film amorphous silicon-based multilayers. The annealing procedure that was carried out in vacuum at temperatures up to 1100 °C is integrated in a X-ray diffraction (XRD) setup for real-time monitoring of the formation phases of the nanostructures. The microstructure of the crystallized films is investigated through experimental measurements combined with atomistic simulations of realistic nanocrystalline silicon (nc-Si) models. The multilayers consisting of uniformly alternating thicknesses of hydrogenated amorphous silicon and silicon oxide (SiO2) were deposited by plasma enhanced chemical vapor deposition on crystalline silicon and Corning glass substrates. The crystallized structure consisting of nc-Si structures embedded in an amorphous matrix were further characterized through XRD, Raman spectroscopy, and Fourier transform infrared measurements. We are able to show the different stages of nanostructure formation and how the sizes and the crystallized mass fraction can be controlled in our experimental synthesis. The crystallized silicon structures with large crystalline filling fractions exceeding 50% have been simulated with a robust classical molecular dynamics technique. The crystalline filling fractions and structural order of nc-Si obtained from this simulation are compared with our Raman and XRD measurements.

  6. Atomistic processes of dislocation generation and plastic deformation during nanoindentation

    SciTech Connect

    Begau, C.; Hartmaier, A.; George, Easo P; Pharr, George M

    2011-01-01

    To enable plastic deformation during nanoindentation of an initially defect-free crystal, it is necessary first to produce dislocations. While it is now widely accepted that the nucleation of the first dislocations occurs at the start of the pop-in event frequently observed in experiments, it is unclear how these initial dislocations multiply during the early stages of plastic deformation and produce pop-in displacements that are typically much larger than the magnitude of the Burgers vector. This uncertainty about the complex interplay between dislocation multiplication and strain hardening during nanoindentation makes a direct correlation between force-displacement curves and macroscopic material properties difficult. In this paper, we study the early phase of plastic deformation during nanoindentation with the help of large-scale molecular dynamics simulations. A skeletonization method to simplify defect structures in atomistic simulations enables the direct observation and quantitative analysis of dislocation nucleation and multiplication processes occurring in the bulk as well as at the surface.

  7. Micromechanical tests of ion irradiated materials: Atomistic simulations and experiments

    SciTech Connect

    Shin, C.; Jin, H. H.; Kwon, J.

    2012-07-01

    We investigated irradiation effects on Fe-Cr binary alloys by using a nano-indentation combined with a continuous stiffness measurement (CSM) technique. We modeled the nano-indentation test by using a finite element method. We could extract the intrinsic hardness and the yield stress of an irradiation hardened region by using a so-called inverse method. SiC micro-pillars of various sizes were fabricated by mask and inductively coupled plasma etching technique and compressed by using flat punch nano-indentation. Compressive fracture strength showed a clear specimen size effect. Brittle-to-Ductile transition at room temperature was observed as the specimen size decreases. The effect of irradiation on the fracture strength of SiC micro-pillars was evaluated by performing ion irradiation with Si ions. We have performed molecular dynamics simulations of nano-indentation and nano-pillar compression tests. Radiation effect was observed which is found to be due to the interaction of dislocations nucleated by spherical indenter with pre-existing radiation defects (voids). These atomistic simulations are expected to significantly contribute to the investigation of the fundamental deformation mechanism of small scale irradiated materials. (authors)

  8. An efficient fully atomistic potential model for dense fluid methane

    NASA Astrophysics Data System (ADS)

    Jiang, Chuntao; Ouyang, Jie; Zhuang, Xin; Wang, Lihua; Li, Wuming

    2016-08-01

    A fully atomistic model aimed to obtain a general purpose model for the dense fluid methane is presented. The new optimized potential for liquid simulation (OPLS) model is a rigid five site model which consists of five fixed point charges and five Lennard-Jones centers. The parameters in the potential model are determined by a fit of the experimental data of dense fluid methane using molecular dynamics simulation. The radial distribution function and the diffusion coefficient are successfully calculated for dense fluid methane at various state points. The simulated results are in good agreement with the available experimental data shown in literature. Moreover, the distribution of mean number hydrogen bonds and the distribution of pair-energy are analyzed, which are obtained from the new model and other five reference potential models. Furthermore, the space-time correlation functions for dense fluid methane are also discussed. All the numerical results demonstrate that the new OPLS model could be well utilized to investigate the dense fluid methane.

  9. An Atomistic study of Helium Resolution in bcc Iron

    SciTech Connect

    Stoller, Roger E; Stewart, David M

    2011-01-01

    The evolution of gas-stabilized bubbles in irradiated materials can be a significant factor in the microstructural processes that lead to mechanical property and dimensional changes in structural materials exposed to high-energy neutrons. Helium generation and accumulation is particularly important under DT fusion irradiation conditions. Although the process of ballistic resolutioning of gas from bubbles has been long-discussed in the literature, there have been few computational studies of this mechanism. Resolutioning could limit bubble growth by ejecting gas atoms back into the metal matrix. A detailed atomistic study of ballistic He resolutioning from bubbles in bcc iron has been carried out using molecular dynamics. A newly-developed Fe-He interatomic potential was employed, with the iron matrix described by the potential of Ackland and co-workers from 1997. The primary variables examined were: irradiation temperature (100 and 600K), iron knock-on atom energy (5 and 20 keV), bubble radius (~0.5 and 1.0 nm), and He-to-vacancy ratio in the bubble (0.25, 0.5 and 1.0) in order to obtain an assessment of this dynamic resolutioning mechanism. The results presented here focus on the 5 keV cascades which indicate a modest, but potentially significant level of He removal by this process.

  10. Atomistic simulation of hydrophobin HFBII conformation in aqueous and fluorous media and at the water/vacuum interface.

    PubMed

    Raffaini, Giuseppina; Milani, Roberto; Ganazzoli, Fabio; Resnati, Giuseppe; Metrangolo, Pierangelo

    2016-01-01

    Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. PMID:26606320

  11. The influence of antieigenvalues and antieigenvectors on the correlation between the polarizations of reagents and products of molecular collisions

    NASA Astrophysics Data System (ADS)

    de Miranda, Marcelo P.; Gordon, Sean D. S.; Aldegunde, Jesús

    2012-08-01

    This article raises and answers a question regarding the extent to which correlation between the angular momentum polarizations of reagents and products of a bimolecular collision is or is not uniform. The question is this: how markedly does product (j‧) polarization change when reagent (j) polarization is changed? Using canonical collision mechanisms theory, and the operator-trigonometric concepts of maximal turning angle, antieigenvalue, and antieigenvector, the authors arrive at the following answer: barring complete or nearly complete insensitivity of the collision to steric effects, one should expect a high degree of nonuniformity in two-, three- or four-vector correlations involving j and j‧.

  12. Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials

    NASA Astrophysics Data System (ADS)

    Fu, Yao; Song, Jeong-Hoon

    2015-08-01

    Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic-continuum bridging.

  13. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  14. Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

    SciTech Connect

    McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.; Schultz, Peter A.; Foster, Michael E.; Bartelt, Norman Charles

    2015-09-01

    In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.

  15. Cold melting of beryllium: Atomistic view on Z-machine experiments

    SciTech Connect

    Dremov, V. V. Rykounov, A. A.; Sapozhnikov, F. A.; Karavaev, A. V.; Yakovlev, S. V.; Ionov, G. V.; Ryzhkov, M. V.

    2015-07-21

    Analysis of phase diagram of beryllium at high pressures and temperatures obtained as a result of ab initio calculations and large scale classical molecular dynamics simulations of beryllium shock loading have shown that the so called cold melting takes place when shock wave propagates through polycrystalline samples. Comparison of ab initio calculation results on sound speed along the Hugoniot with experimental data obtained on Z-machine also evidences for possible manifestation of the cold melting. The last may explain the discrepancy between atomistic simulations and experimental data on the onset of the melting on the Hugoniot.

  16. Applications of single-layered graphene sheets as mass sensors and atomistic dust detectors

    NASA Astrophysics Data System (ADS)

    Sakhaee-Pour, A.; Ahmadian, M. T.; Vafai, A.

    2008-01-01

    Molecular structural mechanics is implemented to model the vibrational behavior of defect-free single-layered graphene sheets (SLGSs) at constant temperature. To mimic these two-dimensional layers, zigzag and armchair models with cantilever and bridge boundary conditions are adopted. Fundamental frequencies of these nanostructures are calculated, and it is perceived that they are independent of the chirality and aspect ratio. The effects of point mass and atomistic dust on the fundamental frequencies are also considered in order to investigate the possibility of using SLGSs as sensors. The results show that the principal frequencies are highly sensitive to an added mass of the order of 10-6 fg.

  17. Temperature dependent structural, elastic, and polar properties of ferroelectric polyvinylidene fluoride (PVDF) and trifluoroethylene (TrFE) copolymers

    NASA Astrophysics Data System (ADS)

    Sun, Fu-Chang; Dongare, Avinash; Asandei, Alexandru; Alpay, Pamir; Nakhmanson, Serge; University of Connecticut Team

    We use molecular dynamics to calculate the structural, elastic, and polar properties of crystalline ferroelectric β-poly(vinylidene fluoride), PVDF (-CH2-CF2-)n with randomized trifluoroethylene TrFE (-CHF-CF2-)n as a function of TrFE content (0-50%) in the temperature range of 0-400 K. There is a very good agreement between the experimentally obtained and the computed values of the lattice parameters, thermal expansion coefficients, elastic constants, polarization, and pyroelectric coefficients. A continuous decrease in Young's modulus with increasing TrFE content was observed and attributed to the increased intramolecular and intermolecular repulsive interactions between fluorine atoms. The computed polarization displayed a similar trend, with the room temperature spontaneous polarization decreasing by 44% from 13.8 μC/cm2 (pure PVDF) to 7.7 μC/cm2 [50/50 poly(VDF-co-TrFE)]. Our results show that molecular dynamics can be used as a practical tool to predict the mechanical and polarization-related behavior of ferroelectric poly(VDF-co-TrFE). Such an atomistic model can thus serve as a guide for practical applications of this important multifunctional polymer.

  18. Atomistic Cohesive Zone Models for Interface Decohesion in Metals

    NASA Technical Reports Server (NTRS)

    Yamakov, Vesselin I.; Saether, Erik; Glaessgen, Edward H.

    2009-01-01

    Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship characterizing the load transfer across the plane of a growing edge crack is extracted from atomistic simulations for use within a continuum finite element model. The methodology for the atomistic derivation of a cohesive-zone law is presented. This procedure can be implemented to build cohesive-zone finite element models for simulating fracture in nanocrystalline or ultrafine grained materials.

  19. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    NASA Astrophysics Data System (ADS)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  20. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    PubMed Central

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-01-01

    Abstract. Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy. PMID:25473883

  1. Atomistic and model description of nanotube electromechanical devices

    NASA Astrophysics Data System (ADS)

    Rotkin, Slava V.

    2003-03-01

    Nanotubes (NTs), which are natural objects on the size scale compatible with nanodevices and bio-molecules, exhibit several unique properties by themselves and in specific environments such as electronic, bio-chemical or electromechanical nanodevices. A compact continuum model has been developed [1] for the multi-scale calculation of NT behavior in various devices, ranging from Nano-Electromechanical Systems (NEMS)[2] to Light-Controlled Molecular Switches [3]. The continuum model parameterization is based on Molecular Dynamics and microscopic modeling. For example, elements of quantum mechanical consideration were introduced through the calculation of the nanotube polarizability, atomistic capacitance [4], and van der Waals interaction [5]. Quantum-chemistry approach was used for computation of an equilibrium structure of chemically modified NTs. An analytical expression will be discussed for quantum capacitance of metallic NTs with arbitrary lateral deformation. Compact model and a quantum mechanical simulation will be compared for the NT charge density calculation. A scattering probability for a potential of charged impurity and ballistic conductance of NT channel have been computed for a light controlled electronic NT switch. Analytical expression for the pull-in voltage for NT NEMS will be presented with quantum corrections and van der Waals interactions taken into account. This calculation will demonstrate that a principal physical limit exists for fabricating NEMS [6]. 1. N.R.Aluru, et.al., in Handbook of Nanoscience, Engineering and Technology, Eds: W.Goddard, et.al.; CRC Press, 2002 2. M.Dequesnes, S.V.Rotkin, N.R.Aluru, Nanotechnology 13, 2002 3. S.V.Rotkin, I.Zharov, Int.J.of Nanoscience 1(3/4) 2002 4. K.A.Bulashevich, S.V.Rotkin, JETPL 75(4) 2002 5. S.V.Rotkin, K.Hess, J.of Comp.Electronics 1(3) 2002 6. S.V.Rotkin, in Microfabr. Syst. and MEMS, Eds: P. J. Hesketh, et.al. ECS Inc., Pennington, NJ, USA 2002

  2. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

    Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

  3. Solvation thermodynamics and heat capacity of polar and charged solutes in water

    SciTech Connect

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-21

    The solvation thermodynamics and in particular the solvation heat capacity of polar and charged solutes in water is studied using atomistic molecular dynamics simulations. As ionic solutes we consider a F{sup -} and a Na{sup +} ion, as an example for a polar molecule with vanishing net charge we take a SPC/E water molecule. The partial charges of all three solutes are varied in a wide range by a scaling factor. Using a recently introduced method for the accurate determination of the solvation free energy of polar solutes, we determine the free energy, entropy, enthalpy, and heat capacity of the three different solutes as a function of temperature and partial solute charge. We find that the sum of the solvation heat capacities of the Na{sup +} and F{sup -} ions is negative, in agreement with experimental observations, but our results uncover a pronounced difference in the heat capacity between positively and negatively charged groups. While the solvation heat capacity {Delta}C{sub p} stays positive and even increases slightly upon charging the Na{sup +} ion, it decreases upon charging the F{sup -} ion and becomes negative beyond an ion charge of q=-0.3e. On the other hand, the heat capacity of the overall charge-neutral polar solute derived from a SPC/E water molecule is positive for all charge scaling factors considered by us. This means that the heat capacity of a wide class of polar solutes with vanishing net charge is positive. The common ascription of negative heat capacities to polar chemical groups might arise from the neglect of non-additive interaction effects between polar and apolar groups. The reason behind this non-additivity is suggested to be related to the second solvation shell that significantly affects the solvation thermodynamics and due to its large spatial extent induces quite long-ranged interactions between solvated molecular parts and groups.

  4. Grain boundary barrier modification due to coupling effect of crystal polar field and water molecular dipole in ZnO-based structures

    SciTech Connect

    Ji, Xu; Zhu, Yuan E-mail: phzktang@ust.hk; Chen, Mingming; Su, Longxing; Chen, Anqi; Zhao, Chengchun; Gui, Xuchun; Xiang, Rong; Huang, Feng; Tang, Zikang E-mail: phzktang@ust.hk

    2014-06-16

    Surface water molecules induced grain boundaries (GBs) barrier modification was investigated in ZnO and ZnMgO/ZnO films. Tunable electronic transport properties of the samples by water were characterized via a field effect transistor (FET) device structure. The FETs fabricated from polar C-plane ZnO and ZnMgO/ZnO films that have lots of GBs exhibited obvious double Schottky-like current-voltage property, whereas that fabricated from nonpolar M-plane samples with GBs and ZnO bulk single-crystal had no obvious conduction modulation effects. Physically, these hallmark properties are supposed to be caused by the electrostatical coupling effect of crystal polar field and molecular dipole on GBs barrier.

  5. Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

    PubMed

    Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

    2016-07-20

    Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs. PMID:27348048

  6. A fully atomistic computer simulation study of cold denaturation of a β-hairpin

    NASA Astrophysics Data System (ADS)

    Yang, Changwon; Jang, Soonmin; Pak, Youngshang

    2014-12-01

    Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.

  7. Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

    2006-03-01

    Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

  8. Domain reduction method for atomistic simulations

    SciTech Connect

    Medyanik, Sergey N. . E-mail: medyanik@northwestern.edu; Karpov, Eduard G. . E-mail: edkarpov@gmail.com; Liu, Wing Kam . E-mail: w-liu@northwestern.edu

    2006-11-01

    In this paper, a quasi-static formulation of the method of multi-scale boundary conditions (MSBCs) is derived and applied to atomistic simulations of carbon nano-structures, namely single graphene sheets and multi-layered graphite. This domain reduction method allows for the simulation of deformable boundaries in periodic atomic lattice structures, reduces the effective size of the computational domain, and consequently decreases the cost of computations. The size of the reduced domain is determined by the value of the domain reduction parameter. This parameter is related to the distance between the boundary of the reduced domain, where MSBCs are applied, and the boundary of the full domain, where the standard displacement boundary conditions are prescribed. Two types of multi-scale boundary conditions are derived: one for simulating in-layer multi-scale boundaries in a single graphene sheet and the other for simulating inter-layer multi-scale boundaries in multi-layered graphite. The method is tested on benchmark nano-indentation problems and the results are consistent with the full domain solutions.

  9. Atomistic Simulations of Fracture in Semiconductors

    NASA Astrophysics Data System (ADS)

    Bernstein, Noam

    Semiconductors are the materials that underlie nearly all modern electron ics. They include elemental solids, such as silicon and germanium, as well as compounds such as gallium arsenide and silicon carbide. Since their main use is in electronic applications, semiconductors are not usually thought of as structural materials. Nevertheless there are important reasons, both technological and scientific, for the study of mechanical properties of semiconductors. The developing field of micro-machines, from micro-electromechanical systems (MEMS) to nanotechnology, relies on fabrication techniques developed for electronic devices to make microscopic mechanical system. To a large extent it is the link between these fabrication techniques, including deposition, masking, and etching, and the materials that has driven the use of semiconductors as structural components. On a more fundamental level, the ability to fabricate extremely pure and nearly defect free samples makes semiconductors excellent model systems for studying the physics of fracture. In this section I will attempt to give an overview of the ways in which atomistic simulations have been applied to fracture in semiconductors using a number of illustrative examples.

  10. Robust atomistic calculation of dislocation line tension

    NASA Astrophysics Data System (ADS)

    Szajewski, B. A.; Pavia, F.; Curtin, W. A.

    2015-12-01

    The line tension Γ of a dislocation is an important and fundamental property ubiquitous to continuum scale models of metal plasticity. However, the precise value of Γ in a given material has proven difficult to assess, with literature values encompassing a wide range. Here results from a multiscale simulation and robust analysis of the dislocation line tension, for dislocation bow-out between pinning points, are presented for two widely-used interatomic potentials for Al. A central part of the analysis involves an effective Peierls stress applicable to curved dislocation structures that markedly differs from that of perfectly straight dislocations but is required to describe the bow-out both in loading and unloading. The line tensions for the two interatomic potentials are similar and provide robust numerical values for Al. Most importantly, the atomic results show notable differences with singular anisotropic elastic dislocation theory in that (i) the coefficient of the \\text{ln}(L) scaling with dislocation length L differs and (ii) the ratio of screw to edge line tension is smaller than predicted by anisotropic elasticity. These differences are attributed to local dislocation core interactions that remain beyond the scope of elasticity theory. The many differing literature values for Γ are attributed to various approximations and inaccuracies in previous approaches. The results here indicate that continuum line dislocation models, based on elasticity theory and various core-cut-off assumptions, may be fundamentally unable to reproduce full atomistic results, thus hampering the detailed predictive ability of such continuum models.

  11. Free energy of steps using atomistic simulations

    NASA Astrophysics Data System (ADS)

    Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

    The properties of solid-liquid interfaces are known to play critical roles in solidification processes. Particularly special importance is given to thermodynamic quantities that describe the equilibrium state of these surfaces. For example, on the solid-liquid-vapor heteroepitaxial growth of semiconductor nanowires the crystal nucleation process on the faceted solid-liquid interface is influenced by the solid-liquid and vapor-solid interfacial free energies, and also by the free energies of associated steps at these faceted interfaces. Crystal-growth theories and mesoscale simulation methods depend on quantitative information about these properties, which are often poorly characterized from experimental measurements. In this work we propose an extension of the capillary fluctuation method for calculation of the free energy of steps on faceted crystal surfaces. From equilibrium atomistic simulations of steps on (111) surfaces of Copper we computed accurately the step free energy for different step orientations. We show that the step free energy remains finite at all temperature up to the melting point and that the results obtained agree with the more well established method of thermodynamic integration if finite size effects are taken into account. The research of RF and MA at UC Berkeley were supported by the US National Science Foundation (Grant No. DMR-1105409). TF acknowledges support through a postdoctoral fellowship from the Miller Institute for Basic Research in Science.

  12. Modeling: The Role of Atomistic Simulations

    SciTech Connect

    Aga, Rachel S; Morris, James R

    2007-01-01

    A major advantage of atomistic simulations is that a detailed picture of the model under investigation is available, and so they have been very instrumental in explaining the connection of macroscopic properties to the atomic scale. Simulations play a significant role in the development and testing of theories. For example, simulations have been extensively used to test the mode-coupling theory (MCT). The theory predicts that at some critical temperature Tc, known as the mode-coupling temperature, the supercooled liquid undergoes a structural arrest, prohibiting the system from accessing all possible states, thus, essentially undergoing an ergodic to nonergodic transition. It gives definite predictions on various correlation functions that can be calculated directly in simulations. Simulations and MCT have played a tremendous role in elucidating a majority of what we now understand about the dynamics of glass-forming systems. Simulations can also be used to compare with experimental results to validate the model, so that one can use simulation results to measure properties not accessible to experiments. In many cases, as will be illustrated in the next sections, results of simulations motivate experimental investigations. Part of the goal of this chapter is to examine the contributions of atomic simulations to the current state of understanding of metallic glasses.

  13. Strain Functionals for Characterizing Atomistic Geometries

    NASA Astrophysics Data System (ADS)

    Kober, Edward; Rudin, Sven

    The development of a set of strain tensor functionals that are capable of characterizing arbitrarily ordered atomistic structures is described. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the moments of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. Other methods used to characterize atomic structures, such as the Steinhardt parameters or the centrosymmetry metric, can be derived from this more general approach. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. They allow material phases, deformations, and a large number of defect structures to be readily identified and classified. Applications to the analysis of shock-loaded samples of Cu, Ta and Ti will be presented. This strain functional basis can also then be used for developing interatomic potential functions, and an initial application to Cu will be presented.

  14. Stress in titania nanoparticles: An atomistic study

    SciTech Connect

    Darkins, Robert; Sushko, Maria L.; Liu, Jun; Duffy, Dorothy M.

    2014-04-24

    Stress engineering is becoming an increasingly important method for controlling electronic, optical, and magnetic properties of nanostructures, although the concept of stress is poorly defined at the nanoscale. We outline a methodology for computing bulk and surface stress in nanoparticles using atomistic simulation. The method is applicable to ionic and non- ionic materials alike and may be extended to other nanostructures. We apply it to spherical anatase nanoparticles ranging from 2 to 6 nm in diameter and obtain a surface stress of 0.89 N/m, in agreement with experimental measurements. Based on the extent that stress inhomogeneities at the surface are transmitted into the bulk, two characteristic length-scales are identified: below 3 nm bulk and surface regions cannot be defined and the available analytic theories for stress are not applicable, and above about 5 nm the stress becomes well-described by the theoretical Young-Laplace equation. The effect of a net surface charge on the bulk stress is also investigated. It is found that moderate surface charges can induce significant bulk stresses, on the order of 100 MPa, in nanoparticles within this size range.

  15. Long Time-Scale Atomistic Simulations

    SciTech Connect

    Sadigh, B; Cai, W; de Koning, M; Oppelstrup, T; Bulatov, V; Kalos, M

    2005-02-11

    During the past two years, we have succeeded in implementing an efficient parallel Importance Sampling Monte-Carlo (ISMC) scheme with application towards rarely occurring transition events, of great abundance in materials science and chemistry. The inefficiency of the standard atomistic modeling techniques for these problems may be traced to the extremely low probability of sampling system trajectories, or paths, that lead to a successful transition event. Instead of following the conventional approach of developing smart algorithms for searching transition paths, we tackle this problem by explicitly enhancing the probability of sampling successful transition events by means of an importance function. By selecting it appropriately, one focuses predominantly on the successful transition paths while discarding most irrelevant ones. In this manner, the rare-event problem is reformulated into an optimization problem for finding the best-possible importance function. Utilizing efficient iterative minimization algorithms, our IS approach can now be used to calculate the rate of occurrence of low-probability transition phenomena of short duration (short successful paths), but which involve collective degrees of freedom of many atoms.

  16. Atomistic simulations of caloric effects in ferroelectrics

    NASA Astrophysics Data System (ADS)

    Lisenkov, Sergey; Ponomareva, Inna

    2013-03-01

    The materials that exhibit large caloric effects have emerged as promising candidates for solid-state refrigeration which is an energy-efficient and environmentally friendly alternative to the conventional refrigeration technology. However, despite recent ground breaking discoveries of giant caloric effects in some materials they appear to remain one of nature's rarities. Here we use atomistic simulations to study electrocaloric and elastocaloric effects in Ba0.5Sr0.5TiO3 and PbTiO3 ferroelectrics. Our study reveals the intrinsic features of such caloric effects in ferroelectrics and their potential to exhibit giant caloric effects. Some of the findings include the coexistence of negative and positive electrocaloric effects in one material and an unusual field-driven transition between them as well as the coexistence of multiple giant caloric effects in Ba0.5Sr0.5TiO3 alloys. These findings could potentially lead to new paradigms for cooling devices. This work is partially supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0005245.

  17. Graviresponse and its regulation from the aspect of molecular levels in higher plants: growth and development, and auxin polar transport in etiolated pea seedlings under microgravity.

    PubMed

    Miyamoto, Kensuke; Hoshino, Tomoki; Hitotsubashi, Reiko; Tanimoto, Eiichi; Ueda, Junichi

    2003-10-01

    In STS-95 space experiments we have demonstrated that microgravity conditions resulted in automorphosis in etiolated pea (Pisum sativum L. cv. Alaska) seedlings (Ueda et al. 1999). Automorphosis-like growth and development in etiolated pea seedlings were also induced under simulated microgravity conditions on a 3-dimensional (3-D) clinostat, epicotyls being the most oriented toward the direction far from the cotyledons. Detail analysis of epicotyl bending revealed that within 36 h after watering, no significant difference in growth direction of epicotyls was observed in between seedlings grown on the 3-D clinostat and under 1 g conditions, differential growth near the cotyledonary node resulting in epicotyl bending of ca. 45 degrees toward the direction far from the cotyledons. Thereafter epicotyls continued to grow almost straightly keeping this orientation on the 3-D clinostat. On the other hand, the growth direction in etiolated seedlings changed to antigravity direction by negative gravitropic response under 1 g conditions. Automorphological epicotyl bending was also phenocopied by the application of auxin polar transport inhibitors such as 9-hydroxyfluorene-9-carboxylic acid, N-(1-naphtyl)phthalamic acid and 2,3,5-triiodobenzoic acid. These results together with the fact that auxin polar transport activity in etiolated pea epicotyls was substantially reduced in space suggested that reduced auxin polar transport is closely related to automorphosis. Strenuous efforts to learn how gravity contributes to the auxin polar transport in etiolated pea epicotyls in molecular bases resulted in successful identification of PsPIN2 and PsAUX1 encoding putative auxin-efflux and influx carrier proteins, respectively. Based on the results of these gene expression under simulated microgravity conditions, a possible role of PsPIN2 and PsAUX1 genes for auxin polar transport in etiolated pea seedlings will be discussed. PMID:14676393

  18. Molecular Arrangement in Self-Assembled Azobenzene-Containing Thiol Monolayers at the Individual Domain Level Studied through Polarized Near-Field Raman Spectroscopy

    PubMed Central

    Chaigneau, Marc; Picardi, Gennaro; Ossikovski, Razvigor

    2011-01-01

    6-[4-(phenylazo)phenoxy]hexane-1-thiol self-assembled monolayers deposited on a gold surface form domain-like structures possessing a high degree of order with virtually all the molecules being identically oriented with respect to the surface plane. We show that, by using polarized near-field Raman spectroscopy, it is possible to derive the Raman scattering tensor of the ordered layer and consequently, the in-plane molecular orientation at the individual domain level. More generally, this study extends the application domain of the near-field Raman scattering selection rules from crystals to ordered organic structures. PMID:21541056

  19. Kohn-Sham-like approach toward a classical density-functional theory of inhomogeneous polar molecular liquids: an application to liquid hydrogen chloride.

    PubMed

    Lischner, Johannes; Arias, T A

    2008-11-21

    The Gordian knot of density-functional theories for classical molecular liquids remains finding an accurate free-energy functional in terms of the densities of the atomic sites of the molecules. Following Kohn and Sham, we show how to solve this problem by considering noninteracting molecules in a set of effective potentials. This shift in perspective leads to an accurate and computationally tractable description in terms of simple three-dimensional functions. We also treat both the linear- and saturation- dielectric responses of polar systems, presenting liquid hydrogen chloride as a case study. PMID:19113431

  20. Bonding, Backbonding, and Spin-Polarized Molecular Orbitals:Basis for Magnetism and Semiconducting Transport in V[TCNE]x~;;2

    SciTech Connect

    Kortright, Jeffrey B; Kortright, Jeffrey B; Lincoln, Derek M; Edelstein, Ruth Shima; Epstein, Arthur J

    2008-05-20

    X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (MCD) at the V L2,3 and C and N K edges reveal bonding/backbonding interactions in films of the 400 K magnetic semiconductor V[TCNE]x~;;2. In V spectra, dxy-like orbitals are modeled assuming V2+ in an octahedral ligand field, while dz2 and dx2-y2 orbitals involved in strong covalent bonding cannot be modeled by atomic calculations. C and N MCD, and differences in XAS from neutral TCNE molecules, reveal spin-polarized molecular orbitals in V[TCNE]x~;;2 associated with backbonding interactions that yield its novel properties.

  1. Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

    PubMed Central

    Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

    2013-01-01

    Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

  2. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    NASA Technical Reports Server (NTRS)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  3. An atomistic model for cross-linked HNBR elastomers used in seals

    NASA Astrophysics Data System (ADS)

    Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

    2015-03-01

    Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

  4. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

    2009-01-01

    Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

  5. Mapping Strain-rate Dependent Dislocation-Defect Interactions by Atomistic Simulations

    SciTech Connect

    Fan, Yue; Osetskiy, Yury N; Yip, Sidney; Yildiz-Botterud, Bilge

    2013-01-01

    Probing the mechanisms of defect-defect interactions at strain rates lower than 106 s-1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose a novel atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation-defect interactions at virtually any strain rate, exemplified within 10-7 to 107 s-1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIA) under shear deformation. Using an activation-relaxation algorithm (1), we uncover a unique strain-rate dependent trigger mechanism that allows the SIA cluster to be absorbed during the process leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain-rate and temperature. Our predictions of a crossover from a defect recovery at the low strain rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s-1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed.

  6. Molecular photoelectron angular distribution rotations in multi-photon resonant ionization of H{sub 2}{sup +} by circularly polarized ultraviolet laser pulses

    SciTech Connect

    Yuan, Kai-Jun Chelkowski, Szczepan; Bandrauk, André D.

    2015-04-14

    We study effects of pulse durations on molecular photoelectron angular distributions (MPADs) in ultrafast circular polarization ultraviolet resonant ionization processes. Simulations performed on aligned H{sub 2}{sup +} by numerically solving time dependent Schrödinger equations show rotations of MPADs with respect to the molecular symmetry axes. It is found that in multi-photon resonant ionization processes, rotation angles are sensitive to pulse durations, which we attribute to the coherent resonant excitation between the ground state and the intermediate excited electronic state induced by Rabi oscillations. Multi-photon nonresonant and single photon ionization processes are simulated and compared which exhibit a constant rotation angle. An asymmetry parameter is introduced to describe the pulse duration sensitivity by perturbation theory models. Influence of pulse frequency detunings on MPADs is also investigated where oscillations of rotations are absent at long pulse durations due to nonresonance excitation.

  7. Impact of Molecular Orientation and Packing Density on Electronic Polarization in the Bulk and at Surfaces of Organic Semiconductors.

    PubMed

    Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

    2016-06-01

    The polarizable environment surrounding charge carriers in organic semiconductors impacts the efficiency of the charge transport process. Here, we consider two representative organic semiconductors, tetracene and rubrene, and evaluate their polarization energies in the bulk and at the organic-vacuum interface using a polarizable force field that accounts for induced-dipole and quadrupole interactions. Though both oligoacenes pack in a herringbone motif, the tetraphenyl substituents on the tetracene backbone of rubrene alter greatly the nature of the packing. The resulting change in relative orientations of neighboring molecules is found to reduce the bulk polarization energy of holes in rubrene by some 0.3 eV when compared to tetracene. The consideration of model organic-vacuum interfaces highlights the significant variation in the electrostatic environment for a charge carrier at a surface although the net change in polarization energy is small; interestingly, the environment of a charge even just one layer removed from the surface can be viewed already as representative of the bulk. Overall, it is found that in these herringbone-type layered crystals the polarization energy has a much stronger dependence on the intralayer packing density than interlayer packing density. PMID:27183361

  8. Visualizing the Positive-Negative Interface of Molecular Electrostatic Potentials as an Educational Tool for Assigning Chemical Polarity

    ERIC Educational Resources Information Center

    Schonborn, Konrad; Host, Gunnar; Palmerius, Karljohan

    2010-01-01

    To help in interpreting the polarity of a molecule, charge separation can be visualized by mapping the electrostatic potential at the van der Waals surface using a color gradient or by indicating positive and negative regions of the electrostatic potential using different colored isosurfaces. Although these visualizations capture the molecular…

  9. Molecular orientation behavior of chiral nematic liquid crystals based on the presence of blue phases using polarized microscopic FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Matsumura, Masanori; Katayama, Norihisa

    2016-07-01

    Study on molecular orientation behavior of highly twisted chiral nematic liquid crystals (N∗LCs) expressing blue phases (BPs) is important for developing new devices. This study examines the change of molecular orientation of N∗LCs due to the presence of BPs. Polarized microscopic FT-IR spectroscopy was used to study the in- and out-of-plane molecular orientations of N∗LCs that undergo a phase transition involving BPs. The band intensity ratio of CN to CH2 stretching modes (CN/CH2) in the IR spectra was used to determine the orientation of N∗LC molecules. The measured spectra indicated that the helical axis of N∗LC molecules was perpendicular to the substrate before heating and inclined on the substrate after cooling the sample which has phase transition from BP I to chiral nematic (N∗). The N∗LC molecule in the cell of rubbed orientation film exhibited the in-plane anisotropy after a heating-cooling ramp only in samples that passed through BP I. These results indicate that the changes of molecular orientation of N∗LC by phase transition are affected by BP I.

  10. Atomistic Simulation of Sea Spray Particles

    NASA Astrophysics Data System (ADS)

    Gokturk, H.

    2012-12-01

    Particles generated by ocean wave spray play an important role in many atmospheric processes such as cloud condensation, cycling of elements like chlorine, and scattering of sunlight reaching the ocean surface [1-2]. Indeed, artificially spraying droplets of seawater to the atmosphere by marine vessels roaming the ocean has been suggested as a geoengineering method to combat global warming [3]. One of the interesting aspects of ocean spray particles is that they include dissolved salt ions. Typically a liter of seawater contains about 3.5 g of salt which is mostly sodium chloride. Hydrated salt ions of the particle create a molecular structure which is different from that of pure water. An objective of this research is to investigate the influence of the dissolved ions on the properties of the particles by using first principle quantum mechanical calculations. Another objective is to probe the interaction of carbon dioxide (CO2) with such particles to understand whether the ions might enhance the absorption of atmospheric CO2 into the particles. Atomic models used in the calculations consist of a salt ion, for example sodium (Na+) ion surrounded by water molecules. Calculations are performed by using the DFT method with B3LYP hybrid functional and Pople type basis sets augmented with polarization and diffuse functions. Results of the calculations indicate that average binding energy of water molecules nearest to the ion is 0.7 eV per molecule for Na+ and 0.5 eV per molecule for Cl-. Water molecules are bound to the ion with significantly greater energy than that of the hydrogen bond (~0.2 eV) which is the binding mechanism of pure water. Higher binding energy of the particles explains why they serve well as condensation nuclei. As expected, binding energy decreases with increasing distance from the ion. It becomes comparable to that of the hydrogen bond at a distance of about 2 nm which corresponds to approximately 7 layers of water molecules surrounding the ion

  11. Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.

    PubMed

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state (2)H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C-(2)H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of (13)C-(1)H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For (2)H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes. PMID:27154600

  12. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids

    PubMed Central

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-01-01

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246

  13. Dielectric response and anhydrous proton conductivity in a chiral framework containing a non-polar molecular rotor.

    PubMed

    Yu, Shan-Shan; Liu, Shao-Xian; Duan, Hai-Bao

    2015-12-28

    Herein, we report a chiral 3D framework with the formula [Co(HPO3)2][H2DABCO] (DABCO = 1,4-diazabicyclo[2.2.2]octane). This compound exhibits two distinct dielectric anomalies, one attributed to the transfer of protons between non-polar DABCO and the inorganic framework, and the other to the in-plane oscillatory fluctuation of the DABCO molecule. It also exhibits proton conductivity under high-temperature anhydrous conditions. PMID:26584424

  14. Production of Molecular Iodine and Tri-iodide in the Frozen Solution of Iodide: Implication for Polar Atmosphere.

    PubMed

    Kim, Kitae; Yabushita, Akihiro; Okumura, Masanori; Saiz-Lopez, Alfonso; Cuevas, Carlos A; Blaszczak-Boxe, Christopher S; Min, Dae Wi; Yoon, Ho-Il; Choi, Wonyong

    2016-02-01

    The chemistry of reactive halogens in the polar atmosphere plays important roles in ozone and mercury depletion events, oxidizing capacity, and dimethylsulfide oxidation to form cloud-condensation nuclei. Among halogen species, the sources and emission mechanisms of inorganic iodine compounds in the polar boundary layer remain unknown. Here, we demonstrate that the production of tri-iodide (I3(-)) via iodide oxidation, which is negligible in aqueous solution, is significantly accelerated in frozen solution, both in the presence and the absence of solar irradiation. Field experiments carried out in the Antarctic region (King George Island, 62°13'S, 58°47'W) also showed that the generation of tri-iodide via solar photo-oxidation was enhanced when iodide was added to various ice media. The emission of gaseous I2 from the irradiated frozen solution of iodide to the gas phase was detected by using cavity ring-down spectroscopy, which was observed both in the frozen state at 253 K and after thawing the ice at 298 K. The accelerated (photo-)oxidation of iodide and the subsequent formation of tri-iodide and I2 in ice appear to be related with the freeze concentration of iodide and dissolved O2 trapped in the ice crystal grain boundaries. We propose that an accelerated abiotic transformation of iodide to gaseous I2 in ice media provides a previously unrecognized formation pathway of active iodine species in the polar atmosphere. PMID:26745029

  15. Probing the Sequence of Conformationally-Induced Polarity Changes in the Molecular Chaperonin GroEL with Fluorescence Spectroscopy

    PubMed Central

    Kim, So Yeon; Semyonov, Alexander N.; Twieg, Robert J.; Horwich, Arthur L.; Frydman, Judith; Moerner, W. E.

    2006-01-01

    Hydrophobic interactions play a major role in binding non-native substrate proteins in the central cavity of the bacterial chaperonin GroEL. The sequence of local conformational changes by which GroEL and its cofactor GroES assist protein folding can be explored using the polarity-sensitive fluorescence probe Nile Red. A specific single-cysteine mutant of GroEL (Cys261), whose cysteine is located inside the central cavity at the apical region of the protein, was covalently labeled with synthetically prepared Nile Red maleimide (NR). Bulk fluorescence spectra of Cys261-NR were measured to examine the effects of binding of the stringent substrate, malate dehydrogenase (MDH), GroES, and nucleotide on the local environment of the probe. After binding denatured substrate, the fluorescence intensity increased by 32±7%, suggesting enhanced hydrophobicity at the position of the label. On the other hand, in the presence of ATP, the fluorescence intensity decreased by 13±3%, implying increased local polarity. In order to explore the sequence of local polarity changes, substrate, GroES, and various nucleotides were added in different orders; the resulting changes in emission intensity provide insight into the sequence of conformational changes occurring during GroEL-mediated protein folding. PMID:16375456

  16. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

    PubMed

    Fenley, Andrew T; Muddana, Hari S; Gilson, Michael K

    2014-01-01

    Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. PMID:25503996

  17. Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

    PubMed Central

    Gilson, Michael K.

    2014-01-01

    Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. PMID:25503996

  18. Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

    SciTech Connect

    Chen, Wei-Ren; Do, Changwoo; Hong, Kunlun; Liu, Emily; Liu, Yun; Porcar, L.; Smith, Gregory Scott; Wu, Bin; Egami, T; Smith, Sean C

    2012-01-01

    Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 (G4) polyelectrolyte polyamidoamine (PAMAM) starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, (r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work which provides a link between the neutron scattering experiment and MD computation. The simulations enable scattering calculations of not only the hydrocarbons, but also the contribution to the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we question the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

  19. The first atomistic modelling-aided reproduction of morphologically defective single walled carbon nanohorns.

    PubMed

    Furmaniak, Sylwester; Terzyk, Artur P; Kaneko, Katsumi; Gauden, Piotr A; Kowlaczyk, Piotr; Itoh, Tsutomu

    2013-01-28

    A new modelling-aided approach for the atomistic model of single walled carbon nanohorn (SWNH) creation is presented, based on experimental evidence, on realistic potential of carbon-carbon interactions and on molecular simulations. A new model of SWNHs is next used to predict Ar adsorption properties and to check the molecular fundamentals of the adsorption mechanism. The influence of the apex angle value, nanohorn diameter and nanohorn length on the shapes of isotherms, enthalpy, high resolution α(s)-plots and adsorption potential distribution curves is checked. Finally the comparison with new experimental Ar adsorption results is shown and the conclusions on the porosity of real SWNH aggregates are given. PMID:23229231

  20. An object oriented Python interface for atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

    2016-01-01

    Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

  1. Atomistic Simulation of Carbon Nanotube Ropes and Hydrogen Absorption

    NASA Astrophysics Data System (ADS)

    Li, Ju; Yip, Sidney; Fujiwara, Joshua

    2001-06-01

    Atomistic Simulation of Carbon Nanotube Ropes and Hydrogen Absorption Ju Li, Sidney Yip, Massachusetts Institute of Technology, Department of Nuclear Engineering, Cambridge, MA 02139; Joshua Fujiwara, Honda R&D Co., Ltd., Wako Research Center, JAPAN. Using Brenner type Reactive Empirical Bond Order (REBO) interatomic potentials, we perform atomistic simulations to calculate the optimized structures, tensile and bending strengths, and thermal conductivities of both straight and twisted single-walled nanotube ropes (bundles) where results from direct simulation are checked against those from the Green-Kubo linear response theory. Preliminary calculations are performed to study hydrogen absorption by SWNTs at room temperature and 77K.

  2. The GTP-bound and Sumoylated Form of the rab17 Small Molecular Weight GTPase Selectively Binds Syntaxin 2 in Polarized Hepatic WIF-B Cells.

    PubMed

    Striz, Anneliese C; Tuma, Pamela L

    2016-04-29

    A major focus for our laboratory is identifying the molecules and mechanisms that regulate polarized apical protein sorting in hepatocytes, the major epithelial cells of the liver. These trafficking pathways are regulated, in part, by small molecular weight rab GTPases. We chose to investigate rab17, whose expression is restricted to polarized epithelial cells, is enriched in liver, and has been implicated in regulating basolateral to apical transcytosis. To initiate our studies, we generated three recombinant adenoviruses expressing wild type, constitutively active (GTP bound), or dominant-negative (GDP bound) rab17. Immunoblotting revealed rab17 immunoreactive species at 25 kDa (the predicted rab17 molecular mass) and 40 kDa. We determined that mono-sumoylation of the 25-kDa rab17 is responsible for the shift in molecular mass, and that rab17 prenylation is required for sumoylation. We further determined that sumoylation selectively promotes interactions with syntaxin 2 (but not syntaxins 3 or 4) and that these interactions are nucleotide dependent. Furthermore, a K68R-mutated rab17 led to the redistribution of syntaxin 2 and 5' nucleotidase from the apical membrane to subapical puncta, whereas multidrug resistance protein 2 distributions were not changed. Together these data are consistent with the proposed role of rab17 in vesicle fusion with the apical plasma membrane and further implicate sumoylation as an important mediator of protein-protein interactions. The selectivity in syntaxin binding and apical protein redistribution further suggests that rab17 and syntaxin 2 mediate fusion of transcytotic vesicles at the apical surface. PMID:26957544

  3. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy

    SciTech Connect

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R.

    2014-04-15

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

  4. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy.

    PubMed

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R

    2014-04-01

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

  5. Polarity, viscosity, and ionic conductivity of liquid mixtures containing [C4C1im][Ntf2] and a molecular component.

    PubMed

    Lopes, J N Canongia; Gomes, Margarida F Costa; Husson, Pascale; Pádua, Agílio A H; Rebelo, Luis Paulo N; Sarraute, Sabine; Tariq, Mohammad

    2011-05-19

    In this study, we have focused on binary mixtures composed of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)-imide, [C(4)C(1)im][Ntf(2)], and a selection of six molecular components (acetonitrile, dichloromethane, methanol, 1-butanol, t-butanol, and water) varying in polarity, size, and isomerism. Two Kamlet-Taft parameters, the polarizability π* and the hydrogen bond acceptor β coefficient were determined by spectroscopic measurements. In most cases, the solvent power (dipolarity/polarizability) of the ionic liquid is only slightly modified by the presence of the molecular component unless large quantities of this component are present. The viscosity and electrical conductivity of these mixtures were measured as a function of composition and the relationship between these two properties were studied through Walden plot curves. The viscosity of the ionic liquid dramatically decreases with the addition of the molecular component. This decrease is not directly related to the volumetric properties of each mixture or its interactions. The conductivity presents a maximum as a function of the composition and, except for the case of water, the conductivity maxima decrease for more viscous systems. The Walden plots indicate enhanced ionic association as the ionic liquid gets more diluted, a situation that is the inverse of that usually found for conventional electrolyte solutions. PMID:21517046

  6. A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra.

    PubMed

    Alves, Cassio; Iacovelli, Federico; Falconi, Mattia; Cardamone, Francesca; Morozzo Della Rocca, Blasco; de Oliveira, Cristiano L P; Desideri, Alessandro

    2016-05-23

    A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures. PMID:27050675

  7. Intergranular fracture in UO{sub 2}: derivation of traction-separation law from atomistic simulations

    SciTech Connect

    Zhang, Yongfeng; Millett, P.C.; Tonks, M.R.; Bai, Xian-Ming; Biner, S.B.

    2013-07-01

    In this study, the intergranular fracture behavior of UO{sub 2} was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt Σ5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior. (authors)

  8. Fracture toughness from atomistic simulations: Brittleness induced by emission of sessile dislocations

    SciTech Connect

    Farkas, D.

    1998-08-04

    Using atomistic simulations of crack response for intermetallic materials the author shows that when the emitted dislocations are sessile and stay in the immediate vicinity of the crack tip the emitted dislocations can actually lead to brittle failure. She present the results of an atomistic simulation study of the simultaneous dislocation emission and crack propagation process in this class of materials. She used a molecular statics technique with embedded atom (EAM) potentials developed for NiAl. The crystal structure of NiAl is the CsCl type (B2) with a lattice parameter of 0.287 nm, which is reproduced by the potential together with the cohesive energy and elastic constants. The compound stays ordered up to the melting point, indicating a strong tendency towards chemical ordering with a relatively high energy of the antiphase boundary (APB). As a result of this relatively large energy the dislocations of 1/2<111> type Burgers vectors imply a high energy and the deformation process occurs via the larger <100> type dislocations.

  9. Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2013-10-01

    In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

  10. Atomistic Mechanism of Plastic Deformation During Nano-indentation of Titanium Aluminide

    NASA Astrophysics Data System (ADS)

    Rino, Jose; Dasilva, Claudio

    2013-06-01

    The mechanisms governing defect nucleation in solids are of great interest in all material science branches. Atomistic computer simulations such as Molecular Dynamics (MD), has been providing more understanding of subsurface deformations, bringing out details of atomic structures and dynamics of defects within the material. In the present work we show the first simulation measurements within an atomistic resolution of the mechanical properties of titanium aluminide intermetallic compound (TiAl), which is a promising candidate for high temperature applications with remarkable properties, such as: attractive combination of low density, high melting temperature, high elastic modulus, and strength retention at elevated temperatures, besides its good creep properties. Through calculations of local pressure, local shear stress and spatial rearrangements of atoms beneath the indenter, it was possible to quantify the indentation damage on the structure. We have founded that prismatic dislocations mediate the emission and interaction of dislocations and the activated slip planes are associated with the Thompson tetrahedron. Furthermore, using the load-penetration depth response, we were able to estimate the elastic modulus and the hardness of the TiAl alloy. All our findings are in well agreement with experimental results.

  11. Electrochemical phase formation: classical and atomistic theoretical models.

    PubMed

    Milchev, Alexander

    2016-08-01

    The process of electrochemical phase formation at constant thermodynamic supersaturation is considered in terms of classical and atomistic nucleation theories. General theoretical expressions are derived for important thermodynamic and kinetic quantities commenting also upon the correlation between the existing theoretical models and experimental results. Progressive and instantaneous nucleation and growth of multiple clusters of the new phase are briefly considered, too. PMID:27108683

  12. Statistically Reliable 'Atomistic' Simulation of Sub 100 nm MOSFETs

    NASA Technical Reports Server (NTRS)

    Asenov, Asen

    2000-01-01

    A 3D 'atomistic' simulation technique to study random impurity induced threshold voltage lowering and fluctuations in sub 0. 1 micron MOSFETs is presented. It allows statistical analysis of random impurity effects down to the individual impurity level-Efficient algorithms based on a single solution of Poisson's equation, followed by the solution of a simplified current continuity equation are used in the simulations.

  13. Bridging the macroscopic and atomistic descriptions of the electrocaloric effect.

    PubMed

    Ponomareva, I; Lisenkov, S

    2012-04-20

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba(0.5)Sr(0.5)TiO(3) alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency. PMID:22680758

  14. Bridging the Macroscopic and Atomistic Descriptions of the Electrocaloric Effect

    NASA Astrophysics Data System (ADS)

    Ponomareva, I.; Lisenkov, S.

    2012-04-01

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba0.5Sr0.5TiO3 alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency.

  15. Efficient production of polar molecular Bose-Einstein condensates via an all-optical R-type atom-molecule adiabatic passage

    NASA Astrophysics Data System (ADS)

    Qian, Jing; Zhou, Lu; Zhang, Keye; Zhang, Weiping

    2010-03-01

    We propose a scheme of 'R-type' photoassociative adiabatic passage (PAP) to create polar molecular condensates from two different species of ultracold atoms. Due to the presence of a quasi-coherent population trapping state in the scheme, it is possible to associate atoms into molecules with a low-power photoassociation (PA) laser. One remarkable advantage of our scheme is that a tunable atom-molecule coupling strength can be achieved by using a time-dependent PA field, which exhibits larger flexibility than using a tunable magnetic field. In addition, our results show that the PA intensity required in the 'R-type' PAP could be greatly reduced compared to that in a conventional 'Λ-type' one.

  16. Formation of molecular complexes of salicylic acid, acetylsalicylic acid, and methyl salicylate in a mixture of supercritical carbon dioxide with a polar cosolvent

    NASA Astrophysics Data System (ADS)

    Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.

    2015-08-01

    The solvate structures formed by salicylic acid, acetylsalicylic acid, and methyl salicylate in supercritical (SC) carbon dioxide with a polar cosolvent (methanol, 0.03 mole fractions) at a density of 0.7 g/cm3 and a temperature of 318 K were studied by the molecular dynamics method. Salicylic and acetylsalicylic acids were found to form highly stable hydrogen-bonded complexes with methanol via the hydrogen atom of the carboxyl group. For methyl salicylate in which the carboxyl hydrogen is substituted by a methyl radical, the formation of stable hydrogen bonds with methanol was not revealed. The contribution of other functional groups of the solute to the interactions with the cosolvent was much smaller. An analysis of correlations between the obtained data and the literature data on the cosolvent effect on the solubility of the compounds in SC CO2 showed that the dissolving ability of SC CO2 with respect to a polar organic substance in the presence of a cosolvent increased only when stable hydrogen-bonded complexes are formed between this substance and the cosolvent.

  17. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system. PMID:27117093

  18. Molecular dynamics of glycine ions in alanine doped TGS single crystal as probed by polarized laser raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Bajpai, P. K.; Verma, A. L.

    2012-10-01

    Polarized Raman spectra of pure and alanine doped tri-glycine sulfate (TGS) single crystals at 12 K in different scattering geometries are analyzed. Sub species modes due to three crystallographically distinguishable glycine ions G (I), G (II) and G (III) are assigned. It is observed that alanine doping does not change the crystalline field and acts as local perturbation only. The major changes due to doping are observed in the relative intensities of different modes; most of the modes associated with G (I) and SO42- ions show reversal behavior in relative intensity at high doping concentration. The observed spectral changes are analyzed in terms of reorientation of G (I) ions with sub species modes of G (II)/ G (III) following the reorientation due to complex hydrogen bonding network.

  19. Effective ionic charge polarization using typical supporting electrolyte and charge injection phenomena in molecularly doped polymer light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Itoh, Eiji; Yamashita, Takanori; Miyairi, Keiichi

    2002-11-01

    An effective method of enhancing charge injection and electroluminescence efficiency of polymer-based light-emitting diodes is introduced. Spin-coated films of poly (N-vinylcarbazole) blended with electron-transport material (Bu-PBD), laser dye (Coumarin6), and the typical supporting electrolyte [tetraethylammonium perchlorate (TEAP)] were examined and it was found that the injection current and luminance of the light emitting diodes doped with TEAP were enhanced dramatically after heat treatment at 80 degC and appropriate biasing in an external electric field of 1.5 x108 V/m at this temperature. A charge injection model based on Fowler-Nordheim tunneling is proposed, taking into account electric field distortion due to the accumulation of ionic space charges at the electrode/film interface. The relaxation time of ionic polarization is found to be related to the cation size of the electrolyte.

  20. Development of Polarizable Models for Molecular Mechanical Calculations III: Polarizable Water Models Conforming to Thole Polarization Screening Schemes

    PubMed Central

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong

    2012-01-01

    As an integrated step towards a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well, but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations. PMID:22712654

  1. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

    PubMed

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Luo, Ray

    2012-07-19

    As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations. PMID:22712654

  2. Calculation of molecular mean excitation energies via the polarization propagator formalism: H2 and H2O

    NASA Astrophysics Data System (ADS)

    Geertsen, Jan; Oddershede, Jens; Sabin, John R.

    1986-08-01

    We present ab initio calculations of oscillator-strength sum rules S(μ) and mean exciton energies Iμ for -1<=μ<=1. We use the polarization propagator formalism at the random-phase approximation level. Calculations are performed for H2 and H2O using large basis sets: 90 uncontracted Gaussian-type orbitals (CGTO's) for H2 and 101 CGTO's for water. We find that I0=19.12 eV for H2 (including thermal averaging) and 72.46 eV for H2O. They agree very well with previous semiempirical estimates. The same holds for the other Iμ moments. The fulfillment of the Thomas-Reiche-Kuhn sum rule in both the dipole length and velocity formulations shows that the basis sets employed are satisfactory. We have also investigated the ``shell-wise'' contributions to S(0) and I0 for H2O.

  3. QSRR Models for Kováts’ Retention Indices of a Variety of Volatile Organic Compounds on Polar and Apolar GC Stationary Phases Using Molecular Connectivity Indexes

    PubMed Central

    Faham, Shadab

    2010-01-01

    Quantitative structure-retention relationship (QSRR) approaches, based on molecular connectivity indices are useful to predict the gas chromatography of Kováts relative retention indices (GC-RRIs) of 132 volatile organic compounds (VOCs) on different 12 (4 apolar and 8 polar) stationary phases (C67, C103, C78, C∞, POH, TTF, MTF, PCL, PBR, TMO, PSH and PCN) at 130 °C. Full geometry optimization based on Austin model 1 semi-empirical molecular orbital method was carried out. The sets of 30 molecular descriptors were derived directly from the topological structures of the compounds from DRAGON program. By means of the final variable selection method, which is elimination selection stepwise regression algorithms, three optimal descriptors were selected to develop a QSRR model to predict the RRI of organic compounds on each stationary phase with a correlation coefficient between 0.9378 and 0.9673 and a leave-one-out cross-validation correlation coefficient between 0.9325 and 0.9653. The root mean squares errors over different 12 phases were within the range of 0.0333–0.0458. Furthermore, the accuracy of all developed models was confirmed using procedures of Y-randomization, external validation through an odd–even number and division of the entire dataset into training and test sets. A successful interpretation of the complex relationship between GC RRIs of VOCs and the chemical structures was achieved by QSRR. The three connectivity indexes in the models are also rationally interpreted, which indicated that all organic compounds’ RRI was precisely represented by molecular connectivity indexes. Electronic supplementary material The online version of this article (doi:10.1365/s10337-010-1741-4) contains supplementary material, which is available to authorized users. PMID:21088689

  4. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

    PubMed

    Lagardère, Louis; Lipparini, Filippo; Polack, Étienne; Stamm, Benjamin; Cancès, Éric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

    2015-06-01

    In this article, we present a parallel implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The smooth particle mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the direct inversion in the iterative subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy and force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package, which is the first implementation of a polarizable model that makes large-scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of SPME and a noticeable improvement of the memory management, giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to nonoptimized, sequential implementations, giving new directions for polarizable molecular dynamics with periodic boundary conditions using massively parallel implementations. PMID:26575557

  5. Polarized Neutron Diffraction as a Tool for Mapping Molecular Magnetic Anisotropy: Local Susceptibility Tensors in Co(II) Complexes.

    PubMed

    Ridier, Karl; Gillon, Béatrice; Gukasov, Arsen; Chaboussant, Grégory; Cousson, Alain; Luneau, Dominique; Borta, Ana; Jacquot, Jean-François; Checa, Ruben; Chiba, Yukako; Sakiyama, Hiroshi; Mikuriya, Masahiro

    2016-01-11

    Polarized neutron diffraction (PND) experiments were carried out at low temperature to characterize with high precision the local magnetic anisotropy in two paramagnetic high-spin cobalt(II) complexes, namely [Co(II) (dmf)6 ](BPh4 )2 (1) and [Co(II) 2 (sym-hmp)2 ](BPh4 )2 (2), in which dmf=N,N-dimethylformamide; sym-hmp=2,6-bis[(2-hydroxyethyl)methylaminomethyl]-4-methylphenolate, and BPh4 (-) =tetraphenylborate. This allowed a unique and direct determination of the local magnetic susceptibility tensor on each individual Co(II) site. In compound 1, this approach reveals the correlation between the single-ion easy magnetization direction and a trigonal elongation axis of the Co(II) coordination octahedron. In exchange-coupled dimer 2, the determination of the individual Co(II) magnetic susceptibility tensors provides a clear outlook of how the local magnetic properties on both Co(II) sites deviate from the single-ion behavior because of antiferromagnetic exchange coupling. PMID:26728231

  6. Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers.

    PubMed

    Upadhyay, Sanjay K; Wang, Yukun; Zhao, Tangzhen; Ulmschneider, Jakob P

    2015-06-01

    The membrane disruption and pore-forming mechanism of melittin has been widely explored by experiments and computational studies. However, the precise mechanism is still enigmatic, and further study is required to turn antimicrobial peptides into future promising drugs against microbes. In this study, unbiased microsecond (µs) time scale (total 17 µs) atomistic molecular dynamics simulation were performed on multiple melittin systems in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membrane to capture the various events during the membrane disorder produced by melittin. We observed bent U-shaped conformations of melittin, penetrated deeply into the membrane in all simulations, and a special double U-shaped structure. However, no peptide transmembrane insertion, nor pore formation was seen, indicating that these processes occur on much longer timescales, and suggesting that many prior computational studies of melittin were not sufficiently unbiased. PMID:25963936

  7. The bridging scale for two-dimensional atomistic/continuum coupling

    NASA Astrophysics Data System (ADS)

    Park, Harold S.; Karpov, Eduard G.; Liu, Wing Kam; Klein, Patrick A.

    2005-01-01

    In this paper, we present all necessary generalisations to extend the bridging scale, a finite-temperature multiple scale method which couples molecular dynamics (MD) and finite element (FE) simulations, to two dimensions. The crucial development is a numerical treatment of the boundary condition acting upon the reduced atomistic system, as such boundary conditions are analytically intractable beyond simple one-dimension systems. The approach presented in this paper offers distinct advantages compared to previous works, specifically the compact size of the resulting time history kernel, and the fact that the time history kernel can be calculated using an automated numerical procedure for arbitrary multi-dimensional lattice structures and interatomic potentials. We demonstrate the truly two-way nature of the coupled FE and reduced MD equations of motion via two example problems, wave propagation and dynamic crack propagation. Finally, we compare both problems to benchmark full MD simulations to validate the accuracy and efficiency of the proposed method.

  8. Difference in aggregation between functional and toxic amyloids studied by atomistic simulations

    NASA Astrophysics Data System (ADS)

    Carballo Pacheco, Martin; Ismail, Ahmed E.; Strodel, Birgit

    Amyloids are highly structured protein aggregates, normally associated with neurodegenerative diseases such as Alzheimer's disease. In recent years, a number of nontoxic amyloids with physiologically normal functions, called functional amyloids, have been found. It is known that soluble small oligomers are more toxic than large fibrils. Thus, we study with atomistic explicit-solvent molecular dynamics simulations the oligomer formation of the amyloid- β peptide Aβ25 - 35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Our simulations show that monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. In addition, we observe faster aggregation by functional amyloids than toxic amyloids, which could explain their lack of toxicity.

  9. Peculiarities of sliding friction in graphene, graphene fluoride, graphite: Comparison of experiment with atomistic simulations

    NASA Astrophysics Data System (ADS)

    Barabanova, Liudmyla; McCausland, Jeffrey; Buldum, Alper; Lyuksyutov, Sergei

    Friction is the major source of energy dissipation at the nanoscale. We use atomic force microscopy (AFM) to study slide friction based on analysis of trace-minus-retrace (TMR) signals. To obtain the signals a directional dependence of the sliding friction using a rotational technique was used at the edges and interiors of the samples graphene (G), graphene fluoride (GF), and graphite. The friction coefficient experimental results were based on a methodology assuming orthotropic friction and found to be in the range of 10-3 to 10-1 over all samples. Supplementing experimental measurements, we also performed atomistic modeling and simulations to investigate tribological properties of G including the edges. Molecular dynamics simulations and geometry optimization calculations were carried and compared with experimental measurements. It is suggested that the atoms at the apex of the asperities and at the graphene edges have important effect on friction.

  10. Atomistic effects on friction and contact area in single and multi asperity contacts

    NASA Astrophysics Data System (ADS)

    Luan, Binquan; Robbins, Mark

    2008-03-01

    Contact and friction are universal phenomena in our daily life. Theoretical studies of macroscopic contact and friction are usually based on continuum theories such as Hertz theory and Amontons's laws. Recent advances in nanotechnology have stimulated research into friction at the nanometer scale where new phenomena emerge. Contact and friction in single- and multi-asperity contacts with nanometer dimensions were studied using molecular dynamics simulations (MD) and a hybrid method. The hybrid method retains a full atomistic treatment near contacts and replaces more distant regions with a more efficient finite element description. Our results demonstrate that atomic-scale changes in surface structure produce huge changes in friction and contact area and substantial deviations from the predictions of continuum theories. Unanticipated surface plasticity is observed near peaks on crystalline surfaces. In the case of multiasperity amorphous systems, the rate of local plastic deformation near the surface is directly related to the frictional dissipation of energy.

  11. Frozen-density embedding theory with average solvent charge densities from explicit atomistic simulations.

    PubMed

    Laktionov, Andrey; Chemineau-Chalaye, Emilie; Wesolowski, Tomasz A

    2016-08-21

    Besides molecular electron densities obtained within the Born-Oppenheimer approximation (ρB(r)) to represent the environment, the ensemble averaged density (〈ρB〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444]. This makes it possible to introduce an approximation in the evaluation of the solvent effect on quantum mechanical observables consisting of replacing the ensemble averaged observable by the observable evaluated at ensemble averaged ρB(r). This approximation is shown to affect negligibly the solvatochromic shift in the absorption of hydrated acetone. The proposed model provides a continuum type of representation of the solvent, which reflects nevertheless its local structure, and it is to be applied as a post-simulation analysis tool in atomistic level simulations. PMID:26984532

  12. The role of halide ions in the anisotropic growth of gold nanoparticles: a microscopic, atomistic perspective.

    PubMed

    Meena, Santosh Kumar; Celiksoy, Sirin; Schäfer, Philipp; Henkel, Andreas; Sönnichsen, Carsten; Sulpizi, Marialore

    2016-05-21

    We provide a microscopic view of the role of halides in controlling the anisotropic growth of gold nanorods through a combined computational and experimental study. Atomistic molecular dynamics simulations unveil that Br(-) adsorption is not only responsible for surface passivation, but also acts as the driving force for CTAB micelle adsorption and stabilization on the gold surface in a facet-dependent way. The partial replacement of Br(-) by Cl(-) decreases the difference between facets and the surfactant density. Finally, in the CTAC solution, no halides or micellar structures protect the gold surface and further gold reduction should be uniformly possible. Experimentally observed nanoparticle's growth in different CTAB/CTAC mixtures is more uniform and faster as the amount of Cl(-) increases, confirming the picture from the simulations. In addition, the surfactant layer thickness measured on nanorods exposed to CTAB and CTAC quantitatively agrees with the simulation results. PMID:27118188

  13. Atomistic modeling of dislocation-interface interactions

    SciTech Connect

    Wang, Jian; Valone, Steven M; Beyerlein, Irene J; Misra, Amit; Germann, T. C.

    2011-01-31

    Using atomic scale models and interface defect theory, we first classify interface structures into a few types with respect to geometrical factors, then study the interfacial shear response and further simulate the dislocation-interface interactions using molecular dynamics. The results show that the atomic scale structural characteristics of both heterophases and homophases interfaces play a crucial role in (i) their mechanical responses and (ii) the ability of incoming lattice dislocations to transmit across them.

  14. Exploring Conceptual Frameworks of Models of Atomic Structures and Periodic Variations, Chemical Bonding, and Molecular Shape and Polarity: A Comparison of Undergraduate General Chemistry Students with High and Low Levels of Content Knowledge

    ERIC Educational Resources Information Center

    Wang, Chia-Yu; Barrow, Lloyd H.

    2013-01-01

    The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…

  15. Glide-Shuffle Competition in Silicon: An Atomistic Study

    NASA Astrophysics Data System (ADS)

    Li, Ju; Cai, Wei; Chang, Jinpeng; Yip, Sidney

    2001-06-01

    Glide-Shuffle Competition in Silicon: An Atomistic Study Ju Li, Wei Cai, Jinpeng Chang, Sidney Yip, Massachusetts Institute of Technology, Department of Nuclear Engineering, Cambridge, MA 02139 Recent experiments by Suzuki et al and Rabier et al suggest that low-T and high-T plasticity in Si and III-IV compounds may be governed by different mechanisms. We perform direct atomistic calculations to obtain the core energies, Peierls-Nabarro stresses, and kink formation and migration energies of full shuffle- and glide-set dislocations and glide-set partial dislocations in Si using the Stillinger-Weber potential. These results are compared with previous calculations, and their implications will be discussed. Dynamical simulations of some of the full dislocations in motion show qualitatively different behavior with their counterparts in bcc metals.

  16. Atomistic Simulation of Displacement Cascades in Zircon

    SciTech Connect

    Devanathan, Ram; Weber, William J.; Corrales, Louis R.; BP McGrail and GA Cragnolino

    2002-05-06

    Low energy displacement cascades in zircon (ZrSiO4) initiated by a Zr primary knock-on atom have been investigated by molecular dynamics simulations using a Coulombic model for long-range interactions, Buckingham potential for short-range interactions and Ziegler-Biersack potentials for close pair interactions. Displacements were found to occur mainly in the O sublattice, and O replacements by a ring mechanism were predominant. Clusters containing Si interstitials bridged by O interstitials, vacancy clusters and anti-site defects were found to occur. This Si-O-Si bridging is considerable in quenched liquid ZrSiO4.

  17. Atomistic Simulation of Collision Cascades in Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2006-09-01

    Defect production in energetic collision cascades in zircon has been studied by molecular dynamics simulation using a partial charge model combined with the Ziegler-Biersack-Littmark potential. Energy dissipation, defect accumulation, Si-O-Si polymerization, and Zr coordination number were examined for 10 keV and 30 keV U recoils simulated in the constant NVE ensemble. For both energies an amorphous core was produced with features similar to that of melt quenched zircon. Disordered Si ions in this core were polymerized with an average degree of polymerization of 1.5, while disordered Zr ions showed a coordination number of about 6 in agreement with EXAFS results. These results suggest that nano-scale phase separation into silica- and zirconia-rich regions occurs in the amorphous core.

  18. Atomistic approach for simulating plasmons in nanostructures

    NASA Astrophysics Data System (ADS)

    Sakko, Arto; Rossi, Tuomas P.; Enkovaara, Jussi; Nieminen, Risto M.

    2014-05-01

    Recent experimental and theoretical works have demonstrated that quantum mechanical effects play an important role in materials design of some novel nano-plasmonic materials. In this work, electronic structure calculations are used to study these effects for the optical properties of metal nanostructures and small flakes of graphene. Their optical response is shown to depend on their exact atomic composition, and their similarities (size-dependent resonance frequency) and differences (metallic vs. semiconducting material) are discussed. The open-source computer code GPAW is used for the simulations, which can be done for systems of thousands of valence electrons. The calculations automatically include quantum effects such as tunneling, nonlocal response, and molecular orbital hybridization.

  19. Atomistic Simulation of Single Asperity Contact

    NASA Astrophysics Data System (ADS)

    Philip; Kromer; Marder, Michael

    2003-03-01

    In the standard (Bowden and Tabor) model of friction, the macroscopic behavior of sliding results from the deformation of microscopic asperities in contact. A recent idea instead extracts macroscopic friction from the aggregate behavior of traveling, self-healing interfacial cracks: certain families of cracks are found to be mathematically forbidden, and the envelope of allowed cracks dictates the familiar Coulomb law of friction. To explore the connection between the new and traditional pictures of friction, we conducted molecular dynamics (MD) simulations of single-asperity contact subjected to an oscillatory sliding force -- a geometry important for the problem of fretting (damage due to small-scale vibratory contact). Our simulations reveal the importance of traveling interface cracks to the dynamics of slip at the interface, and illuminate the dynamics of crack initiation and suppression.

  20. Atomistic insights into aqueous corrosion of copper.

    SciTech Connect

    Jeon, B.; Sankaranarayanan, S. K. R. S.; van Duin, A. C. T.; Ramanathan, S.

    2011-06-21

    Corrosion is a fundamental problem in electrochemistry and represents a mode of failure of technologically important materials. Understanding the basic mechanism of aqueous corrosion of metals such as Cu in presence of halide ions is hence essential. Using molecular dynamics simulations incorporating reactive force-field (ReaxFF), the interaction of copper substrates and chlorine under aqueous conditions has been investigated. These simulations incorporate effects of proton transfer in the aqueous media and are suitable for modeling the bond formation and bond breakage phenomenon that is associated with complex aqueous corrosion phenomena. Systematic investigation of the corrosion process has been carried out by simulating different chlorine concentration and solution states. The structural and morphological differences associated with metal dissolution in the presence of chloride ions are evaluated using dynamical correlation functions. The simulated atomic trajectories are used to analyze the charged states, molecular structure and ion density distribution which are utilized to understand the atomic scale mechanism of corrosion of copper substrates under aqueous conditions. Increased concentration of chlorine and higher ambient temperature were found to expedite the corrosion of copper. In order to study the effect of solution states on the corrosion resistance of Cu, partial fractions of proton or hydroxide in water were configured, and higher corrosion rate at partial fraction hydroxide environment was observed. When the Cl{sup -} concentration is low, oxygen or hydroxide ion adsorption onto Cu surface has been confirmed in partial fraction hydroxide environment. Our study provides new atomic scale insights into the early stages of aqueous corrosion of metals such as copper.

  1. 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.

  2. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    NASA Astrophysics Data System (ADS)

    Vedula, Ravi Pramod Kumar

    profiles, inherent in strain-engineered Ge nanofins, on their transport properties. Fully atomistic simulations, involving a combination molecular dynamics simulations with first-principles based force-fields and semi-empirical tight binding calculations, coupled with linearized Boltzmann model are used to calculate the hole transport properties of realistic Ge nanofins (heights 5-15nm and widths 5nm-40nm). Our simulations predict the technological limit of phonon limited hole mobility improvement in Ge channel PMOS devices (H<15nm) and present geometric guidelines for patterning nanofins to engineer high performance uniaxial devices conducive to the existing top-down fabrication approaches. From these calculations, we demonstrate that realistic modeling of the devices requires a reduction in the empiricism of fitting parameters and incorporation of new multi-scale, multi-resolution approach spanning across various spatial and temporal scales. Such physics based predictive multiscale models facilitate an integrated approach for rapid development and pave the way for designing new advanced materials and devices.

  3. Indium and impurity incorporation in InGaN films on polar, nonpolar, and semipolar GaN orientations grown by ammonia molecular beam epitaxy

    SciTech Connect

    Browne, David A.; Young, Erin C.; Lang, Jordan R.; Hurni, Christophe A.; Speck, James S.

    2012-07-15

    The effects of NH{sub 3} flow, group III flux, and substrate growth temperature on indium incorporation and surface morphology have been investigated for bulk InGaN films grown by ammonia molecular beam epitaxy. The incorporation of unintentional impurity elements (H, C, O) in InGaN films was studied as a function of growth temperature for growth on polar (0001) GaN on sapphire templates, nonpolar (1010) bulk GaN, and semipolar (1122), (2021) bulk GaN substrates. Enhanced indium incorporation was observed on both (1010) and (2021) surfaces relative to c-plane, while reduced indium incorporation was observed on (1122) for co-loaded conditions. Indium incorporation was observed to increase with decreasing growth temperature for all planes, while being relatively unaffected by the group III flux rates for a 1:1 Ga:In ratio. Indium incorporation was found to increase at the expense of a decreased growth rate for higher ammonia flows; however, smooth surface morphology was consistently observed for growth on semipolar orientations. Increased concentrations of oxygen and hydrogen were observed on semipolar and nonpolar orientations with a clear trend of increased hydrogen incorporation with indium content.

  4. Atomistic simulations of brittle crack growth.

    SciTech Connect

    Hoyt, Jeffrey John

    2007-04-01

    Ceramic materials such as lead zirconium titanates (PZT), low temperature co-fired ceramics and silica glasses are used in several of Sandia's mission critical components. Brittle fracture, either during machining and processing or after many years in service, remains a serious reliability and cost issue. Despite its technological importance, brittle fracture remains poorly understand, especially the onset and propagation of sub-critical cracks. However, some insights into the onset of fracture can be gleaned from the atomic scale structure of the amorphous material. In silica for example, it is well known [1] that the Si-O-Si bonds are relatively weak and, in angle distribution functions determined from scattering experiments, the bonds exhibit a wide spread around a peak at 150. By contrast the O-Si-O bonds are strong with a narrow peak in the distribution around the 109 dictated by the SiO{sub 4} tetrahedron. In addition, slow energy release in silica, as deduced from dissolution experiments, depends on the distribution of 3-fold and higher rings in the amorphous structure. The purpose of this four month LDRD project was to investigate the atomic structure of silica in the bulk and in the vicinity of a crack tip using molecular dynamics simulations. Changes in the amorphous structure in the neighborhood of an atomically sharp tip may provide important clues as to the initiation sites and the stress intensity required to propagate a sub-critical crack.

  5. TUTORIAL: Electrical resistance: an atomistic view

    NASA Astrophysics Data System (ADS)

    Datta, Supriyo

    2004-07-01

    This tutorial article presents a 'bottom-up' view of electrical resistance starting from something really small, like a molecule, and then discussing the issues that arise as we move to bigger conductors. Remarkably, no serious quantum mechanics is needed to understand electrical conduction through something really small, except for unusual things like the Kondo effect that are seen only for a special range of parameters. This article starts with energy level diagrams (section 2), shows that the broadening that accompanies coupling limits the conductance to a maximum of q2/h per level (sections 3, 4), describes how a change in the shape of the self-consistent potential profile can turn a symmetric current-voltage characteristic into a rectifying one (sections 5, 6), shows that many interesting effects in molecular electronics can be understood in terms of a simple model (section 7), introduces the non-equilibrium Green function (NEGF) formalism as a sophisticated version of this simple model with ordinary numbers replaced by appropriate matrices (section 8) and ends with a personal view of unsolved problems in the field of nanoscale electron transport (section 9). Appendix A discusses the Coulomb blockade regime of transport, while appendix B presents a formal derivation of the NEGF equations. MATLAB codes for numerical examples are listed in appendix C. (The appendices are available in the online version only.)

  6. Long-time atomistic simulations with the Parallel Replica Dynamics method

    NASA Astrophysics Data System (ADS)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  7. An atomistic methodology of energy release rate for graphene at nanoscale

    SciTech Connect

    Zhang, Zhen; Lee, James D.; Wang, Xianqiao

    2014-03-21

    Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough.

  8. Atomistic simulation of structure and dynamics of the plastic crystal diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate

    NASA Astrophysics Data System (ADS)

    Chen, F.; Jin, L.; de Leeuw, S. W.; Pringle, J. M.; Forsyth, M.

    2013-06-01

    Molecular dynamics simulations have been performed to investigate the interrelations between structures, transport mechanisms, and phase transitions of an organic ionic plastic crystal material, diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate ([P1,2,2,4][PF6]), in both solid and liquid phases. Examination of the temperature dependence of supercell parameters and radial distribution functions provides evidence of plastic phase transitions. Nonlinear increments of cell size within the temperature range 123-413 K are consistent with the plastic phase transitions identified from experimental analysis. The time- and temperature-dependent microstructure and dynamics have been intensively studied through analysis of trajectory files. The rotational motion and diffusion of the matrix ions are quantitatively analysed via rotational correlation functions and mean square displacements. We present new information on the evolution of molecular motions in different phases, and compare and contrast our findings with previously reported hypotheses based on nuclear magnetic resonance results. This work provides valuable information at an atomistic level to explain the experimental observations, which helps further understanding of the molecular motions underlying the plastic phase transitions.

  9. Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B

    SciTech Connect

    Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert; Loos, Katja; Fels, Gregor

    2011-04-01

    Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using docking tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.

  10. Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

    PubMed

    Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

    2013-01-01

    Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

  11. Atomistic MD simulation reveals the mechanism by which CETP penetrates into HDL enabling lipid transfer from HDL to CETP

    PubMed Central

    Cilpa-Karhu, Geraldine; Jauhiainen, Matti; Riekkola, Marja-Liisa

    2015-01-01

    Inhibition of cholesterol ester transfer protein (CETP), a protein mediating transfer of neutral lipids between lipoproteins, has been proposed as a means to elevate atheroprotective HDL subpopulations and thereby reduce atherosclerosis. However, off-target and adverse effects of the inhibition have raised doubts about the molecular mechanism of CETP-HDL interaction. Recent experimental findings have demonstrated the penetration of CETP into HDL. However, atomic level resolution of CETP penetration into HDL, a prerequisite for a better understanding of CETP functionality and HDL atheroprotection, is missing. We constructed an HDL particle that mimics the actual human HDL mass composition and investigated for the first time, by large-scale atomistic molecular dynamics, the interaction of an upright CETP with a human HDL-mimicking model. The results demonstrated how CETP can penetrate the HDL particle surface, with the formation of an opening in the N barrel domain end of CETP, put in evidence the major anchoring role of a tryptophan-rich region of this domain, and unveiled the presence of a phenylalanine barrier controlling further access of HDL-derived lipids to the tunnel of CETP. The findings reveal novel atomistic details of the CETP-HDL interaction mechanism and can provide new insight into therapeutic strategies. PMID:25424006

  12. Cell polarity: mechanochemical patterning.

    PubMed

    Goehring, Nathan W; Grill, Stephan W

    2013-02-01

    Nearly every cell type exhibits some form of polarity, yet the molecular mechanisms vary widely. Here we examine what we term 'chemical systems' where cell polarization arises through biochemical interactions in signaling pathways, 'mechanical systems' where cells polarize due to forces, stresses and transport, and 'mechanochemical systems' where polarization results from interplay between mechanics and chemical signaling. To reveal potentially unifying principles, we discuss mathematical conceptualizations of several prototypical examples. We suggest that the concept of local activation and global inhibition - originally developed to explain spatial patterning in reaction-diffusion systems - provides a framework for understanding many cases of cell polarity. Importantly, we find that the core ingredients in this framework - symmetry breaking, self-amplifying feedback, and long-range inhibition - involve processes that can be chemical, mechanical, or even mechanochemical in nature. PMID:23182746

  13. Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks.

    PubMed

    Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

    2016-01-28

    Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones. PMID:26730607

  14. SUPRAMOLECULAR SYSTEMS BEHAVIOR AT THE AIR-WATER INTERFACE. MOLECULAR DYNAMIC SIMULATION STUDY

    SciTech Connect

    Sandoval, C.; Saavedra, M.; Gargallo, L.; Radic, D.

    2008-08-28

    Atomistic molecular dynamics simulation (MDS) was development to investigate the structural and dynamic properties of a monolayer of supramolecular systems. The simulations were performed at room temperature, on inclusion complexes (ICs) of {alpha}-cyclodextrin (CD) with poly(ethylene-oxide)(PEO), poly({epsilon}-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF). The simulations were carried out for a surface area of 30A ring . The trajectories of the MDS show that the system more stable was IC-PEC, being the less stable IC-PEO. The disordered monolayer for the systems was proved by the orientation correlation function and the radial distribution function between the polar groups of ICs and the water molecules. We found that the system IC-PEC was more stable that the systems IC-PTHF and IC-PEO.

  15. Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX.

    PubMed

    Lee, Kibaek; Joshi, Kaushik; Chaudhuri, Santanu; Stewart, D Scott

    2016-05-14

    We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model is based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations. PMID:27179475

  16. Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

    NASA Astrophysics Data System (ADS)

    Lee, Kibaek; Joshi, Kaushik; Chaudhuri, Santanu; Stewart, D. Scott

    2016-05-01

    We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model is based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.

  17. Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

    NASA Astrophysics Data System (ADS)

    Rezaei Mianroodi, Jaber; Svendsen, Bob

    2015-04-01

    The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical

  18. The Landau-Lifshitz equation in atomistic models

    NASA Astrophysics Data System (ADS)

    Ellis, M. O. A.; Evans, R. F. L.; Ostler, T. A.; Barker, J.; Atxitia, U.; Chubykalo-Fesenko, O.; Chantrell, R. W.

    2015-09-01

    The Landau-Lifshitz (LL) equation, originally proposed at the macrospin level, is increasingly used in Atomistic Spin Dynamic (ASD) models. These models are based on a spin Hamiltonian featuring atomic spins of fixed length, with the exchange introduced using the Heisenberg formalism. ASD models are proving a powerful approach to the fundamental understanding of ultrafast magnetization dynamics, including the prediction of the thermally induced magnetization switching phenomenon in which the magnetization is reversed using an ultra-fast laser pulse in the absence of an externally applied field. This paper outlines the ASD model approach and considers the role and limitations of the LL equation in this context.

  19. Atomistic simulation of a superionic transition in UO2

    NASA Astrophysics Data System (ADS)

    Korneva, M. A.; Starikov, S. V.

    2016-01-01

    The results of the atomistic simulation of a superionic transition and melting of uranium dioxide are presented. The temperature dependences of the concentration of defects in the oxygen sublattice and changes in the heat capacity and isothermal compressibility upon the superionic transition are calculated. It is shown that the curve of the superionic transition in the PT diagram can be described by the Ehrenfest's equation. The possibility of describing the superionic transition within the framework of the theory of second- order phase transitions is discussed. Based on the results obtained, it is considered that this structural transformation can occur in other materials.

  20. Ergodicity, mixing, and time reversibility for atomistic nonequilibrium steady states

    SciTech Connect

    Hoover, W.G.; Kum, O.

    1997-11-01

    Ergodic mixing is prerequisite to any statistical-mechanical calculation of properties derived from atomistic dynamical simulations. Thus the time-reversible thermostats and ergostats used in simulating Gibbsian equilibrium dynamics or nonequilibrium steady-state dynamics should impose ergodicity and mixing. Though it is hard to visualize many-dimensional phase-space distributions, recent developments provide several practical numerical approaches to the problem of ergodic mixing. Here we apply three of these approaches to a useful nonequilibrium test problem, an oscillator in a temperature gradient. {copyright} {ital 1997} {ital The American Physical Society}

  1. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGESBeta

    Stukowski, Alexander

    2012-05-28

    Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

  2. Atomistic methodologies for material properties of 2D materials at the nanoscale

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen

    Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our

  3. Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

    DOE PAGESBeta

    Taylor, Christopher D.

    2012-01-01

    Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies ofmore » the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.« less

  4. Nuclear magnetic resonance inverse spectra of InGaAs quantum dots: Atomistic level structural information

    NASA Astrophysics Data System (ADS)

    Bulutay, Ceyhun; Chekhovich, E. A.; Tartakovskii, A. I.

    2014-11-01

    A wealth of atomistic information is contained within a self-assembled quantum dot (QD), associated with its chemical composition and the growth history. In the presence of quadrupolar nuclei, as in InGaAs QDs, much of this is inherited to nuclear spins via the coupling between the strain within the polar lattice and the electric quadrupole moments of the nuclei. Here, we present a computational study of the recently introduced inverse spectra nuclear magnetic resonance technique to assess its suitability for extracting such structural information. We observe marked spectral differences between the compound InAs and alloy InGaAs QDs. These are linked to the local biaxial and shear strains, and the local bonding configurations. The cation alloying plays a crucial role especially for the arsenic nuclei. The isotopic line profiles also largely differ among nuclear species: While the central transition of the gallium isotopes have a narrow linewidth, those of arsenic and indium are much broader and oppositely skewed with respect to each other. The statistical distributions of electric field gradient (EFG) parameters of the nuclei within the QD are analyzed. The consequences of various EFG axial orientation characteristics are discussed. Finally, the possibility of suppressing the first-order quadrupolar shifts is demonstrated by simply tilting the sample with respect to the static magnetic field.

  5. Strain Engineering of Graphene: Atomistic Simulation of Y-junctions and Nanobubbles

    NASA Astrophysics Data System (ADS)

    Qi, Zenan; Bahamon, Dario; Park, Harold; Pereira, Vitor; Campbell, David; Castro Neto, Antonio

    2014-03-01

    We have studied the effects of two and three-dimensional states of strain on electronic transport in monolayer graphene. Using a combined atomistic simulation approach with molecular mechanics, molecular dynamics, tight binding exact diagonalization and Landauer-Büttiker formulism, we have explored how various deformation patterns induce tunable pseudomagnetic field (PMF) distributions and furthermore how the Landau levels arising from PMF affect the quantum transport properties. Specifically, graphene Y-junction structures are found, under triaxial strains, to behave like pseudomagnetic quantum dots that selectively guide electron movement; valley degeneracy is broken when both strain-induced PMF and external real magnetic fields are present. Furthermore, graphene nano-bubbles with different geometries obtained by gas pressure can also be controlled as functional blocks due to PMF-restricted quantum transport by manipulation of strain. The simulation results show the promising potential to utilize graphene as a tunable building block for electronic NEMS/MEMS devices by strain engineering. Authors acknowledge supports of NRF-CRP award, NSF and Banco Santander.

  6. Atomistic surface erosion and thin film growth modelled over realistic time scales

    SciTech Connect

    Scott, Chris; Blackwell, Sabrina; Vernon, Louis; Kenny, Steven; Smith, Roger; Walls, Michael

    2011-11-07

    We present results of atomistic modelling of surface growth and sputtering using a multi-time scale molecular dynamics-on-the-fly kinetic Monte Carlo scheme which allows simulations to be carried out over realistic experimental times. The method uses molecular dynamics to model the fast processes and then calculates the diffusion barriers for the slow processes on-the-fly, without any preconceptions about what transitions might occur. The method is applied to the growth of metal and oxide materials at impact energies typical for both vapour deposition and magnetron sputtering. The method can be used to explain growth processes, such as the filling of vacancies and the formation of stacking faults. By tuning the variable experimental parameters on the computer, a parameter set for optimum crystalline growth can be determined. The method can also be used to model sputtering where the particle interactions with the surface occur at a higher energy. It is shown how a steady state can arise in which interstitial clusters are continuously being formed below the surface during an atom impact event which also recombine or diffuse to the surface between impact events. For fcc metals the near surface region remains basically crystalline during the erosion process with a pitted topography which soon attains a steady state roughness.

  7. Proton generation and transport in the fuel cell environment: atomistic computer simulations

    NASA Astrophysics Data System (ADS)

    Spohr, Eckhard

    2007-12-01

    Hydrogen atoms in direct methanol fuel cells are produced ’in situ’ by dissociation of methanol on precious metal catalysts (Pt, Pt/Ru) in an aqueous environment. The abstraction of the first hydrogen atom via C H bond cleavage is generally considered to be the rate-limiting step of dissociative methanol adsorption on the catalyst surface. This oxidation reaction on platinum particles in a fuel cell is investigated by means of a combined approach of classical molecular dynamics (MD) simulations and ab initio calculations in order to obtain an understanding of the role of the solvent for the stabilization of intermediates and for the enhancement of proton desorption from the catalyst surface and subsequent transfer into the nearby polymer electrolyte membrane (PEM). The anodically generated protons need to migrate efficiently through the membrane to the cathode were they are consumed. At the same time water and methanol (in a direct methanol fuel cell) transport should be slow. Humidified PEMs are considered to consist of a nanometer-scale phase-separated bicontinuous network of polymer regions providing structural integrity, and of aqueous regions providing the pathways for proton conduction. MD simulations provide a powerful theoretical tool for the investigation and clarification of the relationship between molecular structure and these transport phenomena. In order to atomistically model larger fractions of a humidified PEM, a coarse-grained model of humidified polymer electrolyte membranes has been developed.

  8. Atomistic Simulation of Tensile Deformation Behavior of ∑5 Tilt Grain Boundaries in Copper Bicrystal

    PubMed Central

    Zhang, Liang; Lu, Cheng; Tieu, Kiet

    2014-01-01

    Experiments on polycrystalline metallic samples have indicated that Grain boundary (GB) structure can affect many material properties related to fracture and plasticity. In this study, atomistic simulations are employed to investigate the structures and mechanical behavior of both symmetric and asymmetric ∑5[0 0 1] tilt GBs of copper bicrystal. First, the equilibrium GB structures are generated by molecular statics simulation at 0K. The results show that the ∑5 asymmetric GBs with different inclination angles (φ) are composed of only two structural units corresponding to the two ∑5 symmetric GBs. Molecular dynamics simulations are then conducted to investigate the mechanical response and the underlying deformation mechanisms of bicrystal models with different ∑5 GBs under tension. Tensile deformation is applied under both ‘free’ and ‘constrained’ boundary conditions. Simulation results revealed different mechanical properties of the symmetric and asymmetric GBs and indicated that stress state can play an important role in the deformation mechanisms of nanocrystalline materials. PMID:25082227

  9. Atomistically-informed Dislocation Dynamics in fcc Crystals

    SciTech Connect

    Martinez, E; Marian, J; Arsenlis, T; Victoria, M; Perlado, J M

    2006-09-06

    We develop a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our findings to the plastic behavior of monocrystalline fcc metals.

  10. Atomistic Simulation of High-Density Uranium Fuels

    DOE PAGESBeta

    Garcés, Jorge Eduardo; Bozzolo, Guillermo

    2011-01-01

    We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

  11. 3d visualization of atomistic simulations on every desktop

    NASA Astrophysics Data System (ADS)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

  12. Atomistic calculation of the thermoelectric properties of Si nanowires

    NASA Astrophysics Data System (ADS)

    Bejenari, I.; Kratzer, P.

    2014-07-01

    The thermoelectric properties of 1.6-nm-thick Si square nanowires with [100] crystalline orientation are calculated over a wide temperature range from 0 K to 1000 K, taking into account atomistic electron-phonon interaction. In our model, the [010] and [001] facets are passivated by hydrogen and there are Si-Si dimers on the nanowire surface. The electronic structure was calculated by using the sp3 spin-orbit-coupled atomistic second-nearest-neighbor tight-binding model. The phonon dispersion was calculated from a valence force field model of the Brenner type. A scheme for calculating electron-phonon matrix elements from a second-nearest-neighbor tight-binding model is presented. Based on Fermi's golden rule, the electron-phonon transition rate was obtained by combining the electron and phonon eigenstates. Both elastic and inelastic scattering processes are taken into consideration. The temperature dependence of transport characteristics was calculated by using a solution of the linearized Boltzmann transport equation obtained by means of the iterative orthomin method. At room temperature, the electron mobility is 195 cm2 V-1 s-1 and increases with temperature, while a figure of merit ZT =0.38 is reached for n-type doping with a concentration of n =1019 cm-3.

  13. Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

    1999-01-01

    We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

  14. Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension.

    PubMed

    Muddana, Hari S; Gullapalli, Ramachandra R; Manias, Evangelos; Butler, Peter J

    2011-01-28

    Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing. PMID:21152516

  15. Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences.

    PubMed

    Cronin, Matthew A; Rincon, Gonzalo; Meredith, Robert W; MacNeil, Michael D; Islas-Trejo, Alma; Cánovas, Angela; Medrano, Juan F

    2014-01-01

    We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears. PMID:24477675

  16. Polar organic marker compounds in atmospheric aerosol in the Po Valley during the Supersito campaigns - Part 1: Low molecular weight carboxylic acids in cold seasons

    NASA Astrophysics Data System (ADS)

    Pietrogrande, Maria Chiara; Bacco, Dimitri; Visentin, Marco; Ferrari, Silvia; Poluzzi, Vanes

    2014-04-01

    In the framework of the “Supersito” project, three intensive experimental campaigns were conducted in the Po Valley (Northern Italy) in cold seasons, such as late autumn, pre-winter and deep-winter, over three years from 2011 to 2013. As a part of a study on polar marker compounds, including carboxylic acids, sugar derivatives and lignin phenols, the present study reports a detailed discussion on the atmospheric concentrations of 14 low molecular weight carboxylic acids, mainly dicarboxylic and oxo-hydroxy carboxylic acids, as relevant markers of primary and secondary organic aerosols. PM2.5 samples were collected in two monitoring sites, representing urban and rural background stations. The total quantities of carboxylic acids were 262, 167 and 249 ng m-3 at the urban site and 308, 115, 248 ng m-3 at the rural site in pre-winter, fall and deep-winter, respectively. These high concentrations can be explained by the large human emission sources in the urbanized region, combined with the stagnant atmospheric conditions during the cold seasons that accumulate the organic precursors and accelerate the secondary atmospheric reactions. The distribution profiles of the investigated markers suggest the dominant contributions of primary anthropogenic sources, such as traffic, domestic heating and biomass burning. These results are confirmed by comparison with additional emission tracers, such as anhydro-saccharides for biomass burning and fatty acids originated from different anthropogenic sources. In addition, some secondary constituents were detected in both sites, as produced by in situ photo-chemical reactions from both biogenic (e.g. pinonic acid) and anthropogenic precursors (e.g. phthalic and adipic acids). The impact of different sources from human activities was elucidated by investigating the week pattern of carboxylic and fatty acid concentrations. The weekly trends of analytes during the warmer campaign (fall 2012; mean temperature: 12 °C) may be related to

  17. Size effects of 109° domain walls in rhombohedral barium titanate single crystals—A molecular statics analysis

    NASA Astrophysics Data System (ADS)

    Endres, Florian; Steinmann, Paul

    2016-01-01

    Ferroelectric functional materials are of great interest in science and technology due to their electromechanically coupled material properties. Therefore, ferroelectrics, such as barium titanate, are modeled and simulated at the continuum scale as well as at the atomistic scale. Due to recent advancements in related manufacturing technologies the modeling and simulation of smart materials at the nanometer length scale is getting more important not only to predict but also fundamentally understand the complex material behavior of such materials. In this study, we analyze the size effects of 109° nanodomain walls in ferroelectric barium titanate single crystals in the rhombohedral phase using a recently proposed extended molecular statics algorithm. We study the impact of domain thicknesses on the spontaneous polarization, the coercive field, and the lattice constants. Moreover, we discuss how the electromechanical coupling of an applied electric field and the introduced strain in the converse piezoelectric effect is affected by the thickness of nanodomains.

  18. Material fields in atomistics as pull-backs of spatial distributions

    NASA Astrophysics Data System (ADS)

    Chandra Admal, Nikhil; Tadmor, Ellad B.

    2016-04-01

    The various fields defined in continuum mechanics have both a material and a spatial description that are related through the deformation mapping. In contrast, continuum fields defined for atomistic systems using the Irving-Kirkwood or Murdoch-Hardy procedures correspond to a spatial description. It is uncommon to define atomistic fields in the reference configuration due to the lack of a unique definition for the deformation mapping in atomistic systems. In this paper, we construct referential atomistic distributions as pull-backs of the spatial distributions obtained in the Murdoch-Hardy procedure with respect to a postulated deformation mapping that tracks particles. We then show that some of these referential distributions are independent of the choice of the deformation mapping and only depend on the reference and current configuration of particles. Therefore, the fields obtained from these distributions can be calculated without explicitly constructing a deformation map, and by construction they satisfy the balance equations. In particular, we obtain definitions for the first and second atomistic Piola-Kirchhoff stress tensors. We demonstrate the validity of these definitions through a numerical example involving finite deformation of a slab containing a notch under tension. An interesting feature of the atomistic first Piola-Kirchhoff stress tensor is the absence of a kinetic part, which in the atomistic Cauchy stress tensor accounts for thermal fluctuations. We show that this effect is implicitly included in the atomistic first Piola-Kirchhoff stress tensor through the motion of the particles. An open source program to compute the atomistic Cauchy and first Piola-Kirchhoff stress fields called MDStressLab is available online at

  19. Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.

    PubMed

    Koch, Denise M; Peslherbe, Gilles H

    2008-01-17

    Sodium iodide has long been a paradigm for ionic and covalent curve crossing and ultrafast nonadiabatic dynamics, and our interest lies in the influence of solvation on this process. The NaI(H2O)n photodissociation dynamics are simulated with the molecular dynamics with quantum transitions method. A quantum mechanics/molecular mechanics (QM/MM) description is adopted for the NaI(H2O)n electronic states, in which a semiempirical valence bond approach is used to describe the NaI electronic structure, and a polarizable optimized potential for cluster simulations model is used to describe solute-solvent and solvent-solvent interactions. In contrast to previous work with a nonpolarizable MM model [Koch et al., J. Phys. Chem. A, 2006, 110, 1438], this approach predicts that the NaI ionic ground- to covalent first-excited-state Franck-Condon energy gaps reach a plateau by cluster size 16, in relatively good agreement with experiment and electronic structure calculations; this allows us to safely extend our previous simulations to larger cluster sizes, i.e., n > 4. The simulations suggest that the disappearance of the two-photon ionization probe signals observed in femtosecond pump-probe experiments of NaI(H2O)n, n >/= 4, is due to the shift of the NaI curve-crossing region toward larger NaI internuclear separations because of solvent stabilization of the NaI ionic state. Further, the latter causes the adiabatic ground and excited states to acquire pure ionic and covalent character, respectively, by cluster 8, resulting in NaI ionic ground-state recombination or dissociation. To make a connection with electron transfer in solution, free energy curves have been generated as a function of a solvent coordinate similar to that of solution theory. Inspection of the free energy curves together with the results of excited-state simulations reveal that the electron-transfer process in clusters is not governed by the collective motion of the solvent molecules, as in solution, but

  20. Polarization induced hole doping in graded Al{sub x}Ga{sub 1-x}N (x = 0.7 {approx} 1) layer grown by molecular beam epitaxy

    SciTech Connect

    Li, Shibin; Zhang, Ting; Wu, Jiang; Yang, Yajie; Wang, Zhiming; Wu, Zhiming; Chen, Zhi; Jiang, Yadong

    2013-02-11

    Polarization induced hole doping on the order of {approx}10{sup 18} cm{sup -3} is achieved in linearly graded Al{sub x}Ga{sub 1-x}N (x = 0.7 {approx} 1) layer grown by molecular beam epitaxy. Graded Al{sub x}Ga{sub 1-x}N and conventional Al{sub 0.7}Ga{sub 0.3}N layers grown on AlN are beryllium (Be) doped via epitaxial growth. The hole concentration in graded Al{sub x}Ga{sub 1-x}N:Be (x = 0.7 {approx} 1) layers demonstrates that polarization generates hole charges from Be dopant. The Al{sub 0.7}Ga{sub 0.3}N layer is not conductive owing to the absence of carriers generated from the Be dopant without the inducement of polarization. Polarization doping provides an approach to high efficiency p-type doping in high Al composition AlGaN.

  1. Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

    DOE PAGESBeta

    Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; Luskin, Mitchell

    2015-11-16

    Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

  2. An Atomistic View on Human Hemoglobin Carbon Monoxide Migration Processes

    PubMed Central

    Lucas, M. Fátima; Guallar, Víctor

    2012-01-01

    A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed. PMID:22385860

  3. Protein displacements under external forces: An atomistic Langevin dynamics approach

    NASA Astrophysics Data System (ADS)

    Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

    2009-02-01

    We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

  4. Emergence of linear elasticity from the atomistic description of matter

    NASA Astrophysics Data System (ADS)

    Cakir, Abdullah; Pica Ciamarra, Massimo

    2016-08-01

    We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

  5. Atomistic simulation of static magnetic properties of bit patterned media

    NASA Astrophysics Data System (ADS)

    Arbeláez-Echeverri, O. D.; Agudelo-Giraldo, J. D.; Restrepo-Parra, E.

    2016-09-01

    In this work we present a new design of Co based bit pattern media with out-of-plane uni-axial anisotropy induced by interface effects. Our model features the inclusion of magnetic impurities in the non-magnetic matrix. After the material model was refined during three iterations using Monte Carlo simulations, further simulations were performed using an atomistic integrator of Landau-Lifshitz-Gilbert equation with Langevin dynamics to study the behavior of the system paying special attention to the super-paramagnetic limit. Our model system exhibits three magnetic phase transitions, one due to the magnetically doped matrix material and the weak magnetic interaction between the nano-structures in the system. The different magnetic phases of the system as well as the features of its phase diagram are explained.

  6. How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations

    PubMed Central

    Äijänen, Tarja; Koivuniemi, Artturi; Javanainen, Matti; Rissanen, Sami; Rog, Tomasz; Vattulainen, Ilpo

    2014-01-01

    Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL)-cholesterol and decrease low density lipoprotein (LDL)-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases. PMID:25412509

  7. Experimentally driven atomistic model of 1,2 polybutadiene

    NASA Astrophysics Data System (ADS)

    Gkourmpis, Thomas; Mitchell, Geoffrey R.

    2014-02-01

    We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120-400 K. Analysis of the experimental data yields bond lengths for CC and C  C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

  8. Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

    NASA Astrophysics Data System (ADS)

    Van de Put, Maarten L.; Vandenberghe, William G.; Sorée, Bart; Magnus, Wim; Fischetti, Massimo V.

    2016-06-01

    A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.

  9. Experimentally driven atomistic model of 1,2 polybutadiene

    SciTech Connect

    Gkourmpis, Thomas; Mitchell, Geoffrey R.

    2014-02-07

    We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

  10. An atomistic-continuum Cosserat rod model of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chandraseker, Karthick; Mukherjee, Subrata; Paci, Jeffrey T.; Schatz, George C.

    2009-06-01

    The focus of the present work is an atomistic-continuum model of single-walled carbon nanotubes (CNTs) based on an elastic rod theory which can exhibit geometric as well as material nonlinearity [Healey, T.J., 2002. Material symmetry and chirality in nonlinearly elastic rods. Mathematics and Mechanics of Solids 7, 405-420]. In particular, the single-walled carbon nanotube (SWNT) is modeled as a one-dimensional elastic continuum with some finite thickness bounded by the lateral surface. Exploitation of certain symmetries in the underlying atomic structure leads to suitable representations of the continuum elastic strain energy density in terms of strain measures that capture extension, twist, bending, and shear deformations [Healey, T.J., 2002. Material symmetry and chirality in nonlinearly elastic rods. Mathematics and Mechanics of Solids 7, 405-420]. Bridging between the atomic scale and the effective continuum is carried out by parameterization of the continuum elastic energy and determination of the parameters using unit cell atomistic simulations over a range of deformation magnitudes and types. Specifically, the proposed model takes into account (a) bending, (b) twist, (c) shear, (d) extension, (e) coupled extension and twist, and (f) coupled bending and shear deformations. The extracted parameters reveal benefits of accounting for important anisotropic and large-strain effects as improvements over employing traditional, linearly elastic, isotropic, small-strain, continuum models to simulate deformations of atomic systems such as SWNTs. It is envisioned that the proposed approach and the extracted model parameters can serve as a useful input to simulations of SWNT deformations using existing nonlinearly elastic continuum codes based, for example, on the finite element method (FEM).

  11. An Atomistic Statistically Effective Energy Function for Computational Protein Design.

    PubMed

    Topham, Christopher M; Barbe, Sophie; André, Isabelle

    2016-08-01

    Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical

  12. Polarization developments

    SciTech Connect

    Prescott, C.Y.

    1993-07-01

    Recent developments in laser-driven photoemission sources of polarized electrons have made prospects for highly polarized electron beams in a future linear collider very promising. This talk discusses the experiences with the SLC polarized electron source, the recent progress with research into gallium arsenide and strained gallium arsenide as a photocathode material, and the suitability of these cathode materials for a future linear collider based on the parameters of the several linear collider designs that exist.

  13. Neuronal polarization.

    PubMed

    Takano, Tetsuya; Xu, Chundi; Funahashi, Yasuhiro; Namba, Takashi; Kaibuchi, Kozo

    2015-06-15

    Neurons are highly polarized cells with structurally and functionally distinct processes called axons and dendrites. This polarization underlies the directional flow of information in the central nervous system, so the establishment and maintenance of neuronal polarization is crucial for correct development and function. Great progress in our understanding of how neurons establish their polarity has been made through the use of cultured hippocampal neurons, while recent technological advances have enabled in vivo analysis of axon specification and elongation. This short review and accompanying poster highlight recent advances in this fascinating field, with an emphasis on the signaling mechanisms underlying axon and dendrite specification in vitro and in vivo. PMID:26081570

  14. Polarization Aberrations

    NASA Technical Reports Server (NTRS)

    Mcguire, James P., Jr.; Chipman, Russell A.

    1990-01-01

    The analysis of the polarization characteristics displayed by optical systems can be divided into two categories: geometrical and physical. Geometrical analysis calculates the change in polarization of a wavefront between pupils in an optical instrument. Physical analysis propagates the polarized fields wherever the geometrical analysis is not valid, i.e., near the edges of stops, near images, in anisotropic media, etc. Polarization aberration theory provides a starting point for geometrical design and facilitates subsequent optimization. The polarization aberrations described arise from differences in the transmitted (or reflected) amplitudes and phases at interfaces. The polarization aberration matrix (PAM) is calculated for isotropic rotationally symmetric systems through fourth order and includes the interface phase, amplitude, linear diattenuation, and linear retardance aberrations. The exponential form of Jones matrices used are discussed. The PAM in Jones matrix is introduced. The exact calculation of polarization aberrations through polarization ray tracing is described. The report is divided into three sections: I. Rotationally Symmetric Optical Systems; II. Tilted and Decentered Optical Systems; and Polarization Analysis of LIDARs.

  15. Atomistic simulation of CO2 solubility in poly(ethylene oxide) oligomers

    NASA Astrophysics Data System (ADS)

    Hong, Bingbing; Panagiotopoulos, Athanassios Z.

    2014-06-01

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henry's constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henry's constant. Dependence of the calculated Henry's constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length.

  16. The atomistic mechanism of carbon nanotube cutting catalyzed by nickel under an electron beam.

    PubMed

    Lebedeva, Irina V; Chamberlain, Thomas W; Popov, Andrey M; Knizhnik, Andrey A; Zoberbier, Thilo; Biskupek, Johannes; Kaiser, Ute; Khlobystov, Andrei N

    2014-12-21

    The cutting of single-walled carbon nanotubes by an 80 keV electron beam catalyzed by nickel clusters is imaged in situ using aberration-corrected high-resolution transmission electron microscopy. Extensive molecular dynamics simulations within the CompuTEM approach provide insight into the mechanism of this process and demonstrate that the combination of irradiation and the nickel catalyst is crucial for the cutting process to take place. The atomistic mechanism of cutting is revealed by a detailed analysis of irradiation-induced reactions of bond reorganization and atom ejection in the vicinity of the nickel cluster, showing a highly complex interplay of different chemical transformations catalysed by the metal cluster. One of the most prevalent pathways includes three consecutive stages: formation of polyyne carbon chains from the carbon nanotube, dissociation of the carbon chains into single and pairs of adatoms adsorbed on the nickel cluster, and ejection of these adatoms leading to the cutting of the nanotube. Significant variations in the atom ejection rate are discovered depending on the process stage and nanotube diameter. The revealed mechanism and kinetic characteristics of the cutting process provide fundamental knowledge for the development of new methodologies for control and manipulation of carbon structures at the nanoscale. PMID:25363681

  17. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    DOE PAGESBeta

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized tomore » compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.« less

  18. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    SciTech Connect

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized to compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.

  19. Atomistic Studies of Cation Transport in Tetragonal ZrO2 During Zirconium Corrosion

    SciTech Connect

    Xian-Ming Bai; Yongfeng Zhang; Michael R. Tonks

    2013-10-01

    Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is one of the major degradation mechanisms of these alloys. During corrosion the transport of oxidizing species in zirconium dioxide (ZrO2) determines the corrosion kinetics. Previously it has been argued that the outward diffusion of cation ions is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO2. The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration barriers of some defect clusters can be much lower than those of point defects. The migration of Zr interstitials at some special grain boundaries is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed.

  20. DL-FIND: an open-source geometry optimizer for atomistic simulations.

    PubMed

    Kästner, Johannes; Carr, Joanne M; Keal, Thomas W; Thiel, Walter; Wander, Adrian; Sherwood, Paul

    2009-10-29

    Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed. PMID:19639948

  1. Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

    NASA Astrophysics Data System (ADS)

    Konuk Onat, Mine; Durukanoglu, Sondan

    2012-02-01

    We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the <100> axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

  2. Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

    NASA Astrophysics Data System (ADS)

    Guin, Laurent; Raphanel, Jean L.; Kysar, Jeffrey W.

    2016-06-01

    Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.

  3. Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

    DOE PAGESBeta

    Bondi, Robert James; Fox, Brian Philip; Marinella, Matthew J.

    2016-03-22

    In this study, first-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influencemore » on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.« less

  4. Atomistic-scale simulations of energetic materials with ReaxFF reactive force fields

    NASA Astrophysics Data System (ADS)

    Goddard, W. A., III; Strachan, A.

    2005-07-01

    Understanding the response of energetic materials to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of million atom systems to capture the complex chemical and mechanical behavior involved: nonequilibrium energy/mass transfer, molecule excitation and decomposition under high strain/heat rates, formation of defects, plastic flow, and phase transitions. To enable such simulations, we developed the ReaxFF reactive force fields based on quantum mechanics (QM) calculations of reactants, products, high-energy intermediates and transition states, but using functional forms suitable for large-scale molecular dynamics simulations of chemical reactions under extreme conditions. We will present an overview of recent progress in ReaxFF developments, including the extension of ReaxFF to new nitramine- based (nitromethane, HMX, PETN, TATB) and peroxide-based (TATP) explosives. To demonstrate the versatility and transferability of ReaxFF, we will present applications to solid composite propellants such as Al/Al2O3-metal nanoparticles embedded into solid explosive matrices (RDX, PETN).

  5. Driving force for crystallization of anionic lipid membranes revealed by atomistic simulations.

    PubMed

    Qiao, Bao Fu; Olvera de la Cruz, Monica

    2013-05-01

    Crystalline vesicles are promising nanomaterials due to their mechanical stability in various environments. To control their fabrication, it is essential to understand the effects of different experimental conditions on crystallization. Here we perform atomistic molecular dynamics simulations of anionic lipid membranes of 1,2-dilauroyl-sn-glycero-3-phosphol-L-serine. In the presence of Na(+) monovalent counterions, we access the phase transition from the liquid-like disordered liquid-crystalline phase to the ordered gel phase by lowering the temperature of the system. The phase transition is conclusively evidenced by the scattering structure factor. Quantitative calculations show that the enhancement of the intertail van der Waals interaction (about -6 k(B)T) plays a dominant role in driving the phase transition rather than the increase in the cohesive interaction (-0.5 k(B)T) between lipids and counterions. Meanwhile, in the presence of multivalent counterions of Zn(2+) or La(3+) the gel phase is found throughout the temperature range investigated. Moreover, the van der Waals interaction per hydrocarbon group is ∼20% stronger in the gel phase (∼ -1.8 k(B)T regardless of the counterions) than in the liquid-crystalline phase (-1.5 k(B)T). PMID:23565965

  6. Finite-temperature elasticity of fcc Al: Atomistic simulations and ultrasonic measurements

    NASA Astrophysics Data System (ADS)

    Pham, Hieu H.; Williams, Michael E.; Mahaffey, Patrick; Radovic, Miladin; Arroyave, Raymundo; Cagin, Tahir

    2011-08-01

    Though not very often, there are some cases in the literature where discrepancies exist in the temperature dependence of elastic constants of materials. A particular example of this case is the behavior of C12 coefficient of a simple metal, aluminum. In this paper we attempt to provide insight into various contributions to temperature dependence in elastic properties by investigating the thermoelastic properties of fcc aluminum as a function of temperature through the use of two computational techniques and experiments. First, ab initio calculations based on density functional theory (DFT) are used in combination with quasiharmonic theory to calculate the elastic constants at finite temperatures through a strain-free energy approach. Molecular dynamics (MD) calculations using tight-binding potentials are then used to extract the elastic constants through a fluctuation-based formalism. Through this dynamic approach, the different contributions (Born, kinetic, and stress fluctuations) to the elastic constants are isolated and the underlying physical basis for the observed thermally induced softening is elucidated. The two approaches are then used to shed light on the relatively large discrepancies in the reported temperature dependence of the elastic constants of fcc aluminum. Finally, the polycrystalline elastic constants (and their temperature dependence) of fcc aluminum are determined using resonant ultrasound spectroscopy (RUS) and compared to previously published data as well as the atomistic calculations performed in this work.

  7. Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

    NASA Astrophysics Data System (ADS)

    Pan, Xiaoliang; Schwartz, Steven

    2015-03-01

    It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

  8. Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting

    PubMed Central

    2011-01-01

    Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear. PMID:22078069

  9. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

    PubMed Central

    Yang, Shengfeng; Chen, Youping

    2015-01-01

    In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

  10. Development and assessment of atomistic models for predicting static friction coefficients

    NASA Astrophysics Data System (ADS)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  11. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    SciTech Connect

    Nomura, K; Seymour, R; Wang, W; Kalia, R; Nakano, A; Vashishta, P; Shimojo, F; Yang, L H

    2009-02-17

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  12. Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

    NASA Astrophysics Data System (ADS)

    Bondi, Robert J.; Fox, Brian P.; Marinella, Matthew J.

    2016-03-01

    First-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influence on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.

  13. Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling.

    PubMed

    Zacharias, Martin

    2013-01-01

    A hybrid coarse-grained (CG) and atomistic (AT) model for protein simulations and rapid searching and refinement of peptide-protein complexes has been developed. In contrast to other hybrid models that typically represent spatially separate parts of a protein by either a CG or an AT force field model, the present approach simultaneously represents the protein by an AT (united atom) and a CG model. The interactions of the protein main chain are described based on the united atom force field allowing a realistic representation of protein secondary structures. In addition, the AT description of all other bonded interactions keeps the protein compatible with a realistic bonded geometry. Nonbonded interactions between side chains and side chains and main chain are calculated at the level of a CG model using a knowledge-based potential. Unrestrained molecular dynamics simulations on several test proteins resulted in trajectories in reasonable agreement with the corresponding experimental structures. Applications to the refinement of docked peptide-protein complexes resulted in improved complex structures. Application to the rapid refinement of docked protein-protein complex is also possible but requires further optimization of force field parameters. PMID:22911567

  14. Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Fernández, M. A.; Sabater, C.; Dednam, W.; Palacios, J. J.; Calvo, M. R.; Untiedt, C.; Caturla, M. J.

    2016-02-01

    The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as "jump to contact" (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.

  15. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized Systems

    NASA Astrophysics Data System (ADS)

    Ho, Phay; Knight, Christopher; Young, Linda; Tegze, Miklos; Faigel, Gyula

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Contract No. DE-AC02-06CH11357.

  16. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  17. Atomistic modeling of phonon bandstructure and transport for optimal thermal management in nanoscale devices

    NASA Astrophysics Data System (ADS)

    Sundaresan, Sasi Sekaran

    Monte Carlo based statistical approach to solve Boltzmann Transport Equation (BTE) has become a norm to investigate heat transport in semiconductors at sub-micron regime, owing mainly to its ability to characterize realistically sized device geometries qualitatively. One of the primary issues with this technique is that the approach predominantly uses empirically fitted phonon dispersion relations as input to determine the properties of phonons so as to predict the thermal conductivity of specified material geometry. The empirically fitted dispersion relations assume harmonic approximation thereby failing to account for thermal expansion, interaction of lattice waves, effect of strain on spring stiffness, and accurate phonon-phonon interaction. To circumvent this problem, in this work, a coupled molecular mechanics-Monte Carlo (MM-MC) platform has been developed and used to solve the phonon Boltzmann Transport Equation (BTE) for the calculation of thermal conductivity of several novel and emerging nanostructures. The use of the quasi-anharmonic MM approach (as implemented in the open source NEMO 3-D software toolkit) not only allows one to capture the true atomicity of the underlying lattice but also enables the simulation of realistically-sized structures containing millions of atoms. As compared to the approach using an empirically fitted phonon dispersion relation, here, a 17% increase in the thermal conductivity for a silicon nanowire due to the incorporation of atomistic corrections in the LA (longitudinal acoustic) branch alone has been reported. The atomistically derived thermal conductivity as calculated from the MM-MC framework is then used in the modular design and analysis of (i) a silicon nanowire based thermoelectric cooler (TEC) unit, and (ii) a GaN/InN based nanostructured light emitting device (LED). It is demonstrated that the use of empirically fitted phonon bandstructure parameters overestimates the temperature difference between the hot and the

  18. Ultracold polar KRb molecules

    NASA Astrophysics Data System (ADS)

    Neyenhuis, Brian; Chotia, Amodsen; Moses, Steven; Ye, Jun; Jin, Deborah

    2011-05-01

    Ultracold polar molecules in the quantum degenerate regime open the possibility of realizing quantum gases with long-range, and spatially anisotropic, interparticle interactions. Currently, we can create a gas of ultracold fermionic ground-state KRb molecules in with a peak density of 1012 cm-3 and a temperature just 1.4 times the Fermi temperature. We will report on efforts to further cool this gas of molecules. One possibility is to evaporatively cool a spin-polarized molecular Fermi gas confined in quasi-2D, where we would rely on dipole-dipole interactions for rethermalization. We acknowledge funding from NIST, NSF, and AFOSR-MURI.

  19. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    NASA Technical Reports Server (NTRS)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; Biegel, Bryan (Technical Monitor)

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  20. Atomistic-continuum coupling for solid mechanics enforcing momentum balance and continuity

    NASA Astrophysics Data System (ADS)

    Kraczek, B.; Johnson, D. D.; Xia, C.; Haber, R. B.

    2004-03-01

    We investigate an atomistic-continuum coupling strategy for solid mechanics based on the theoretical framework of Spacetime Discontinuous Galerkin (SDG) finite element methods. SDG methods weakly enforce momentum balance and continuity over computational cells that directly discretize a spacetime analysis domain. The explicit incorporation of spacetime momentum flux within this formulation supports a straightforward exchange of stress and force between the continuum and atomistic regions with no ad hoc coupling assumptions. We employ a simple MD model for the atomistics and only consider problems in 1d øtimes time. However, this coupling strategy should be applicable to other O(N) atomistic methods and extensible to higher spatial dimensions. We focus on the effects of continuum basis truncation and unresolved length-scales in the present investigation.

  1. Tracking Microstructure of Crystalline Materials: A Post-Processing Algorithm for Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Panzarino, Jason F.; Rupert, Timothy J.

    2014-03-01

    Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. To understand the fundamental principles that govern material behavior at the atomic scale and directly connect to experimental works, it is necessary to quantify the microstructure of materials simulated with atomistics. Specifically, quantitative tools for identifying crystallites, their crystallographic orientation, and overall sample texture do not currently exist. Here, we develop a post-processing algorithm capable of characterizing such features, while also documenting their evolution during a simulation. In addition, the data is presented in a way that parallels the visualization methods used in traditional experimental techniques. The utility of this algorithm is illustrated by analyzing several types of simulation cells that are commonly found in the atomistic modeling literature but could also be applied to a variety of other atomistic studies that require precise identification and tracking of microstructure.

  2. Polar Bear

    USGS Publications Warehouse

    Amstrup, S.D.; DeMaster

    1988-01-01

    Polar bears are long-lived, late-maturing carnivores that have relatively low rates of reproduction and natural mortality. Their populations are susceptible to disturbance from human activities, such as the exploration and development of mineral resources or hunting. Polar bear populations have been an important renewable resource available to coastal communities throughout the Arctic for thousands of years.

  3. Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning 13C nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose

    NASA Astrophysics Data System (ADS)

    Lefort, Ronan; Bordat, Patrice; Cesaro, Attilio; Descamps, Marc

    2007-01-01

    This paper uses chemical shift surfaces to simulate experimental C13 cross polarization magic angle spinning spectra for amorphous solid state disaccharides, paying particular attention to the glycosidic linkage atoms in trehalose, sucrose, and lactose. The combination of molecular mechanics with density functional theory/gauge invariant atomic orbital ab initio methods provides reliable structural information on the conformational distribution in the glass. The results are interpreted in terms of an enhanced flexibility that trehalose possesses in the amorphous solid state, at least on the time scale of C13 nuclear magnetic resonance measurements. Implications of these findings for the fragility of trehalose glass and bioprotectant action are discussed.

  4. Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

    PubMed Central

    Komarov, Pavel V; Khokhlov, Alexei R

    2013-01-01

    Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

  5. Polarization control at spin-driven ferroelectric domain walls

    NASA Astrophysics Data System (ADS)

    Leo, Naëmi; Bergman, Anders; Cano, Andres; Poudel, Narayan; Lorenz, Bernd; Fiebig, Manfred; Meier, Dennis

    2015-04-01

    Unusual electronic states arise at ferroelectric domain walls due to the local symmetry reduction, strain gradients and electrostatics. This particularly applies to improper ferroelectrics, where the polarization is induced by a structural or magnetic order parameter. Because of the subordinate nature of the polarization, the rigid mechanical and electrostatic boundary conditions that constrain domain walls in proper ferroics are lifted. Here we show that spin-driven ferroelectricity promotes the emergence of charged domain walls. This provides new degrees of flexibility for controlling domain-wall charges in a deterministic and reversible process. We create and position a domain wall by an electric field in Mn0.95Co0.05WO4. With a magnetic field we then rotate the polarization and convert neutral into charged domain walls, while its magnetic properties peg the wall to its location. Using atomistic Landau-Lifshitz-Gilbert simulations we quantify the polarization changes across the two wall types and highlight their general occurrence.

  6. Polarized rainbow.

    PubMed

    Können, G P; de Boer, J H

    1979-06-15

    The Airy theory of the rainbow is extended to polarized light. For both polarization directions a simple analytic expression is obtained for the intensity distribution as a function of the scattering angle in terms of the Airy function and its derivative. This approach is valid at least down to droplet diameters of 0.3 mm in visible light. The degree of polarization of the rainbow is less than expected from geometrical optics; it increases with droplet size. For a droplet diameter >1 mm the locations of the supernumerary rainbows are equal for both polarization directions, but for a diameter <1 mm the supernumerary rainbows of the weaker polarization component are located between those in the strong component. PMID:20212586

  7. Nanosculpt: A methodology for generating complex realistic configurations for atomistic simulations

    PubMed Central

    Prakash, A.; Hummel, M.; Schmauder, S.; Bitzek, E.

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nanosculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data. PMID:27054098

  8. Nano sculpt: A methodology for generating complex realistic configurations for atomistic simulations.

    PubMed

    Prakash, A; Hummel, M; Schmauder, S; Bitzek, E

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data. PMID:27054098

  9. Atomistic Models of General Anesthetics for Use in in Silico Biological Studies

    PubMed Central

    2015-01-01

    While small molecules have been used to induce anesthesia in a clinical setting for well over a century, a detailed understanding of the molecular mechanism remains elusive. In this study, we utilize ab initio calculations to develop a novel set of CHARMM-compatible parameters for the ubiquitous modern anesthetics desflurane, isoflurane, sevoflurane, and propofol for use in molecular dynamics (MD) simulations. The parameters generated were rigorously tested against known experimental physicochemical properties including dipole moment, density, enthalpy of vaporization, and free energy of solvation. In all cases, the anesthetic parameters were able to reproduce experimental measurements, signifying the robustness and accuracy of the atomistic models developed. The models were then used to study the interaction of anesthetics with the membrane. Calculation of the potential of mean force for inserting the molecules into a POPC bilayer revealed a distinct energetic minimum of 4–5 kcal/mol relative to aqueous solution at the level of the glycerol backbone in the membrane. The location of this minimum within the membrane suggests that anesthetics partition to the membrane prior to binding their ion channel targets, giving context to the Meyer–Overton correlation. Moreover, MD simulations of these drugs in the membrane give rise to computed membrane structural parameters, including atomic distribution, deuterium order parameters, dipole potential, and lateral stress profile, that indicate partitioning of anesthetics into the membrane at the concentration range studied here, which does not appear to perturb the structural integrity of the lipid bilayer. These results signify that an indirect, membrane-mediated mechanism of channel modulation is unlikely. PMID:25303275

  10. Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment.

    PubMed

    Eastwood, Michael P; Chitra, Tarun; Jumper, John M; Palmo, Kim; Pan, Albert C; Shaw, David E

    2013-10-24

    Understanding the nature of the glass transition--the dramatic slowing of dynamics and eventual emergence of a disordered solid from a cooling liquid--is a fundamental challenge in physical science. A central characteristic of glass-forming liquids is a non-exponential main relaxation process. The extent of deviation from exponential relaxation typically becomes more pronounced on cooling. Theories that predict a growth of spatially heterogeneous dynamics as temperature is lowered can explain these observations. In apparent contradiction to these theories, however, some experiments suggest that certain substances--notably including the intensely studied molecular glass-former ortho-terphenyl (OTP)--have a main relaxation process whose shape is essentially temperature independent, even though other observables predicted to be correlated with the degree of dynamical heterogeneity are temperature dependent. Here we report the first simulations based on an atomistic model of OTP that reach equilibrium at temperatures well into the supercooled regime. We first show that the results of these simulations are in reasonable quantitative agreement with experimental data for several basic properties over a wide range of temperatures. We then focus on rotational relaxation, finding nearly exponential behavior at high temperatures with clearly increasing deviations as temperature is lowered. The much weaker temperature dependence observed in light-scattering experiments also emerges from the same simulation data when we calculate correlation functions similar to those probed experimentally; this highlights the diversity of temperature dependencies that can be obtained with different probes. Further analysis suggests that the temperature insensitivity observed in the light-scattering experiments stems from the dependence of these measurements on internal as well as rotational molecular motion. Within the temperature range of our OTP simulations, our results strongly suggest that

  11. Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations

    NASA Astrophysics Data System (ADS)

    Agrawal, Anupriya

    Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.

  12. Polar Glaciology

    NASA Technical Reports Server (NTRS)

    Robin, G. D.

    1984-01-01

    Two fields of research on polar ice sheets are likely to be of dominant interest during the 1990s. These are: the role of polar ice sheets in the hydrological cycle ocean-atmosphere-ice sheets-oceans, especially in relation to climate change; and the study and interpretation of material in deep ice cores to provide improved knowledge of past climates and of the varying levels of atmospheric constituents such as CO2, NOx, SO2, aerosols, etc., over the past 200,000 years. Both topics require a better knowledge of ice dynamics. Many of the studies that should be undertaken in polar regions by Earth Observing System require similar instruments and techniques to those used elsewhere over oceans and inland surfaces. However to study polar regions two special requirements need to be met: Earth Observing System satellite(s) need to be in a sufficiently high inclination orbit to cover most of the polar regions. Instruments must also be adapted, often by relatively limited changes, to give satisfactory data over polar ice. The observational requirements for polar ice sheets in the 1990s are summarized.

  13. Atomistic modeling of electronic structure and transport in disordered nanostructures

    NASA Astrophysics Data System (ADS)

    Kharche, Neerav

    As the Si-CMOS technology approaches the end of the International Technology Roadmap for Semiconductors (ITRS), the semiconductor industry faces a formidable challenge to continue the transistor scaling according to Moore's law. To continue the scaling of classical devices, alternative channel materials such as SiGe, carbon nanotubes, nanowires, and III-V based materials are being investigated along with novel 3D device geometries. Researchers are also investigating radically new quantum computing devices, which are expected to perform calculations faster than the existing classical Si-CMOS based structures. Atomic scale disorders such as interface roughness, alloy randomness, non-uniform strain, and dopant fluctuations are routinely present in the experimental realization of such devices. These disorders now play an increasingly important role in determining the electronic structure and transport properties as device sizes enter the nanometer regime. This work employs the atomistic tight-binding technique, which is ideally suited for modeling systems with local disorders on an atomic scale. High-precision multi-million atom electronic structure calculations of (111) Si surface quantum wells and (100) SiGe/Si/SiGe heterostructure quantum wells are performed to investigate the modulation of valley splitting induced by atomic scale disorders. The calculations presented here resolve the existing discrepancies between theoretically predicted and experimentally measured valley splitting, which is an important design parameter in quantum computing devices. Supercell calculations and the zone-unfolding method are used to compute the bandstructures of inhomogeneous nanowires made of AlGaAs and SiGe and their connection with the transmission coefficients computed using non-equilibrium Green's function method is established. A unified picture of alloy nanowires emerges, in which the nanodevice (transmission) and nanomaterials (bandstructure) viewpoints complement each other

  14. Pure AlN layers in metal-polar AlGaN/AlN/GaN and AlN/GaN heterostructures grown by low-temperature ammonia-based molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Kaun, Stephen W.; Mazumder, Baishakhi; Fireman, Micha N.; Kyle, Erin C. H.; Mishra, Umesh K.; Speck, James S.

    2015-05-01

    When grown at a high temperature (820 °C) by ammonia-based molecular beam epitaxy (NH3-MBE), the AlN layers of metal-polar AlGaN/AlN/GaN heterostructures had a high GaN mole fraction (∼0.15), as identified by atom probe tomography in a previous study (Mazumder et al 2013 Appl. Phys. Lett. 102 111603). In the study presented here, growth at low temperature (<740 °C) by NH3-MBE yielded metal-polar AlN layers that were essentially pure at the alloy level. The improved purity of the AlN layers grown at low temperature was correlated to a dramatic increase in the sheet density of the two-dimensional electron gas (2DEG) at the AlN/GaN heterointerface. Through application of an In surfactant, metal-polar AlN(3.5 nm)/GaN and AlGaN/AlN(2.5 nm)/GaN heterostructures grown at low temperature yielded low 2DEG sheet resistances of 177 and 285 Ω/□, respectively.

  15. The non-uniqueness of the atomistic stress tensor and its relationship to the generalized Beltrami representation

    NASA Astrophysics Data System (ADS)

    Admal, Nikhil Chandra; Tadmor, E. B.

    2016-08-01

    The non-uniqueness of the atomistic stress tensor is a well-known issue when defining continuum fields for atomistic systems. In this paper, we study the non-uniqueness of the atomistic stress tensor stemming from the non-uniqueness of the potential energy representation. In particular, we show using rigidity theory that the distribution associated with the potential part of the atomistic stress tensor can be decomposed into an irrotational part that is independent of the potential energy representation, and a traction-free solenoidal part. Therefore, we have identified for the atomistic stress tensor a discrete analog of the continuum generalized Beltrami representation (a version of the vector Helmholtz decomposition for symmetric tensors). We demonstrate the validity of these analogies using a numerical test. A program for performing the decomposition of the atomistic stress tensor called MDStressLab is available online at

  16. Development and evaluation of supercritical fluid chromatography/mass spectrometry for polar and high-molecular-weight coal components: Technical progress report for the period October 1, 1985 - September 30, 1986

    SciTech Connect

    Chess, E.K.; Kalinoski, H.T.; Wright, B.W.; Smith, R.D.

    1987-02-01

    Technical progress toward the programmatic goals of developing and evaluating SFC/MS for the analysis of higher-molecular-weight compounds was made in the following areas: Studies have been conducted to characterize the requirements for and to facilitate the transfer of thermal energy to the capillary flow restrictor region. Such studies have resulted in a new interface probe design which allows better transport of higher molecular weight, less volatile compounds decreasing the mass discrimination at the supercritical fluid chromatograph mass spectrometer interface region. Calibration of the magnetic sector mass spectrometer to 1400 daltons has been developed. A digital syringe pump controller, interfaced to an Apple IIe computer allows much finer and more reproducible control of the pressure (density) of the supercritical fluid mobile phase. Nonpolar supercritical fluid mobile phases have been modified by the addition of small amounts of polar fluids to create fluids with higher solvating powers than, but with similar operating parameters. An in-depth knowledge of the fluid behavior is required for successful utilization of these modified fluids. Polar-modified fluids have been used with three types of supercritical fluid introduction to the mass spectrometer: direct fluid injection, supercritical fluid chromatography, and supercritical fluid extraction. Capillary columns evaluated for stability indicated that our present methods for preparing columns are sufficient, for many of the stationary phase and supercritical fluid combinations tested, to create columns that can be used successfully with supercritical fluid chromatography. 9 refs., 11 figs.

  17. Polarizing cues.

    PubMed

    Nicholson, Stephen P

    2012-01-01

    People categorize themselves and others, creating ingroup and outgroup distinctions. In American politics, parties constitute the in- and outgroups, and party leaders hold sway in articulating party positions. A party leader's endorsement of a policy can be persuasive, inducing co-partisans to take the same position. In contrast, a party leader's endorsement may polarize opinion, inducing out-party identifiers to take a contrary position. Using survey experiments from the 2008 presidential election, I examine whether in- and out-party candidate cues—John McCain and Barack Obama—affected partisan opinion. The results indicate that in-party leader cues do not persuade but that out-party leader cues polarize. This finding holds in an experiment featuring President Bush in which his endorsement did not persuade Republicans but it polarized Democrats. Lastly, I compare the effect of party leader cues to party label cues. The results suggest that politicians, not parties, function as polarizing cues. PMID:22400143

  18. Polar motion

    NASA Technical Reports Server (NTRS)

    Kolenkiewicz, R.

    1973-01-01

    Tracking of the Beacon Explorer-C satellite by a precision laser system was used to measure the polar motion and solid earth tide. The tidal perturbation of satellite latitude is plotted as variation in maximum latitude in seconds of arc on earth's surface as a function of the date, and polar motion is shown by plotting the variation in latitude of the laser in seconds of arc along the earth's surface as a function of date

  19. Polarization of Starlight

    NASA Astrophysics Data System (ADS)

    Whittet, D. C. B.

    The polarization of starlight is universally attributed to directional extinction arising when dust grains along the line of sight are aligned in the presence of a magnetic field. This phenomenon provides a powerful tool for studying the optical properties of the dust (size, shape, refractive index) and for charting the galactic magnetic field. Current observational constraints at all wavelengths are consistent with a picture in which only the larger grains in the size range responsible for extinction are efficient polarizers. Small grains are much less well aligned and/or more isotropic in shape than large grains. The polarizing grains include silicates, but it is not clear whether they contain appreciable quantities of carbon. The degree of alignment is highly sensitive to ambient physical conditions as well as to particle size. The polarization efficiency per unit extinction declines with increasing density within dark clouds, hindering attempts to map the intracloud magnetic field. However, spectropolarimetric studies of interstellar ice absorption features seen in deeply embedded YSOs indicate that mantled grains within dense molecular clouds can be surprisingly efficient polarizers, suggesting that a qualitatively different alignment mechanism is operating compared with diffuse regions of the ISM. This talk will present a brief overview of key observations and their interpretation, highlight areas of uncertainty, and suggest avenues of future research. The physics of grain alignment is reviewed elsewhere in this meeting (see paper by Roberge).

  20. AtomEye: an efficient atomistic configuration viewer

    NASA Astrophysics Data System (ADS)

    Li, Ju

    2003-03-01

    AtomEye is free atomistic visualization software for all major UNIX platforms. It is based on a newly developed graphics core library of higher quality than the X-window standard, with area-weighted anti-aliasing. An order-N neighbourlist algorithm is used to compute the bond connectivity. The functionalities of AtomEye include: parallel and perspective projections with full three-dimensional navigation; customizable bond and coordination number calculation; colour-encoding of arbitrary user-defined quantities; local atomic strain invariant; coloured atom tiling and tracing; up to 16 cutting planes; periodic boundary condition translations; high-quality JPEG, PNG and EPS screenshots; and animation scripting. The program is efficient compared to OpenGL hardware acceleration by employing special algorithms to treat spheres (atoms) and cylinders (bonds), in which they are rendered as primitive objects rather than as composites of polygons. AtomEye can handle more than one million atoms on a PC with 1 GB memory. It is a robust, low-cost tool for surveying nanostructures and following their evolutions.