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Sample records for polarized atomistic molecular

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    PubMed

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

  17. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    PubMed

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems. PMID:24554590

  18. Atomistic molecular-dynamics simulations of the size and shape of polyethylene in hexane at infinite dilution

    NASA Astrophysics Data System (ADS)

    Zifferer, Gerhard; Kornherr, Andreas

    2005-05-01

    Parameters characteristic of size and shape of single polyethylene chains consisting of 15-60 monomer units dissolved in hexane are calculated by use of molecular-dynamics simulations based on a fully atomistic representation of the system. Results are compared with corresponding calculations in vacuum as well as Monte Carlo simulations of coarse-grained chains. The major concern of the study is a careful check of actual limits and possibilities of atomistic simulations of global properties of polymers. As expected such simulations are still restricted to rather small chain lengths but are already large enough to obey the characteristics of polymer coils.

  19. Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation

    SciTech Connect

    Dumpala, Santoshrupa; Broderick, Scott R.; Rajan, Krishna; Khalilov, Umedjon; Neyts, Erik C.; Duin, Adri C. T. van; Provine, J; Howe, Roger T.

    2015-01-05

    In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO{sub 2} and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Molecular organization in freely suspended nano-thick 8CB smectic films. An atomistic simulation.

    PubMed

    Palermo, Mattia Felice; Muccioli, Luca; Zannoni, Claudio

    2015-10-21

    We present an atomistic molecular dynamics simulation of freely suspended films of the smectic liquid crystal 8CB formed by nl = 2, 3,…,10, 20 theoretical monolayers, determining their orientational and positional order as a function of the film thickness. We find that films are always composed by bilayers of antiparallel molecules, and that in the case of odd nl, the system prefers to self-assemble in (nl + 1)/2 bilayers, with an increase of surface tension with respect to even nl samples. We also show that external layers have higher positional and orientational order, and that upon heating the disordering of the system proceeds from the inside, with the central layers progressively losing their smectic character, while the external ones are more resistant to temperature changes and keep the film from breaking.

  5. 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

  6. 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

  7. 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

  8. 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

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

    PubMed

    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.

  10. 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.

  11. Defect-mediated polarization switching in ferroelectrics and related materials: from mesoscopic mechanisms to atomistic control.

    PubMed

    Kalinin, Sergei V; Rodriguez, Brian J; Borisevich, Albina Y; Baddorf, Arthur P; Balke, Nina; Chang, Hye Jung; Chen, Long-Qing; Choudhury, Samrat; Jesse, Stephen; Maksymovych, Peter; Nikiforov, Maxim P; Pennycook, Stephen J

    2010-01-19

    The plethora of lattice and electronic behaviors in ferroelectric and multiferroic materials and heterostructures opens vistas into novel physical phenomena including magnetoelectric coupling and ferroelectric tunneling. The development of new classes of electronic, energy-storage, and information-technology devices depends critically on understanding and controlling field-induced polarization switching. Polarization reversal is controlled by defects that determine activation energy, critical switching bias, and the selection between thermodynamically equivalent polarization states in multiaxial ferroelectrics. Understanding and controlling defect functionality in ferroelectric materials is as critical to the future of oxide electronics and solid-state electrochemistry as defects in semiconductors are for semiconductor electronics. Here, recent advances in understanding the defect-mediated switching mechanisms, enabled by recent advances in electron and scanning probe microscopy, are discussed. The synergy between local probes and structural methods offers a pathway to decipher deterministic polarization switching mechanisms on the level of a single atomically defined defect.

  12. Molecular dynamics simulation of oleic acid/oleate bilayers: an atomistic model for a ufasome membrane.

    PubMed

    Han, Sanghwa

    2013-01-01

    When oleic acid and oleate coexist in comparable amounts they form unilamellar vesicles called ufasomes in aqueous phase. Intrinsic pH sensitivity of ufasomes makes it an attractive vehicle for drug delivery. Physical properties of ufasomes have been studied by using spectroscopic techniques but an atomistic model for a ufasome has not been proposed. In this study molecular dynamics simulation was performed on oleic acid/oleate bilayers with the oleate concentration varying from 40 to 70 mol%. All the bilayers reached an equilibrium and stayed stable during a 40 ns simulation. Area per lipid increased with mol% of oleate probably due to charge repulsion between anionic oleate molecules. Oleate was pulled out toward the aqueous phase so that the carboxyl groups of oleic acid and oleate were separated by 0.392 nm in the bilayer of oleic acid/oleate 1:1. Water concentration at the depth of carboxyl group of oleate was five times as high as that of oleic acid. Number of hydrogen bonds between oleic acid and oleate was small in contrast to a proposal that it is an important factor for the bilayer stability. However there was an extensive array of hydrogen bonds between the lipids and water molecules. Acyl chain order was within a normal range for a lipid bilayer but lateral diffusion was an order of magnitude faster in oleic acid/oleate bilayer than in dioleoylphosphatidylcholine bilayer. Cholesterol increased the bilayer thickness and order parameter and decreased the rate of lateral diffusion.

  13. Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations

    PubMed Central

    Delemotte, Lucie; Tarek, Mounir; Klein, Michael L.; Amaral, Cristiano; Treptow, Werner

    2011-01-01

    The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10–15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F233. Analysis indicates that the local electric field within the VSD is focused near the F233 residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments. PMID:21444776

  14. 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

  15. 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

  16. CONDENSED MATTER: STRUCTURE, THERMAL AND MECHANICAL PROPERTIES: Rotational viscosity of a liquid crystal mixture: a fully atomistic molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Zhang, Ran; Peng, Zeng-Hui; Liu, Yong-Gang; Zheng, Zhi-Gang; Xuan, Li

    2009-10-01

    Fully atomistic molecular dynamics (MD) simulations at 293, 303 and 313 K have been performed for the four-component liquid crystal mixture, E7, using the software package Material Studio. Order parameters and orientational time correlation functions (TCFs) were calculated from MD trajectories. The rotational viscosity coefficients (RVCs) of the mixture were calculated using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. Temperature dependences of RVC and density were discussed in detail. Reasonable agreement between the simulated and experimental values was found.

  17. 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.

  18. 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

  19. 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

  20. Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

    PubMed

    Tvaroška, Igor

    2015-02-11

    Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. First order melting transitions of highly ordered dipalmitoyl phosphatidylcholine gel phase membranes in molecular dynamics simulations with atomistic detail

    NASA Astrophysics Data System (ADS)

    Schubert, Thomas; Schneck, Emanuel; Tanaka, Motomu

    2011-08-01

    Molecular dynamics simulations with atomistic detail of the gel phase and melting transitions of dipalmitoyl phosphatidylcholine bilayers in water reveal the dependency of many thermodynamic and structural parameters on the initial system ordering. We quantitatively compare different methods to create a gel phase system and we observe that a very high ordering of the gel phase starting system is necessary to observe behavior which reproduces experimental data. We performed heating scans with speeds down to 0.5 K/ns and could observe sharp first order phase transitions. Also, we investigated the transition enthalpy as the natural intrinsic parameter of first order phase transitions, and obtained a quantitative match with experimental values. Furthermore, we performed systematic investigations of the statistical distribution and heating rate dependency of the microscopic phase transition temperature.

  6. Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations.

    PubMed

    Vargiu, Attilio V; Magistrato, Alessandra

    2014-09-01

    Simulation techniques play an ever increasing role in drug design by providing an atomistic view of the pathways of drugs to their target sites, thus revealing the determinants behind molecular recognition and binding, pinpointing local and allosteric conformational changes of both drugs and receptors, and unveiling key chemical mechanisms in enzymatic-like processes. In particular, molecular dynamics simulations, relying on a force field, quantum mechanical, or hybrid description of the system, have been largely employed to unveil mechanistic, kinetic, and thermodynamic aspects of the binding of anticancer drugs to DNA, ultimately contributing to a better understanding of their mechanism of action. Herein we review recent literature, focusing on selected examples from our work, to show how modern computer simulations can be applied to study the mechanism of action of antitumor drugs such as platinum compounds, organic antibiotics, and metal-based octahedral complexes, which are archetypal examples of the most common classes of DNA binding molecules. We discuss the strengths and limitations of in silico studies in this field, as well as current and future challenges.

  7. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

    PubMed

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  8. 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.

  9. 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}.

  10. 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.

  11. 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

  12. 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.

  13. Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena.

    PubMed

    Prasad, Manish; Sinno, Talid

    2004-11-01

    An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.

  14. 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.

  15. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

    PubMed Central

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R.; Shalashilin, Dmitrii V.

    2014-01-01

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely. PMID:24982247

  16. 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

  17. 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

  18. 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

  19. 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

  20. Atomistic molecular dynamics simulations of H2O diffusivity in liquid and supercritical CO2

    NASA Astrophysics Data System (ADS)

    Moultos, Othonas A.; Orozco, Gustavo A.; Tsimpanogiannis, Ioannis N.; Panagiotopoulos, Athanassios Z.; Economou, Ioannis G.

    2015-09-01

    Molecular dynamics simulations were employed for the calculation of diffusion coefficients of pure CO2 and of H2O in CO2 over a wide range of temperatures (298.15 K < T < 523.15 K) and pressures (5.0 MPa < P < 100.0 MPa), that are of interest to CO2 capture-and-sequestration processes. Various combinations of existing fixed-point-charge force-fields for H2O (TIP4P/2005 and Exponential-6) and CO2 (elementary physical model 2 [EPM2], transferable potentials for phase equilibria [TraPPE], and Exponential-6) were tested. All force-field combinations qualitatively reproduce the trends of the experimental data for infinitely diluted H2O in CO2; however, TIP4P/2005-EPM2, TIP4P/2005-TraPPE and Exponential-6-Exponential-6 were found to be the most consistent. Additionally, for H2O compositions ranging from infinite dilution to ?, the Maxwell-Stefan diffusion coefficient is shown to have a weak non-linear composition dependence.

  1. 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

  2. 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.

  3. Effect of polar surfaces on decomposition of molecular materials.

    PubMed

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

    2014-09-24

    We report polar instability in molecular materials. Polarization-induced explosive decomposition in molecular crystals is explored with an illustrative example of two crystalline polymorphs of HMX, an important energetic material. We establish that the presence of a polar surface in δ-HMX has fundamental implications for material stability and overall chemical behavior. A comparative quantum-chemical analysis of major decomposition mechanisms in polar δ-HMX and nonpolar β-HMX discovered a dramatic difference in dominating dissociation reactions, activation barriers, and reaction rates. The presence of charge on the polar δ-HMX surface alters chemical mechanisms and effectively triggers decomposition simultaneously through several channels with significantly reduced activation barriers. This results in much faster decomposition chemistry and in higher chemical reactivity of δ-HMX phase relatively to β-HMX phase. We predict decomposition mechanisms and their activation barriers in condensed δ-HMX phase, sensitivity of which happens to be comparable to primary explosives. We suggest that the observed trend among polymorphs is a manifestation of polar instability phenomena, and hence similar processes are likely to take place in all polar molecular crystals.

  4. Effect of polar surfaces on decomposition of molecular materials.

    PubMed

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

    2014-09-24

    We report polar instability in molecular materials. Polarization-induced explosive decomposition in molecular crystals is explored with an illustrative example of two crystalline polymorphs of HMX, an important energetic material. We establish that the presence of a polar surface in δ-HMX has fundamental implications for material stability and overall chemical behavior. A comparative quantum-chemical analysis of major decomposition mechanisms in polar δ-HMX and nonpolar β-HMX discovered a dramatic difference in dominating dissociation reactions, activation barriers, and reaction rates. The presence of charge on the polar δ-HMX surface alters chemical mechanisms and effectively triggers decomposition simultaneously through several channels with significantly reduced activation barriers. This results in much faster decomposition chemistry and in higher chemical reactivity of δ-HMX phase relatively to β-HMX phase. We predict decomposition mechanisms and their activation barriers in condensed δ-HMX phase, sensitivity of which happens to be comparable to primary explosives. We suggest that the observed trend among polymorphs is a manifestation of polar instability phenomena, and hence similar processes are likely to take place in all polar molecular crystals. PMID:25170566

  5. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    PubMed

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  6. 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

  7. Extending classical molecular theory with polarization.

    PubMed

    Keyes, Tom; Napoleon, Raeanne L

    2011-01-27

    A classical, polarizable, electrostatic theory of short-ranged atom-atom interactions, incorporating the smeared nature of atomic partial charges, is presented. Detailed models are constructed for CO monomer and for CO interacting with an iron atom, as a first step toward heme proteins. A good representation is obtained of the bond-length-dependent dipole of CO monomer from fitting at the equilibrium distance only. Essential features of the binding of CO to myoglobin (Mb) and model heme compounds, including the binding energy, the position of the minimum in the Fe-C potential, the Fe-C frequency, the bending energy, the linear geometry of FeCO, and the increase of the Stark tuning rate and IR intensity, are obtained, suggesting that a substantial part of the Fe-CO interaction consists of a classical, noncovalent, "electrostatic bond ". The binding energy is primarily polarization energy, and the polarization energy of an OH pair in water is shown to be comparable to the experimental hydrogen bond energy.

  8. A Long-Range Electric Field Solver for Molecular Dynamics of Fluid-Solid Interfaces Based on Atomistic-to-Continuum Modeling

    NASA Astrophysics Data System (ADS)

    Templeton, Jeremy; Jones, Reese; Zimmerman, Jonathan; Wong, Bryan; 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 anistropic 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.

  9. A mesoscale strength model for silica-filled polydimethylsiloxane based on atomistic forces obtained from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hanson, D. E.

    2000-11-01

    We present a novel mesoscale model that describes the tensile stress of silica-filled polydimethylsiloxane (PDMS) under elongation. The model is based on atomistic simulations of a single chain of PDMS, interacting with itself and/or a hydroxylated silica surface. These simulations provide estimates of the microscopic forces required to stretch or uncoil a chain of PDMS, or detach it from a silica surface. For both stretching and detachment, we find that the internal potential energy is linear with the distance the chain end is moved, albeit with differing slopes. From these calculations and recent atomic force microscopy (AFM) experiments, we conclude that the forces are constant. We apply this analysis to the case of uncrosslinked, silica-filled PDMS systems and develop a mesoscale, inter-particle strength model. The strength model includes the atomistic forces determined from the simulations, a small entropic component, and a Gaussian probability distribution to describe the distribution of chain lengths of PDMS strands connecting two silica particles and the chain lengths in the free ends. We obtain an analytic stress/strain expression whose predictions agree with experiment. This model also suggests mechanisms to explain the phenomena of hysteresis and permanent set.

  10. 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.

  11. 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.

  12. 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

  13. The molecular basis of mechanisms underlying polarization vision

    PubMed Central

    Roberts, Nicholas W.; Porter, Megan L.; Cronin, Thomas W.

    2011-01-01

    The underlying mechanisms of polarization sensitivity (PS) have long remained elusive. For rhabdomeric photoreceptors, questions remain over the high levels of PS measured experimentally. In ciliary photoreceptors, and specifically cones, little direct evidence supports any type of mechanism. In order to promote a greater interest in these fundamental aspects of polarization vision, we examined a varied collection of studies linking membrane biochemistry, protein–protein interactions, molecular ordering and membrane phase behaviour. While initially these studies may seem unrelated to polarization vision, a common narrative emerges. A surprising amount of evidence exists demonstrating the importance of protein–protein interactions in both rhabdomeric and ciliary photoreceptors, indicating the possible long-range ordering of the opsin protein for increased PS. Moreover, we extend this direction by considering how such protein paracrystalline organization arises in all cell types from controlled membrane phase behaviour and propose a universal pathway for PS to occur in both rhabdomeric and cone photoreceptors. PMID:21282166

  14. 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.

  15. Polarizing properties of molecular ensembles: new approaches to calculations

    NASA Astrophysics Data System (ADS)

    Bokarev, Andrey N.; Plastun, Inna L.

    2016-04-01

    Polarizing properties of molecular ensembles with different structures are investigated by numerical simulation. Carbon nanotubes with zigzag configuration and nucleobases are considered. By numerical simulation total polarizability is investigated for different structures of molecules ensembles. New semi-analytical procedure for calculation of total polarizability for ensembles with different configuration is offered and tested by its application to ensembles which contain single-wall carbon nanotubes and nucleobases.

  16. Phase separation in H2O:N2 mixture - molecular dynamics simulations using atomistic force fields

    SciTech Connect

    Maiti, A; Gee, R; Bastea, S; Fried, L

    2006-09-25

    A class II atomistic force field with Lennard-Jones 6-9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N{sub 2} and H{sub 2}O in the temperature range 700-2500 K and pressure range 0.1-10 GPa. A standard 6th order parameter-mixing scheme is then employed to study a 2:1 (molar) H{sub 2}O:N{sub 2} mixture, to investigate in particular the possibility of phase-separation under detonation conditions. The simulations demonstrate several important results, including: (1) the accuracy of computed EOS for both N{sub 2} and H{sub 2}O over the entire range of temperature and pressure considered; (2) accurate mixing-demixing phase boundary as compared to experimental data; and (3) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models.

  17. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    PubMed

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

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

    PubMed

    Chen, Shuang; Zeng, Xiao Cheng

    2014-04-30

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

  19. 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

  20. Polar solvation dynamics of lysozyme from molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

    2012-05-01

    The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.

  1. Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.

    PubMed

    Kohagen, Miriam; Lepšík, Martin; Jungwirth, Pavel

    2014-11-20

    Calcium represents a key biological signaling ion with the EF-hand loops being its most prevalent binding motif in proteins. We show using molecular dynamics simulations with umbrella sampling that including electronic polarization effects via ionic charge rescaling dramatically improves agreements with experiment in terms of the strength of calcium binding and structures of the calmodulin binding sites. The present study thus opens way to accurate calculations of interactions of calcium and other computationally difficult high-charge-density ions in biological contexts.

  2. Atomistic simulations of the Fe K-edge EXAFS in FeF3 using molecular dynamics and reverse Monte Carlo methods

    NASA Astrophysics Data System (ADS)

    Jonane, Inga; Timoshenko, Janis; Kuzmin, Alexei

    2016-10-01

    Atomistic simulations of the experimental Fe K-edge extended x-ray absorption fine structure (EXAFS) of rhombohedral (space group R\\bar{3}c) FeF3 at T = 300 K were performed using classical molecular dynamics and reverse Monte Carlo (RMC) methods. The use of two complementary theoretical approaches allowed us to account accurately for thermal disorder effects in EXAFS and to validate the developed force-field model, which was constructed as a sum of two-body Buckingham-type (Fe-F and F-F), three-body harmonic (Fe-F-Fe) and Coulomb potentials. We found that the shape of the Fe K-edge EXAFS spectrum of FeF3 is a more sensitive probe for the determination of potential parameters than the values of structural parameters (a, c, x(F)) available from diffraction studies. The best overall agreement between the experimental and theoretical EXAFS spectra calculated using ab initio multiple-scattering approach was obtained for the iron effective charge q(Fe) = 1.71. The RMC method coupled with the evolutionary algorithm was used for more elaborate analysis of the EXAFS data. The obtained results suggest that our force-field model slightly underestimates the amplitude of thermal vibrations of fluorine atoms in the direction perpendicular to the Fe-F bonds.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  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.

    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

  9. Crystallography from Haüy to Laue: controversies on the molecular and atomistic nature of solids.

    PubMed

    Kubbinga, Henk

    2012-01-01

    The history of crystallography has been assessed in the context of the emergence and spread of the molecular theory. The present paper focuses on the 19th century, which saw the emancipation of crystallography as a science sui generis. Around 1800, Laplace's molecularism called the tune in the various sciences (physics, chemistry, biology, crystallography). In crystallography, two schools opposed each other: that of Weiss, in Berlin, and that of Haüy, in Paris. Symmetry proved essential. It will be shown how the lattice theory arose in an essentially molecular framework and how group theory imposed itself. The salt hydrates suggested the idea of (two or more) superimposed molecular lattices. Gradually it became clear that an ultimate lattice theory ought to be atomic. The experiments of Laue, Friedrich and Knipping confirmed that atomic basis.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Yang, H. F.; Liu, Z. T.; Fan, C. C.; Yao, Q.; Xiang, P.; Zhang, K. L.; Li, M. Y.; Liu, J. S.; Shen, D. W.

    2016-08-01

    By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO3 and iso-polarity LaAlO3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO3 (111) substrate was more suitable than Nb-doped SrTiO3. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO3 based superlattices.

  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. 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.

  4. General Reactive Atomistic Simulation Program

    SciTech Connect

    Thompson, Aidan P.

    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, 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.

  5. General Reactive Atomistic Simulation Program

    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

  6. Molecular simulation study of polar order in orthogonal bent-core smectic liquid crystals.

    PubMed

    Peroukidis, Stavros D; Vanakaras, Alexandros G; Photinos, Demetri J

    2015-06-01

    We explore the phase behavior and structure of orthogonal smectic liquid crystals consisting of bent-core molecules (BCMs) by means of Monte Carlo molecular simulations. A simple athermal molecular model is introduced that describes the basic features of the BCMs. Phase transitions between uniaxial and biaxial (antiferroelectric) orthogonal smectics are obtained. The results indicate the presence of local in-plane polar correlations in the uniaxial smectic phase. The macroscopic uniaxial-biaxial transformation is rationalized in terms of local polar correlations giving rise to polar domains. The size of these polar domains grows larger under the action of an external vector field and their internal ordering is enhanced, leading to field-induced biaxial order-disorder transitions.

  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. Photoelectron momentum distributions of atomic and molecular systems in strong circularly or elliptically polarized laser fields

    NASA Astrophysics Data System (ADS)

    He, Pei-Lun; Takemoto, Norio; He, Feng

    2015-06-01

    Photoelectron momentum distributions of a hydrogen atom in an elliptically polarized laser field and a hydrogen molecular ion in a circularly polarized laser field are studied by simulating the time-dependent Schrödinger equation. We demonstrate that, in both systems, the Coulomb interaction between a liberated electron and its parent ion is essential for the photoelectron momentum angular drift in a laser polarization plane. By decomposing the wave packet into the rescattered and directly ionized components in the case of a hydrogen molecular ion, we reveal that the rescattered component drifts by a larger angle. The drift angle of the photoelectron of the hydrogen atom decreases monotonically with longer wavelength, while a nonmonotonic dependence is shown for H2+. We attribute such nonmonotonicity to the fluctuation of the instant of ionization for H2 + as the laser wavelength is changed.

  9. Field-free molecular alignment induced by elliptically polarized laser pulses: Noninvasive three-dimensional characterization

    SciTech Connect

    Hertz, E.; Guerin, S.; Jauslin, H. R.; Lavorel, B.; Faucher, O.; Daems, D.

    2007-10-15

    An investigation of field-free molecular alignment produced by elliptically polarized laser pulses is reported. Experiments are conducted in CO{sub 2} at room temperature. A noninvasive all-optical technique, based on the cross defocusing of a probe pulse, is used to measure the alignment along two orthogonal directions which is sufficient to provide a three-dimensional characterization. The field-free molecular alignment produced by a laser of elliptical polarization is in good agreement in terms of amplitude and shape with theoretical predictions. It turns out to be almost equivalent to the superposition of the effects that one would obtain with two individual cross-polarized pulses. The investigation highlights notably the occurrence of field-free two-direction alignment alternation for a suitably chosen degree of ellipticity. The analogy between this specific ellipticity and the well-known 'magic angle' used in time-resolved spectroscopy to prevent rotational contributions is discussed.

  10. Protons in polar media: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

    The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations

  11. 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.

  12. Molecular Structure of Frizzled, a Drosophila Tissue Polarity Gene

    PubMed Central

    Adler, P. N.; Vinson, C.; Park, W. J.; Conover, S.; Klein, L.

    1990-01-01

    The function of the frizzled (fz) locus is required to coordinate the cytoskeletons of pupal epidermal cells so that a parallel array of cuticular hairs and bristles is produced. We report here the molecular cloning and characterization of the fz locus. The locus is very large. Mutations that inactivate the gene are spread over 100 kb of genomic DNA. The major mRNA product of the gene is a 4-kb RNA that is encoded by 5 exons spread over more than 90 kb of genomic DNA. Conceptual translation of this mRNA indicates that it encodes an integral membrane protein that is likely to contain both extracellular and cytoplasmic domains. PMID:2174014

  13. 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.

  14. 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

  15. 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.

  16. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, G.; Megariotis, G.; Theodorou, D. N.

    2016-08-01

    This study concerns atomistic and coarse-grained Molecular Dynamics simulations of pristine hexabenzocoronene (HBC) molecular crystals. HBC is a symmetric graphene flake of nanometric size that falls in the category of polyaromatic hydrocarbons, finding numerous applications in the field of organic electronics. The HBC molecule is simulated in its crystalline phase initially by means of an all-atom representation, where the molecules self- organize into well aligned molecular stacks, which in turn create a perfect monoclinic molecular crystal. The atomistic model reproduces fairly well the structural experimental properties and thus can be used as a reliable starting point for the development of a coarsegrained model following a bottom-up approach. The coarse-grained model is developed by applying Iterative Boltzmann Inversion, a systematic coarse-graining method which reproduces a set of target atomistic radial distribution functions and intramolecular distributions at the coarser level of description. This model allows the simulation of HBC crystals over longer time and length scales. The crystalline phase is analyzed in terms of the Saupe tensor and thermomechanical properties are probed at the atomistic level.

  17. The effect of solvent polarity on the molecular surface properties and adhesion of Escherichia coli.

    PubMed

    Abu-Lail, Nehal I; Camesano, Terri A

    2006-08-01

    The elasticity and molecular surface characteristics of Escherichia coli JM109 were investigated via atomic force microscopy (AFM) in solvents expressing different polarities. The nature of bacterial adhesion and surface characteristics was probed in formamide, water, and methanol, with dielectric constants of 111, 80, and 33, respectively. Solvent polarity affected the elasticity of the bacterium, the conformation of the cell surface biopolymers, the height of the surface biopolymers, and measured adhesion forces between the bacterium and silicon nitride. By applying the Hertz model to force-indentation data, we determined that the Young's modulus was greatest in the least polar solvent, with values of 182 +/- 34.6, 12.8 +/- 0.1, and 0.8 +/- 0.3 MPa in methanol, water, and formamide, respectively. The thickness of the biopolymer brush layer on the bacterial surface was quantified using a steric model, and these values increased as polarity increased, with values of 27, 93, and 257 nm in methanol, water, and formamide, respectively. The latter results suggest that highly polar conditions favor extension of the biopolymer brush layer. Cross-sectional analysis performed on tapping mode images of the bacterial cells in methanol, water, and formamide further supported this hypothesis. The image height values are larger, since the image analysis measures the height of the bacterium and the polymer layer, but the trend with respect to solvent polarity was the same as was obtained from the steric model of the brush length. Measured adhesion forces scaled inversely with solvent polarity, with greatest adhesion observed in the least polar solvent, methanol. The combined conformational changes to the bacterial surface and biopolymer layer result in different presentations of macromolecules to a substrate surface, and therefore affect the adhesion forces between the bacterial molecules and the substrate. These results suggest that polarity of the solvent environment can be

  18. 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

  19. 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

  20. Atomistic k ṡ p theory

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Pseudopotentials, tight-binding models, and k ṡ 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 ṡ p theory. In its usual formulation, k ṡ 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 ṡ 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 sp3 tight-binding model. We can thus directly derive the parameters in the sp3 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 ṡ 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 ṡ p models to be combined in the same system.

  1. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry

    PubMed Central

    Isegawa, Miho; Fiedler, Luke; Leverentz, Hannah R.; Wang, Yingjie; Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G.

    2013-01-01

    The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries. PMID:23704835

  2. Liquid Crystal Phases of Molecular Bananas: Polarity and Chirality as Broken Symmetries

    NASA Astrophysics Data System (ADS)

    Clark, Noel

    2006-03-01

    The study of the interplay of chirality and polarity has been a particularly rich theme of soft matter science since Meyer's seminal discovery that tilted smectics of chiral molecules are macroscopically polar. This event, and the subsequent realization of polar domains and high-speed electro-optic switching in chiral smectics, engaged the liquid crystal community in a worldwide pursuit of novel smectics for applications, featured by the synthesis of more than 50,000 new liquid crystal compounds, and by a consequent broad diversification of the palette of liquid crystal phases and possibilities for supermolecular ordering. A current important activity in this scenario is the study of polar order in synthetically achiral molecules, for example, in molecular bananas, which, as their shape suggests, might be expected to organize in a polar way. Indeed they do, but beyond this, almost everything learned about them has been surprising, including their persistent tendency to exhibit chirality as a spontaneously broken symmetry. I will discuss some of these new phases and phenomena, including the discovery of fluid conglomerates (Pasteur's experiment in a fluid), triclinic fluid order, chiral twist grain boundary phases of achiral molecules, chirality flipping and field-induced deracemization, ferroelectric and antiferroelectric phases with supermolecular- scale polarization modulation, and chiral thermotropic sponge phases.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Orientation of molecular groups of fibers in nonoriented samples determined by polarized ATR-FTIR spectroscopy.

    PubMed

    Belbachir, Karima; Lecomte, Sophie; Ta, Ha-Phuong; Petibois, Cyril; Desbat, Bernard

    2011-12-01

    A method based on polarized attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy is proposed for determining the infrared dichroic absorption ratio of a single fiber from a sample deposited flat on a germanium crystal without the requirement of fiber orientation. The method shows its efficiency on cellulose fibers of paper and has been applied to protein fibers (type I collagen and β-amyloid) and polysaccharide fibers (cellulose and starch). The method gives access to the dichroic ratio of strong absorptions bands, which is not easily accessible with conventional absorption techniques. Then, the orientation of the molecular groups of organic fibers can be easily determined by polarized ATR-FTIR spectroscopy. By extension, this method will be useful to determine the molecular orientation of fibers in structured complex samples, such as biological tissues and plants. Spatially resolved information on the organization of the fiber network will be easily extracted by utilizing a focal plane array detector for imaging measurements.

  8. 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.

  9. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insights into a separation process.

    PubMed

    Jiang, De-en; Dai, Sheng

    2008-08-21

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are found. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  10. 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 .

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Bidirectional molecular transport shapes cell polarization in a two-dimensional model of eukaryotic chemotaxis.

    PubMed

    Feng, Shiliang; Zhu, Weiping

    2014-12-21

    Chemotacting eukaryotic cells can sense shallow gradients of chemoattractants and respond by assuming an asymmetric shape with well-defined front and back regions. Such a striking polarization phenomenon is produced largely through the interconversions and interactions between several cellular components, including Rac GTPase (Rac), phosphoinositide 3-kinase (PI3K), tensin homology protein (PTEN), phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2). Here, we developed a mathematical model of cell polarization by exploring bidirectional molecular transport that arose from phosphoinositides (PIs) and Rac-mediated feedback loops. We assumed a static gradient of activated Rac derived from an external signal field as the internal trigger signal. The evolution of PI(3,4,5)P3 and PI(4,5)P2 along with PI3K and PTEN that act as activator and inhibitor, respectively, were described by a pair of coupled transient reaction-diffusion equations. The entire system was solved using a Lattice-Boltzmann method with an embedded Monte-Carlo method to track the stochastic translocation behaviors of discrete PI3K/PTEN molecules. We first showed that, upon a graded external stimulus, the Rac to PI(3,4,5)P3 cascade exhibited a short range positive-feedback loop, while the PTEN to PI(4,5)P2 cascade contributed another long range negative-feedback loop, which dominated the "forward" and "backward" molecular transport, respectively. Second, polarization was governed by the ratio of [PI3K] to [PTEN], and manifested a switch-like behavior. Third, with a uniform stimulus, spontaneous polarization could occur in PTEN-deficient cells.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Atomistic Calculation of Mechanical Behavior

    NASA Astrophysics Data System (ADS)

    Li, Ju

    Mechanical behavior is stress-related behavior. This can mean the material response is driven by externally applied stress (or partially), or the underlying processes are mediated by an internal stress field; very often both are true. Due to defects and their collective behavior [1], the spatiotemporal spectrum of stress field in a real material tends to have very large spectral width, with non-trivial coupling between different scales, which is another way of saying that the mechanical behavior of real materials tends to be multiscale. The concept of stress field is usually valid when coarse-grained above a few nm; in favorable circumstances like when crystalline order is preserved locally, it may be applicable down to sub-nm lengthscale [2]. But overall, the atomic scale is where the stress concept breaks down, and atomistic simulations [3-5] provide very important termination or matching condition for stress-based theories. Large-scale atomistic simulations (chap 2.27) are approaching μm lengthscale and are starting to reveal the collective behavior of defects [6]. But studying defect unit processes is still a main task of atomistic simulation.

  5. 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.

  6. Polarization-Dependent Measurements of Molecular Super Rotors with Oriented Angular Momenta

    NASA Astrophysics Data System (ADS)

    Murray, Matthew J.; Toro, Carlos; Liu, Qingnan; Mullin, Amy S.

    2014-05-01

    Controlling molecular motion would enable manipulation of energy flow between molecules. Here we have used an optical centrifuge to investigate energy transfer between molecular super rotors with oriented angular momenta. The polarizable electron cloud of the molecules interacts with the electric field of linearly polarized light that angularly accelerates over the time of the optical pulse. This process drives molecules into high angular momentum states that are oriented with the optical field and have energies far from equilibrium. High resolution transient IR spectroscopy reveals the dynamics of collisional energy transfer for these super excited rotors. The results of this study leads to a more fundamental understanding of energy balance in non-equilibrium environments and the physical and chemical properties of gases in a new regime of energy states. Results will be presented for several super rotor species including carbon monoxide, carbon dioxide, and acetylene. Polarization-dependent measurements reveal the extent to which the super rotors maintain spatial orientation of high angular momentum states.

  7. Molecular evidence links cryptic diversification in polar planktonic protists to Quaternary climate dynamics.

    PubMed

    Darling, Kate F; Kucera, Michal; Pudsey, Carol J; Wade, Christopher M

    2004-05-18

    It is unknown how pelagic marine protists undergo diversification and speciation. Superficially, the open ocean appears homogeneous, with few clear barriers to gene flow, allowing extensive, even global, dispersal. Yet, despite the apparent lack of opportunity for genetic isolation, diversity is prevalent within marine taxa. A lack of candidate isolating mechanisms would seem to favor sympatric over allopatric speciation models to explain the diversity and biogeographic patterns observed in the oceans today. However, the ocean is a dynamic system, and both current and past circulation patterns must be considered in concert to gain a true perspective of gene flow through time. We have derived a comprehensive picture of the mechanisms potentially at play in the high latitudes by combining molecular, biogeographic, fossil, and paleoceanographic data to reconstruct the evolutionary history of the polar planktonic foraminifer Neogloboquadrina pachyderma sinistral. We have discovered extensive genetic diversity within this morphospecies and that its current "extreme" polar affinity did not appear until late in its evolutionary history. The molecular data demonstrate a stepwise progression of diversification starting with the allopatric isolation of Atlantic Arctic and Antarctic populations after the onset of the Northern Hemisphere glaciation. Further diversification occurred only in the Southern Hemisphere and seems to have been linked to glacial-interglacial climate dynamics. Our findings demonstrate the role of Quaternary climate instability in shaping the modern high-latitude plankton. The divergent evolutionary history of N. pachyderma sinistral genotypes implies that paleoceanographic proxies based on this taxon should be calibrated independently.

  8. Effect of molecular organization on the image histograms of polarization SHG microscopy

    PubMed Central

    Psilodimitrakopoulos, Sotiris; Amat-Roldan, Ivan; Loza-Alvarez, Pablo; Artigas, David

    2012-01-01

    Based on its polarization dependency, second harmonic generation (PSHG) microscopy has been proven capable to structurally characterize molecular architectures in different biological samples. By exploiting this polarization dependency of the SHG signal in every pixel of the image, average quantitative structural information can be retrieved in the form of PSHG image histograms. In the present study we experimentally show how the PSHG image histograms can be affected by the organization of the SHG active molecules. Our experimental scenario grounds on two inherent properties of starch granules. Firstly, we take advantage of the radial organization of amylopectin molecules (the SHG source in starch) to attribute shifts of the image histograms to the existence of tilted off the plane molecules. Secondly, we use the property of starch to organize upon hydration to demonstrate that the degree of structural order at the molecular level affects the width of the PSHG image histograms. The shorter the width is the more organized the molecules in the sample are, resulting in a reliable method to measure order. The implication of this finding is crucial to the interpretation of PSHG images used for example in tissue diagnostics. PMID:23082306

  9. 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.

  10. 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

  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.

    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

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    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.

  17. Atomistic DMD Simulations of Spontaneous Formation of Nematic and Smectic Phase in a Model Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Linhananta, Apichart; Mackay, Ian

    2009-03-01

    We present atomistic discontinuous molecular dynamics (DMD) simulations of the bulk liquid crystal phases of the molecular fluid 8CB. The model is based on previous DMD models of protein folding (A. Linhananta, J. Boer and Ian MacKay, J. Chem. Phys., 2005, 122, 114901) in which all atoms including polar hydrogen, but not nonpolar hydrogen, are represented. Bonded pairs interact by infinite square well, while nonbonded atoms interact by hard-sphere square-well potentials. For the model 8CB, molecular parameters are scaled using AMBER and CHARMM force fields. The hard interaction potentials allow very rapid equilibration of ordered phases. Starting the DMD simulations from initial random states, without positional or orientation order, the 8CB systems spontaneously form ordered nematic and smectic phases. The simulations were performed in a 40 A X 40 A X 40 A box with 100 to 500 8CB molecules. At fixed temperature, as the density increases, the phase change from disorder to nematic to smectic. Finally a density-temperature phase diagram is presented.

  18. 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.

  19. 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.

  20. Relationship between molecular association and re-entrant phenomena in polar calamitic liquid crystals.

    PubMed

    Mandle, Richard J; Cowling, Stephen J; Sage, Ian; Colclough, M Eamon; Goodby, John W

    2015-02-19

    The relationship between molecular association and re-entrant phase behavior in polar calamitic liquid crystals has been explored in two families of materials: the 4'-alkoxy-4-cyanobiphenyls (6OCB and 8OCB) and the 4'-alkoxy-4-nitrobiphenyls. Although re-entrant nematic phase behavior has previously been observed in the phase diagram of 6OCB/8OCB, this is not observed in mixtures of the analogous nitro materials. As there is no stabilization of the smectic A phase in mixture studies, it was conjectured that the degree of association for the nitro systems is greater than that for the cyano analogues. This hypothesis was tested by using measured dielectric anisotropies and computed molecular properties to obtain a value of the Kirkwood factor, g, which describes the degree of association of dipoles in a liquid. These computed values of g confirm that the degree of association for nitro materials is greater than that for cyano and offer a useful method for quantifying molecular association in systems exhibiting a re-entrant polymorphism.

  1. 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

  2. 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

  3. A replica reference interaction site model theory for a polar molecular liquid sorbed in a disordered microporous material with polar chemical groups

    NASA Astrophysics Data System (ADS)

    Kovalenko, Andriy; Hirata, Fumio

    2001-11-01

    We develop a replica generalization of the reference interaction site model (replica RISM) integral equation theory to describe the structure and thermodynamics of quenched-annealed systems comprising polar molecular species. It provides a successful approach to realistic models of molecular liquids, and properly allows for the effect of a quenched disordered matrix on the sorbed liquid. The description can be extended to an electrolyte solution in a disordered material containing charged chemical functionalities that determine its adsorption character. The replica reference interaction site model (RISM) equations are complemented with the hypernetted chain (HNC) closure and its partial linearization (PLHNC), adequate to ionic and polar molecular liquids. In these approximations, the excess chemical potentials are derived in a closed analytical form. We extend the description to a quenched-annealed system with soft-core interaction potentials between all species, in which the liquid and matrix equilibrium distributions are characterized in general by two different temperatures. The replica RISM/PLHNC-HNC theory is applied to water sorbed in a quenched disordered microporous network of atoms associated into interconnected branched chains, with activating polar groups grafted to matrix chains. The results are in qualitative agreement with experiment for water confined in disordered materials.

  4. Using Computer-Based Visualization Strategies to Improve Students' Understanding of Molecular Polarity and Miscibility

    NASA Astrophysics Data System (ADS)

    Sanger, Michael J.; Badger, Steven M., II

    2001-10-01

    This study reports how instruction including visualization strategies associated with computer animations and electron density plots affected students' conceptual understanding of two chemistry topics. Two sets of students responded to several conceptual questions about molecular polarities and miscibilities and these responses were compared. One group received instruction including the use of wooden model kits and physical demonstrations; the other received similar instruction with the additional use of computer animations and electron-density plots. Students who viewed electron-density plots were more likely to identify symmetric molecules with polar bonds as being nonpolar and provided more complete descriptions of how soap molecules help remove grease from an object. Students who viewed computer animations and electron density plots were also more likely to explain that the intermolecular attractions among water molecules are responsible for the immiscibility of oil and water, and were more likely to recognize that water molecules are attracted to each other and to sodium and chloride ions but are not strongly attracted to hydrogen molecules. Although other studies have shown that computer animations can improve students' conceptual understanding of chemistry, this is the first to demonstrate that electron-density plots mapped with electrostatic potentials can also be an effective visualization strategy.

  5. 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.

  6. Polarization second harmonic generation microscopy provides quantitative enhanced molecular specificity for tissue diagnostics.

    PubMed

    Kumar, Rajesh; Grønhaug, Kirsten M; Romijn, Elisabeth I; Finnøy, Andreas; Davies, Catharina L; Drogset, Jon O; Lilledahl, Magnus B

    2015-09-01

    Due to specific structural organization at the molecular level, several biomolecules (e.g., collagen, myosin etc.) which are strong generators of second harmonic generation (SHG) signals, exhibit unique responses depending on the polarization of the excitation light. By using the polarization second harmonic generation (p-SHG) technique, the values of the second order susceptibility components can be used to differentiate the types of molecule, which cannot be done by the use of a standard SHG intensity image. In this report we discuss how to implement p-SHG on a commercial multiphoton microscope and overcome potential artifacts in susceptibility (χ) image. Furthermore we explore the potential of p-SHG microscopy by applying the technique to different types of tissue in order to determine corresponding reference values of the ratio of second-order χ tensor elements. These values may be used as a bio-marker to detect any structural alterations in pathological tissue for diagnostic purposes. The SHG intensity image (red) in (a) shows the distribution of collagen fibers in ovary tissue but cannot determine the type of collagen fiber. However, the histogram distribution (b) for the values of the χ tensor element ratio can be used to quantitatively identify the types of collagen fibers.

  7. 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.

  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. Polarization effects stabilize bacteriorhodopsin's chromophore binding pocket: a molecular dynamics study.

    PubMed

    Babitzki, G; Denschlag, R; Tavan, P

    2009-07-30

    Hybrid methods, which combine a quantum mechanical description of a chromophore by density functional theory (DFT) with a molecular mechanics (MM) model of the surrounding protein binding pocket, can enable highly accurate computations of the chromophore's in situ vibrational spectra. As a prerequisite, one needs a MM model of the chromophore-protein complex, which allows a correct sampling of its room-temperature equilibrium fluctuations by molecular dynamics (MD) simulation. Here, we show for the case of bacteriorhodopsin (BR) that MM-MD descriptions with standard nonpolarizable force fields entail a collapse of the chromophore binding pocket. As demonstrated by us, this collapse can be avoided by employing a polarized MM force field derived by DFT/MM hybrid computations. The corresponding MD simulations, which are complemented by a novel Hamiltonian replica exchange approach, then reveal a structural heterogeneity within the binding pocket of the retinal chromophore, which mainly pertains to the structure of the lysine chain covalently connecting the retinal chromophore with the protein backbone.

  12. 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.

  13. 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

  14. 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

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

    PubMed

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

    2013-06-28

    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)] 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)] and F + HD [D. De Fazio, J. Lucas, V. Aquilanti, and S. Cavalli, Phys. Chem. Chem. Phys. 13, 8571 (2011)] 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 on a compact and convenient spherical tensor expression for

  16. 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

  17. 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

  18. NiTi superelasticity via atomistic simulations

    NASA Astrophysics Data System (ADS)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

    The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Communication: Hydration structure and polarization of heavy alkali ions: A first principles molecular dynamics study of Rb+ and Cs+

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Boero, Mauro

    2012-07-01

    Hydration structure and polarization of Rb+ and Cs+ in liquid water at ambient conditions were studied by first principles molecular dynamics. Our systematic analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H2O molecules in the first solvation shell of the ions slightly increases with increasing the atomic number. We also found that the polarization of heavy alkali ions, particularly Cs+, tends to stabilize a peculiar asymmetric hydration structure with relevant consequences in the extraction of the harmful 137Cs resulting from nuclear wastes.

  4. Shear viscosity of polar liquid mixtures via non-equilibrium molecular dynamics: water, methanol, and acetone

    NASA Astrophysics Data System (ADS)

    Wheeler Richard, Dean R.; Rowley, L.

    Non-equilibrium molecular dynamics (NEMD) with isobaric and isokinetic controls were used to simulate the shear viscosity for binary mixtures of water, methanol and acetone, and for ternary mixtures. In all, 22 different liquid composition points were simulated at 298.15 K and 0.1 MPa. A new set of acetone potential parameters was developed, while slight variants to existing water and methanol models were used. Long range Coulombic interactions were computed with the Ewald sum adapted to Lees-Edwards boundary conditions as formulated in Wheeler, D. R., Fuller, N. G., and Rowley, R. L., 1997, Molec. Phys., 92, 55. The attractive (dispersive) part of the Lennard-Jones (LJ) interactions also was handled by a lattice sum. A hybrid mixing rule was used for the LJ cross interactions. Viscosities extrapolated to zero shear compared well with experimental results, having a mean absolute error of 14% and no errors greater than 30%. Although the simulations successfully predicted viscosity maxima for mixtures high in water content, the peak heights tended to be too low, probably due to the limitations of the water model. The results suggest that NEMD may be a viable means of estimating viscosities for polar liquid mixtures with an unrestricted number of components.

  5. 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.

  6. Beyond frontier molecular orbital theory: a systematic electron transfer model (ETM) for polar bimolecular organic reactions.

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

    Polar bimolecular reactions often begin as charge-transfer complexes and may proceed with a high degree of electron transfer character. Frontier molecular orbital (FMO) theory is predicated in part on this concept. We have developed an electron transfer model (ETM) in which we systematically transfer one electron between reactants and then use density functional methods to model the resultant radical or radical ion intermediates. Sites of higher reactivity are revealed by a composite spin density map (SDM) of odd electron character on the electron density surface, assuming that a new two-electron bond would occur preferentially at these sites. ETM correctly predicts regio- and stereoselectivity for a broad array of reactions, including Diels-Alder, dipolar and ketene cycloadditions, Birch reduction, many types of nucleophilic additions, and electrophilic addition to aromatic rings and polyenes. Conformational analysis of radical ions is often necessary to predict reaction stereochemistry. The electronic and geometric changes due to one-electron oxidation or reduction parallel the reaction coordinate for electrophilic or nucleophilic addition, respectively. The effect is more dramatic for one-electron reduction.

  7. Measuring molecular order in poly(3-alkylthiophene) thin films with polarizing spectroscopies.

    PubMed

    Gurau, Marc C; Delongchamp, Dean M; Vogel, Brandon M; Lin, Eric K; Fischer, Daniel A; Sambasivan, Sharadha; Richter, Lee J

    2007-01-16

    We measured the molecular order of poly(3-alkylthiophene) chains in thin films before and after melting through the combination of several polarized photon spectroscopies: infrared (IR) absorption, variable angle spectroscopic ellipsometry (SE), and near-edge X-ray absorption fine structure (NEXAFS). The data from the various techniques can be uniformly treated in the context of the dielectric constant tensor epsilon for the film. The combined spectroscopies allow determination of the orientation distribution of the main-chain axis (SE and IR), the conjugated pi system normal (NEXAFS), and the side-chain axis (IR). We find significant improvement in the backbone order of the films after recrystallization of the material at temperatures just below the melting temperature. Less aggressive thermal treatments are less effective. IR studies show that the changes in backbone structure occur without significant alteration of the structure of the alkyl side chains. The data indicate that the side chains exhibit significant disorder for all films regardless of the thermal history of the sample.

  8. 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

  9. Alignment dependence of photoelectron momentum distributions of atomic and molecular targets probed by few-cycle circularly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Abu-samha, M.; Madsen, Lars Bojer

    2016-08-01

    We present theoretical photoelectron momentum distributions (PMDs) for ionization from Ar(3 p ) and H2+ (σg) orbitals by few-cycle, high-intensity, near-infrared laser fields circularly polarized in the x y plane. The three-dimensional time-dependent Schrödinger equation is solved numerically within the single-active-electron approximation for Ar and within the fixed nuclei approximation for H2+ . The PMDs are investigated for alignment of the probed target orbitals relative to the polarization plane of the laser field. In the atomic case, the PMDs in the polarization plane for aligned 3 p Ar orbitals are, up to an overall scaling factor, insensitive to alignment of the probed orbital, while the lateral PMDs show a signature of the orbital node when that node is sufficiently close to the polarization plane. For the molecular case of H2+ (σg), our results show a significant impact of alignment on the PMDs due to the anisotropic molecular potential and the alignment-dependent coupling between the ground state and excited states.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. A versatile molecular beacon-like probe for multiplexed detection based on fluorescence polarization and its application for a resettable logic gate.

    PubMed

    Zhang, Min; Le, Huynh-Nhu; Wang, Ping; Ye, Bang-Ce

    2012-10-14

    A versatile molecular beacon (MB)-like probe was developed for multiplexed detection based on fluorescence polarization by target-induced allosteric effect and furthermore for resettable logic gate operation.

  18. 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.

  19. 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.

  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. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

    PubMed

    Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

    2015-03-01

    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.

  2. Atomistic Processes of Catalyst Degradation

    SciTech Connect

    2004-11-27

    The purpose of this cooperative research and development agreement (CRADA) between Sasol North America, Inc., and the oak Ridge National Laboratory (ORNL) was to improve the stability of alumina-based industrial catalysts through the combination of aberration-corrected scanning transmission electron microscopy (STEM) at ORNL and innovative sample preparation techniques at Sasol. Outstanding progress has been made in task 1, 'Atomistic processes of La stabilization'. STEM investigations provided structural information with single-atom precision, showing the lattice location of La dopant atoms, thus enabling first-principles calculations of binding energies, which were performed in collaboration with Vanderbilt University. The stabilization mechanism turns out to be entirely due to a particularly strong binding energy of the La tom to the {gamma}-alumina surface. The large size of the La atom precludes incorporation of La into the bulk alumina and also strains the surface, thus preventing any clustering of La atoms. Thus highly disperse distribution is achieved and confirmed by STEM images. la also affects relative stability of the exposed surfaces of {gamma}-alumina, making the 100 surface more stable for the doped case, unlike the 110 surface for pure {gamma}-alumina. From the first-principles calculations, they can estimate the increase in transition temperature for the 3% loading of La used commercially, and it is in excellent agreement with experiment. This task was further pursued aiming to generate useable recommendations for the optimization of the preparation techniques for La-doped aluminas. The effort was primarily concentrated on the connection between the boehmitre-{gamma}-Al{sub 2}O{sub 3} phase transition (i.e. catalyst preparation) and the resulting dispersion of La on the {gamma}-Al{sub 2}O{sub 3} surface. It was determined that the La distribution on boehmite was non-uniform and different from that on the {gamma}-Al{sub 2}O{sub 3} and thus

  3. 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.

  4. 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.

  5. 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

  6. Influence of solvent polarity on preferential solvation of molecular recognition probes in solvent mixtures.

    PubMed

    Amenta, Valeria; Cook, Joanne L; Hunter, Christopher A; Low, Caroline M R; Vinter, Jeremy G

    2012-12-13

    The association constants for formation of 1:1 complexes between a H-bond acceptor, tri-n-butylphosphine oxide, and a H-bond donor, 4-phenylazophenol, have been measured in a range of different solvent mixtures. Binary mixtures of n-octane and a more polar solvent (ether, ester, ketone, nitrile, sulfoxide, tertiary amide, and halogenated and aromatic solvents) have been investigated. Similar behavior was observed in all cases. When the concentration of the more polar solvent is low, the association constant is identical to that observed in pure n-octane. Once a threshold concentration of the more polar solvent in reached, the logarithm of the association constant decreases in direct proportion to the logarithm of the concentration of the more polar solvent. This indicates that one of the two solutes is preferentially solvated by the more polar solvent, and it is competition with this solvation equilibrium that determines the observed association constant. The concentration of the more polar solvent at which the onset of preferential solvation takes place depends on solvent polarity: 700 mM for toluene, 60 mM for 1,1,2,2-tetrachloroethane, 20 mM for the ether, ester, ketone, and nitrile, 0.2 mM for the tertiary amide, and 0.1 mM for the sulfoxide solvents. The results can be explained by a simple model that considers only pairwise interactions between specific sites on the surfaces of the solutes and solvents, which implies that the bulk properties of the solvent have little impact on solvation thermodynamics. PMID:23190174

  7. Functional modelling of planar cell polarity: an approach for identifying molecular function

    PubMed Central

    2013-01-01

    Background Cells in some tissues acquire a polarisation in the plane of the tissue in addition to apical-basal polarity. This polarisation is commonly known as planar cell polarity and has been found to be important in developmental processes, as planar polarity is required to define the in-plane tissue coordinate system at the cellular level. Results We have built an in-silico functional model of cellular polarisation that includes cellular asymmetry, cell-cell signalling and a response to a global cue. The model has been validated and parameterised against domineering non-autonomous wing hair phenotypes in Drosophila. Conclusions We have carried out a systematic comparison of in-silico polarity phenotypes with patterns observed in vivo under different genetic manipulations in the wing. This has allowed us to classify the specific functional roles of proteins involved in generating cell polarity, providing new hypotheses about their specific functions, in particular for Pk and Dsh. The predictions from the model allow direct assignment of functional roles of genes from genetic mosaic analysis of Drosophila wings. PMID:23672397

  8. 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

  9. 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.

  10. 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

  11. Adaptive resolution simulation of an atomistic protein in MARTINI water

    SciTech Connect

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-02-07

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

  12. 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.

  13. 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.

  14. 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.

  15. Concurrent atomistic-continuum simulation of polycrystalline strontium titanate

    NASA Astrophysics Data System (ADS)

    Yang, Shengfeng; Zhang, Ning; Chen, Youping

    2015-08-01

    This paper presents the new development of a concurrent atomistic-continuum (CAC) method in simulation of the dynamic evolution of defects in polycrystalline polyatomic materials. The CAC method is based on a theoretical formulation that extends Kirkwood's statistical mechanical theory of transport processes to a multiscale description of crystalline materials. It solves for both the deformation of lattice cells and the internal deformation within each lattice cell, making it a suitable method for simulations of polyatomic materials. The simulation results of this work demonstrate that CAC can simulate the nucleation of dislocations and cracks from atomistically resolved grain boundary (GB) regions and the subsequent propagation into coarsely meshed grain interiors in polycrystalline strontium titanate without the need of supplemental constitutive equations or additional numerical treatments. With a significantly reduced computational cost, CAC predicts not only the GB structures, but also the dynamic behaviour of dislocations, cracks and GBs, all of which are comparable with those obtained from atomic-level molecular dynamics simulations. Simulation results also show that dislocations tend to initiate from GBs and triple junctions. The angle between the slip planes and the GB planes plays a key role in determining the GB-dislocation reactions.

  16. The Soft Mode Driven Dynamics in Ferroelectric Perovskites at the Nanoscale: An Atomistic Study

    NASA Astrophysics Data System (ADS)

    McCash, Kevin

    The discovery of ferroelectricity at the nanoscale has incited a lot of interest in perovskite ferroelectrics not only for their potential in device application but also for their potential to expand fundamental understanding of complex phenomena at very small size scales. Unfortunately, not much is known about the dynamics of ferroelectrics at this scale. Many of the widely held theories for ferroelectric materials are based on bulk dynamics which break down when applied to smaller scales. In an effort to increase understanding of nanoscale ferroelectric materials we use atomistic resolution computational simulations to investigate the dynamics of polar perovskites. Within the framework of a well validated effective Hamiltonian model we are able to accurately predict many of the properties of ferroelectric materials at the nanoscale including the response of the soft mode to mechanical boundary conditions and the polarization reversal dynamics of ferroelectric nanowires. Given that the focus of our study is the dynamics of ferroelectric perovskites we begin by developing an effective Hamiltonian based model that could simultaneously describe both static and dynamic properties of such materials. Our study reveals that for ferroelectric perovskites that undergo a sequence of phase transitions, such as BaTiO3. for example, the minimal parameter effective Hamiltonian model is unable to reproduce both static and dynamical properties simultaneously. Nevertheless we developed two sets of parameters that accurately describes the static properties and dynamic properties of BaTiO3 independently. By creating a tool that accurately models the dynamical properties of perovskite ferroelectrics we are able to investigate the frequencies of the soft modes in the perovskite crystal. The lowest energy transverse optical soft modes in perovskite ferroelectrics are known to be cause of the ferroelectric phase transition in these materials and affect a number of electrical properties

  17. Polarity formation in crystals with long range molecular interactions: A Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Cannavacciuolo, Luigi; Hulliger, Jürg

    2016-09-01

    Stochastic formation of a bi-polar state in three dimensional arrays of polar molecules with full Coulomb interactions is reproduced by Monte Carlo simulation. The size of the system is comparable to that of a real crystal seed. The spatial decay of the average order parameter is significantly slowed down by the long range interactions and the exact representation of correlation effects in terms of a single characteristic length becomes impossible. Finite size effects and possible scale invariance symmetry of the order parameter are extensively discussed.

  18. Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering.

    PubMed

    Kohagen, Miriam; Mason, Philip E; Jungwirth, Pavel

    2016-03-01

    Modeled ions, described by nonpolarizable force fields, can suffer from unphysical ion pairing and clustering in aqueous solutions well below their solubility limit. The electronic continuum correction takes electronic polarization effects of the solvent into account in an effective way by scaling the charges on the ions, resulting in a much better description of the ionic behavior. Here, we present parameters for the sodium ion consistent with this effective polarizability approach and in agreement with experimental data from neutron scattering, which could be used for simulations of complex aqueous systems where polarization effects are important.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases.

    PubMed

    Avramopoulos, Aggelos; Otero, Nicolás; Karamanis, Panaghiotis; Pouchan, Claude; Papadopoulos, Manthos G

    2016-01-21

    A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG. A Hirshfeld-based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -26.98 kcal/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB), a study of the magnitude of the interaction-induced polarizability of C84H24-NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.

  6. 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

  7. On the deracemization of a chiral molecular beam by interaction with circularly polarized light

    NASA Astrophysics Data System (ADS)

    Kucirka, Jerry; Shekhtman, Alexander G.

    1996-02-01

    A strong electromagnetic field exerts a force on neutral atoms or molecules and this effect has been utilized in atomic beam optics to create the analogs to optical elements such as lenses and mirrors. We extend this concept to the specific interaction of a chiral molecule with a circularly polarized laser wave. Because of the optical activity of chiral molecules this interaction is selective with respect to handedness and this selectivity forms the basis for a “chiral mirror” scheme, here introduced, to produce chirally pure matter.

  8. 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.

  9. Ferroelectric vortices from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Bellaiche, Laurent

    2011-03-01

    In 2004, the use of a first-principles-based effective Hamiltonian led to the prediction of a novel structure in zero-dimensional ferroelectrics, in which the electric dipoles organize themselves to form a vortex. Such structure exhibits the so-called spontaneous toroidal moment, rather than the spontaneous polarization, as its order parameter. Subsequently, various original phenomena, all related to vortices, were predicted in ferroelectric nanostructures. Examples of such phenomena are: (i) the existence of a new order parameter, denoted as the hypertoroidal moment, that is associated with many complex dipolar structures (such as double-vortex states); (ii) the possible control of single and double vortex states by electric fields, via the formation of original intermediate states [4-8]; (iii) the discovery of a new class of quantum materials (denoted as incipient ferrotoroidics), for which zero-point vibrations wash out the vortex state and yield a complex local structure; (iv) the existence of chiral patterns of oxygen octahedral tiltings that originate from the coupling of these tiltings with the ferroelectric vortices. The purpose of this talk is to discuss some of these striking phenomena, as well as, to reveal others (if time allows). These studies are done in collaboration with A.R. Akbarzadeh, H. Fu, I. Kornev, I. Naumov, I. Ponomareva, S. Prosandeev, Wei Ren and D. Sichuga. These works are supported by the NSF grants DMR 0701558 and DMR-0080054 (C-SPIN), DOE grant DE-SC0002220, and ONR grants N00014-08-1-0915 and N00014-07-1-0825 (DURIP).

  10. The molecular genetics and evolution of colour and polarization vision in stomatopod crustaceans.

    PubMed

    Cronin, T W; Porter, M L; Bok, M J; Wolf, J B; Robinson, P R

    2010-09-01

    Stomatopod crustaceans have the most complex assemblage of visual receptor classes known; retinas of many species are thought to express up to 16 different visual pigments. Physiological studies indicate that stomatopods contain up to six distinct middle-wavelength-sensitive (MWS) photoreceptor classes, suggesting that no more than six different MWS opsin gene copies exist per species. However, we previously reported the unexpected expression of 6-15 different MWS genes in retinas of each of five stomatopod species (Visual Neurosci 26: 255-266, 2009). Here, we present a review of the results reported in this publication, plus new results that shed light on the origins of the diverse colour and polarization visual capabilities of stomatopod crustaceans. Using in situ hybridization of opsins in photoreceptor cells, we obtained new results that support the hypothesis of an ancient functional division separating spatial and polarizational vision from colour vision in the stomatopods. Since evolutionary trace analysis indicates that stomatopod MWS opsins have diverged both with respect to spectral tuning and to cytoplasmic interactions, we have now further analyzed these data in an attempt to uncover the origins, diversity and potential specializations among clades for specific visual functions. The presence of many clusters of highly similar transcripts suggests exuberant opsin gene duplication has occurred in the stomatopods, together with more conservative, ancient gene duplication events within the stem crustacean lineage. Phylogenetic analysis of opsin relatedness suggests that opsins specialized for colour vision have diverged from those devoted to polarization vision, and possibly motion and spatial vision.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Excited-state proton coupled charge transfer modulated by molecular structure and media polarization.

    PubMed

    Demchenko, Alexander P; Tang, Kuo-Chun; Chou, Pi-Tai

    2013-02-01

    Charge and proton transfer reactions in the excited states of organic dyes can be coupled in many different ways. Despite the complementarity of charges, they can occur on different time scales and in different directions of the molecular framework. In certain cases, excited-state equilibrium can be established between the charge-transfer and proton-transfer species. The interplay of these reactions can be modulated and even reversed by variations in dye molecular structures and changes of the surrounding media. With knowledge of the mechanisms of these processes, desired rates and directions can be achieved, and thus the multiple emission spectral features can be harnessed. These features have found versatile applications in a number of cutting-edge technological areas, particularly in fluorescence sensing and imaging.

  19. 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

  20. 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

  1. 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

  2. Interface Thermodynamics with Applications to Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Frolov, Timofey

    Interfaces are ubiquitous in natural phenomena. While the description of interfaces in fluid systems is well developed, solid-fluid and solid-solid interfaces are not well understood. This deficiency is especially true for solid-solid interfaces, which play critical roles in materials engineering, solid-state physics and solid-state chemistry. In this thesis, the Gibbs theory of interfaces is generalized to describe phase boundaries under non-hydrostatic stress in multicomponent systems. We obtain equations that describe coherent solid-solid interfaces with shear stresses parallel to the boundary plane, incoherent solid-solid interfaces for certain constraint variations, solid-fluid interfaces, grain boundaries and surfaces. In the second part of the thesis, the developed theory is applied to study particular types of interfaces using atomistic simulations. We modeled solid surface, solid-liquid interface and grain boundaries. The simulations allowed to calculate values of key thermodynamic properties, clarify behavior of these properties with temperature, composition and stress and test the predictions of the theory. Surface surface free energy and surface stress in a single component system were computed as functions of temperature. The values of these two excess properties do not converge near the melting point despite the extensive surface premelting. Solid-liquid interface free energy was computed using the developed thermodynamic integration technique as a function of composition in CuAg binary alloy and as a function of biaxial strain in a single component Cu system. In the later case the equilibrium states between the non-hydrostatically stressed solid and liquid were accurately predicted using the derived Clausius--Clapeyron type equation. We show that for non-hydrostatic equilibrium interfaces stress is not unique and compute different interface stresses using our simulation data. We also studied effects of elastic deformation, temperature and chemical

  3. Dissecting the molecular bridges that mediate the function of Frizzled in planar cell polarity.

    PubMed

    Struhl, Gary; Casal, José; Lawrence, Peter A

    2012-10-01

    Many epithelia have a common planar cell polarity (PCP), as exemplified by the consistent orientation of hairs on mammalian skin and insect cuticle. One conserved system of PCP depends on Starry night (Stan, also called Flamingo), an atypical cadherin that forms homodimeric bridges between adjacent cells. Stan acts together with other transmembrane proteins, most notably Frizzled (Fz) and Van Gogh (Vang, also called Strabismus). Here, using an in vivo assay for function, we show that the quintessential core of the Stan system is an asymmetric intercellular bridge between Stan in one cell and Stan acting together with Fz in its neighbour: such bridges are necessary and sufficient to polarise hairs in both cells, even in the absence of Vang. By contrast, Vang cannot polarise cells in the absence of Fz; instead, it appears to help Stan in each cell form effective bridges with Stan plus Fz in its neighbours. Finally, we show that cells containing Stan but lacking both Fz and Vang can be polarised to make hairs that point away from abutting cells that express Fz. We deduce that each cell has a mechanism to estimate and compare the numbers of asymmetric bridges, made between Stan and Stan plus Fz, that link it with its neighbouring cells. We propose that cells normally use this mechanism to read the local slope of tissue-wide gradients of Fz activity, so that all cells come to point in the same direction.

  4. Polarized Raman analysis of the molecular rearrangement and residual strain on the surface of retrieved polyethylene tibial plates.

    PubMed

    Puppulin, Leonardo; Takahashi, Yasuhito; Zhu, Wenliang; Sugano, Nobuhiko; Pezzotti, Giuseppe

    2011-03-01

    The response to applied strain of EtO-sterilized and γ-irradiated polyethylene materials belonging to tibial inserts has been studied by polarized Raman spectroscopy. Initial calibrations on as-received samples from three different makers were employed to clarify the rearrangement of molecular chains under strain, expressed in terms of Euler angular displacements in space and orientation distribution functions. This body of information was then applied to a quantitative analysis of four tibial inserts (from the same three makers of the unused samples) retrieved after in vivo exposures ranging between 7 months and 5 years 8 months. The main results of the Raman analysis can be summarized as follows: (i) γ-irradiated samples experienced lower texturing on the molecular scale compared to EtO-sterilized samples, likely due to a higher strain recovery capability; and (ii) independent of sterilization method, the amount of plastic strain was mainly developed early after in vivo implantation, whereby out-of-plane molecules rotated under load onto planes parallel to the sample surface until saturation of angular displacements was reached. PMID:20965286

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

    PubMed Central

    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

  6. 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

  7. 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.

  8. General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.

    PubMed

    Mamonov, Artem B; Bhatt, Divesh; Cashman, Derek J; Ding, Ying; Zuckerman, Daniel M

    2009-08-01

    We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Go-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on". PMID:19594147

  9. 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.

  10. Simulation of the Richtmyer-Meshkov and Rayleigh-Taylor Instability Using Atomistic Methods

    NASA Astrophysics Data System (ADS)

    Kadau, Kai; Barber, John L.; Germann, Timothy C.; Lomdahl, Peter S.; Holian, Brad Lee; Alder, Berni J.

    2007-06-01

    We present large-scale atomistic simulations [molecular dynamics (MD) and direct simulation Monte-Carlo (DSMC)] of fluid instabilities that occur when a fluid interface is subjected to shock loading or gravitation [Richtmyer-Meshkov and Rayleigh-Taylor instability]. The atomistic methods reach the parameter range that is of importance for inertial confinement fusion (ICF) capsules subjected to high energy lasers. The results are compared to existing theoretical and experimental work from which we have strong evidence for the importance of fluctuations in such instabilities. References: 1.) Kai Kadau, Timothy C. Germann , Nicolas G. Hadjiconstantinou , Peter S. Lomdahl *, Guy Dimonte , Brad Lee Holian *, and Berni J. Alder, PNAS 101, 5851 (2004). 2.)K. Kadau et al. submitted (2007).

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. ATOMIC AND MOLECULAR PHYSICS: Multiphoton ionization of the hydrogen atom exposed to circularly or linearly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Wang, Pei-Jie; He, Feng

    2009-12-01

    This paper studies the multiphoton ionization of the hydrogen atom exposed to the linearly or circularly polarized laser pulses by solving the time-dependent Schrödinger equation. It finds that the ratio of the ionization probabilities by linearly and circularly polarized laser pulses varies with the numbers of absorbing photons. With the same laser intensity, the circularly polarized laser pulse favors to ionize the atom with more ease than the linearly polarized laser pulse if only two or three photons are necessary to be absorbed. For the higher order multiphoton ionization, the linearly polarized laser pulse has the advantage over circularly polarized laser pulse to ionize the atom.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. ATOMIC AND MOLECULAR PHYSICS: Spontaneous Emission of a Polarized Atom in a Medium Between Two Parallel Mirrors

    NASA Astrophysics Data System (ADS)

    Wang, De-Hua; Huang, Kai-Yun; Xu, Qiang

    2010-01-01

    Using the photon closed orbit theory, the spontaneous emission rate of a polarized atom in a medium between two parallel mirrors is derived and calculated. It is found that the spontaneous emission rate of a polarized atom between the mirrors is related to the atomic position and the polarization direction. The results show that in the vicinity of the mirror, the variation of the spontaneous emission rate depends crucially on the atomic polarization direction. With the increase of the polarization angle, the oscillation in the spontaneous emission rate becomes decreased. For the polarization direction parallel to the mirror plane, the oscillation is the greatest; while for the perpendicular polarization direction, the oscillation is nearly vanished. The agreement between our result and the quantum electrodynamics result suggests the correctness of our calculation. This study further verifies that the atomic spontaneous emission process can be effectively controlled by changing the polarization orientation of the atom.

  7. 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.

  8. 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

  9. ReaxFF molecular dynamics study on oxidation behavior of 3C-SiC: Polar face effects

    NASA Astrophysics Data System (ADS)

    Sun, Yu; Liu, Yi-Jun; Xu, Fei

    2015-09-01

    The oxidation of nanoscale 3C-SiC involving four polar faces (, Si(100), , and Si(111)) is studied by means of a reactive force field molecular dynamics (ReaxFF MD) simulation. It is shown that the consistency of 3C-SiC structure is broken over 2000 K and the low-density carbon chains are formed within SiC slab. By analyzing the oxygen concentration and fitting to rate theory, activation barriers for , Si(100), , and Si(111) are found to be 30.1, 35.6, 29.9, and 33.4 kJ·mol-1. These results reflect lower oxidative stability of C-terminated face, especially along [111] direction. Compared with hexagonal polytypes of SiC, cubic phase may be more energy-favorable to be oxidized under high temperature, indicating polytype effect on SiC oxidation behavior. Project supported by the 111 Project (Grant No. B07050) and the National Natural Science Foundation of China (Grant No. 11402206).

  10. Simultaneous and spectroscopic redox molecular imaging of multiple free radical intermediates using dynamic nuclear polarization-magnetic resonance imaging.

    PubMed

    Hyodo, Fuminori; Ito, Shinji; Yasukawa, Keiji; Kobayashi, Ryoma; Utsumi, Hideo

    2014-08-01

    Redox reactions that generate free radical intermediates are essential to metabolic processes. However, their intermediates can produce reactive oxygen species, which may promote diseases related to oxidative stress. We report here the use of dynamic nuclear polarization-magnetic resonance imaging (DNP-MRI) to conduct redox molecular imaging. Using DNP-MRI, we obtained simultaneous images of free radical intermediates generated from the coenzyme Q10 (CoQ10), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) involved in the mitochondrial electron transport chain as well as the radicals derived from vitamins E and K1. Each of these free radicals was imaged in real time in a phantom comprising a mixture of free radicals localized in either lipophilic or aqueous environments. Changing the frequency of electron spin resonance (ESR) irradiation also allowed each of the radical species to be distinguished in the spectroscopic images. This study is the first to report the spectroscopic DNP-MRI imaging of free radical intermediates that are derived from endogenous species involved in metabolic processes.

  11. The Formin DAAM Functions as Molecular Effector of the Planar Cell Polarity Pathway during Axonal Development in Drosophila

    PubMed Central

    Gombos, Rita; Migh, Ede; Antal, Otilia; Mukherjee, Anindita; Jenny, Andreas

    2015-01-01

    Recent studies established that the planar cell polarity (PCP) pathway is critical for various aspects of nervous system development and function, including axonal guidance. Although it seems clear that PCP signaling regulates actin dynamics, the mechanisms through which this occurs remain elusive. Here, we establish a functional link between the PCP system and one specific actin regulator, the formin DAAM, which has previously been shown to be required for embryonic axonal morphogenesis and filopodia formation in the growth cone. We show that dDAAM also plays a pivotal role during axonal growth and guidance in the adult Drosophila mushroom body, a brain center for learning and memory. By using a combination of genetic and biochemical assays, we demonstrate that Wnt5 and the PCP signaling proteins Frizzled, Strabismus, and Dishevelled act in concert with the small GTPase Rac1 to activate the actin assembly functions of dDAAM essential for correct targeting of mushroom body axons. Collectively, these data suggest that dDAAM is used as a major molecular effector of the PCP guidance pathway. By uncovering a signaling system from the Wnt5 guidance cue to an actin assembly factor, we propose that the Wnt5/PCP navigation system is linked by dDAAM to the regulation of the growth cone actin cytoskeleton, and thereby growth cone behavior, in a direct way. PMID:26180192

  12. The Formin DAAM Functions as Molecular Effector of the Planar Cell Polarity Pathway during Axonal Development in Drosophila.

    PubMed

    Gombos, Rita; Migh, Ede; Antal, Otilia; Mukherjee, Anindita; Jenny, Andreas; Mihály, József

    2015-07-15

    Recent studies established that the planar cell polarity (PCP) pathway is critical for various aspects of nervous system development and function, including axonal guidance. Although it seems clear that PCP signaling regulates actin dynamics, the mechanisms through which this occurs remain elusive. Here, we establish a functional link between the PCP system and one specific actin regulator, the formin DAAM, which has previously been shown to be required for embryonic axonal morphogenesis and filopodia formation in the growth cone. We show that dDAAM also plays a pivotal role during axonal growth and guidance in the adult Drosophila mushroom body, a brain center for learning and memory. By using a combination of genetic and biochemical assays, we demonstrate that Wnt5 and the PCP signaling proteins Frizzled, Strabismus, and Dishevelled act in concert with the small GTPase Rac1 to activate the actin assembly functions of dDAAM essential for correct targeting of mushroom body axons. Collectively, these data suggest that dDAAM is used as a major molecular effector of the PCP guidance pathway. By uncovering a signaling system from the Wnt5 guidance cue to an actin assembly factor, we propose that the Wnt5/PCP navigation system is linked by dDAAM to the regulation of the growth cone actin cytoskeleton, and thereby growth cone behavior, in a direct way.

  13. 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.

  14. 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.

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

    PubMed

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

    2015-04-01

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

  16. Aptamer sandwich-based carbon nanotube sensors for single-carbon-atomic-resolution detection of non-polar small molecular species.

    PubMed

    Lee, Joohyung; Jo, Minjoung; Kim, Tae Hyun; Ahn, Ji-Young; Lee, Dong-ki; Kim, Soyoun; Hong, Seunghun

    2011-01-01

    A portable sensor platform for the detection of small molecular species is crucial for the on-site monitoring of environmental pollutants, food toxicants, and disease-related metabolites. However, it is still extremely difficult to find highly selective and sensitive sensor platforms for general small molecular detection. Herein, we report aptamer sandwich-based carbon nanotube sensor strategy for small molecular detection, where aptamers were utilized to capture target molecules as well as to enhance the sensor signals. We successfully demonstrated the detection of non-polar bisphenol A molecules with a 1 pM sensitivity. Significantly, our sensors were able to distinguish between similar small molecular species with single-carbon-atomic resolution. Furthermore, using the additional biotin modification on labeling aptamer, we enhanced the detection limit of our sensors down to 10 fM. This strategy allowed us to detect non-polar small molecular species using carbon nanotube transistors, thus overcoming the fundamental limitation of field effect transistor-based sensors. Considering the extensive applications of sandwich assay for the detection of rather large biomolecules, our results should open up completely new dimension in small molecular detection technology and should enable a broad range of applications such as environmental protection and food safety.

  17. 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.

  18. 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

  19. Atomistic modeling of metallic nanowires in silicon

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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 104 to 106 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.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

  20. 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

  1. [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

  2. 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.

  3. Computer Science Techniques Applied to Parallel Atomistic Simulation

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    1998-03-01

    Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

  4. 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.

  5. 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)

  6. 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.

  7. 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.

  8. Amp: A modular approach to machine learning in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

    Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which

  9. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties.

    PubMed

    Ertl, P; Rohde, B; Selzer, P

    2000-10-01

    Molecular polar surface area (PSA), i.e., surface belonging to polar atoms, is a descriptor that was shown to correlate well with passive molecular transport through membranes and, therefore, allows prediction of transport properties of drugs. The calculation of PSA, however, is rather time-consuming because of the necessity to generate a reasonable 3D molecular geometry and the calculation of the surface itself. A new approach for the calculation of the PSA is presented here, based on the summation of tabulated surface contributions of polar fragments. The method, termed topological PSA (TPSA), provides results which are practically identical with the 3D PSA (the correlation coefficient between 3D PSA and fragment-based TPSA for 34 810 molecules from the World Drug Index is 0.99), while the computation speed is 2-3 orders of magnitude faster. The new methodology may, therefore, be used for fast bioavailability screening of virtual libraries having millions of molecules. This article describes the new methodology and shows the results of validation studies based on sets of published absorption data, including intestinal absorption, Caco-2 monolayer penetration, and blood-brain barrier penetration.

  10. 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.

  11. 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.

  12. 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.

  13. Visualization and analysis of atomistic simulation data with OVITO-the Open Visualization Tool

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2010-01-01

    The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/.

  14. 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.

  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. 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

  17. Atomistic models of amorphous polybutadienes; 3 -- Static free volume

    SciTech Connect

    Misra, S.; Mattice, W.L.

    1993-12-20

    Atomistic models of polybutadiene have been generated using molecular mechanics and molecular dynamics at a bulk density of 0.89 g cm{sup {minus}3}. Four microstructures formed by cis-1,4-polybutadiene, trans-1,4-polybutadiene, 1,2-polybutadiene, and a random copolymer of the three (55% trans, 35% cis, and 10% vinyl) are analyzed for static free volume. The free volume is determined by hard spherical probes that see the atoms as hard spheres of radii which equal 89% of their van der Waals radii. The total free volume, the free volume distribution, and the shape of the voids are analyzed for all four microstructures. The accessible free volume as a function of the probe size is found to be characteristic of voids in disordered packings of hard spheres. The free volume distributions have some common features across the microstructures. In particular, the free volume distributions as probed by a 1-{angstrom} radius probe show void size concentrations around {approximately}7.5 and 15 {angstrom}{sup 3} (with the exception of trans-polybutadiene, which does not display the latter). The shape factors for all four structures decay to the same asymptotic value of 0.67 {+-} 0.1 over the size range of 0--5 {angstrom}{sup 3}. There is a marked difference in the asphericity and the acylindricity of voids in the four microstructures. Analysis of randomly generated shapes suggests that the voids in the polymer microstructures are mostly elongated in comparison with randomly ``grown`` cavities, probably due to the connectivity of the polymer chains.

  18. Effect of cation asymmetry on the aggregation in aqueous 1-alkyl,3-decylimidazolium bromide solutions: molecular dynamics studies.

    PubMed

    Palchowdhury, Sourav; Bhargava, B L

    2014-06-12

    Self-assembly of cations in aqueous solutions of 1-alkyl,3-decylimidazolium bromide (with four different alkyl chains, methyl, butyl, heptyl, and decyl chain,) have been studied using atomistic molecular dynamics simulations. Polydisperse aggregates of cations are formed in the solution with alkyl tails in the core and the polar head groups present at the surface of the aggregates. The shape of the aggregates is dictated by the length of the alkyl chain. Aggregation numbers increase steadily with the increasing alkyl chain length. The greater asymmetry in the two-substituent chain length leads to a different surface structure compared to that of the cations with alkyl chains of similar length.

  19. Change of Magnetic Field-gas Alignment at the Gravity-driven Alfvénic Transition in Molecular Clouds: Implications for Dust Polarization Observations

    NASA Astrophysics Data System (ADS)

    Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun

    2016-10-01

    Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicular to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.

  20. 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‧.

  1. 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.

  2. Atomistic simulation of oxide dislocations and interfaces

    NASA Astrophysics Data System (ADS)

    Parker, S. C.; de Leeuw, N. H.; Harris, D. J.; Higgins, F. M.; Oliver, Pe M.; Redfern, S. E.; Watson, G. W.

    Atomistic simulation techniques have been used to study screw dislocations, grain boundaries, thin films and surfaces. The results show that the a/2<110> screw dislocations in bulk MgO and NiO are more stable than the a<100> although the latter are stabilised by vacancies. Adsorption of MgO units at the a<100> spiral dislocation shows a complicated two-layer growth mechanism. Self-diffusion through MgO grain boundaries is shown to be faster than in the bulk crystal, with pipe diffusion the energetically most favourable route. Study of thin iron oxide films on MgO found that the most stable MgO/Fe3O4 /(001) interface is an open structure with closely matching spacing between substrate Mg ions and oxygens of the film. The interaction of water with oxides MgO and SiO2 has been investigated. The dominance of the MgO surface is shown through facetting of the less stable and surfaces. The low-coordinated surface sites hence formed are the most reactive towards adsorption of water and dissolution. Similarly, α-quartz surfaces with dangling bonds are more reactive towards water and NaOH than the fully-coordinated surface sites.

  3. 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.

  4. Atomistic modeling of thermodynamic equilibrium of plutonium

    NASA Astrophysics Data System (ADS)

    Lee, Tongsik; Valone, Steve; Baskes, Mike; Chen, Shao-Ping; Lawson, Andrew

    2012-02-01

    Plutonium metal has complex thermodynamic properties. Among its six allotropes at ambient pressure, the fcc delta-phase exhibits a wide range of anomalous behavior: extraordinarily high elastic anisotropy, largest atomic volume despite the close-packed structure, negative thermal expansion, strong elastic softening at elevated temperature, and extreme sensitivity to dilute alloying. An accurate description of these thermodynamic properties goes far beyond the current capability of first-principle calculations. An elaborate modeling strategy at the atomic level is hence an urgent need. We propose a novel atomistic scheme to model elemental plutonium, in particular, to reproduce the anomalous characteristics of the delta-phase. A modified embedded atom method potential is fitted to two energy-volume curves that represent the distinct electronic states of plutonium in order to embody the mechanism of the two-state model of Weiss, in line with the insight originally proposed by Lawson et al. [Philos. Mag. 86, 2713 (2006)]. By the use of various techniques in Monte Carlo simulations, we are able to provide a unified perspective of diverse phenomenological aspects among thermal expansion, elasticity, and phase stability.

  5. 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.

  6. 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.

  7. 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.

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

    PubMed

    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(-) and a Na(+) 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(+) and F(-) 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 ΔC(p) stays positive and even increases slightly upon charging the Na(+) ion, it decreases upon charging the F(-) 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-01

    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- and a Na+ 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+ and F- 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 ΔCp stays positive and even increases slightly upon charging the Na+ ion, it decreases upon charging the F- 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.

  11. 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

  12. 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.

  13. 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.

  14. Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Norman, Paul Erik

    The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic modeling and mesoscopic description

    NASA Astrophysics Data System (ADS)

    Jacobs, William M.; Nicholson, David A.; Zemer, Hagit; Volkov, Alexey N.; Zhigilei, Leonid V.

    2012-10-01

    The exchange of energy between low-frequency mechanical oscillations and high-frequency vibrational modes in carbon nanotubes (CNTs) is a process that plays an important role in a range of dynamic phenomena involving the dissipation of mechanical energy in both individual CNTs and CNT-based materials. The rates and channels through which acoustic energy deposited instantaneously in individual CNTs is dissipated are investigated in a series of atomistic molecular dynamics simulations. Several distinct regimes of energy dissipation, dependent on the initial stretching or bending deformations, are established. The onset of axial or bending buckling marks the transition from a regime of slow thermalization to a regime in which the energy associated with longitudinal and bending oscillations is rapidly damped. In the case of stretching vibrations, an intermediate regime is revealed in which dynamic coupling between longitudinal vibrational modes and the radial “squash” mode causes delayed axial buckling followed by a rapid transfer of energy to high-frequency vibrations. The results of the atomistic simulations are used in the design and parameterization of a “heat bath” description of thermal energy in a mesoscopic model, which is capable of simulating systems consisting of thousands of interacting CNTs. Two complementary methods for the description of mechanical energy dissipation in the mesoscopic model are developed. The relatively slow dissipation of acoustic vibrations in the absence of buckling is described by adding a damping force to the equations of motion of the dynamic elements of the mesoscopic model. The sharp increase in the energy dissipation rate at the onset of buckling is reproduced by incorporating a hysteresis loop into the strain energy that accounts for localized thermalization in the vicinity of buckling kinks. The ability of the mesoscopic model to reproduce the complex multistep processes of acoustic energy dissipation predicted by the

  6. 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…

  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. 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.

  9. Quantum control of molecular handedness in a randomly oriented racemic mixture using three polarization components of electric fields

    NASA Astrophysics Data System (ADS)

    Hoki, Kunihito; González, Leticia; Fujimura, Yuichi

    2002-05-01

    A new laser control scenario is presented for obtaining substantial amounts of enantiomeric enrichment from a randomly oriented racemic mixture. This is carried out by using three polarization components of electric fields; one is used for orientation, the other two for controlling the chirality. The effectiveness is demonstrated by numerical simulations on the enantiomeric enrichment of the axial chiral H2POSH molecule.

  10. 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.

  11. 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.

  12. Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.

    PubMed

    de Jong, Djurre H; Liguori, Nicoletta; van den Berg, Tom; Arnarez, Clement; Periole, Xavier; Marrink, Siewert J

    2015-06-25

    Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain. Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.

  13. 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

  14. 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

  15. 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

  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.

  17. Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field.

    PubMed

    Duan, Rui; Lazim, Raudah; Zhang, Dawei

    2015-09-30

    Human immunodeficiency virus (HIV)-1 protease is one of the most promising drug target commonly utilized to combat Acquired Immune Deficiency Syndrome (AIDS). However, with the emergence of drug resistance arising from mutations, the efficiency of protease inhibitors (PIs) as a viable treatment for AIDS has been greatly reduced. I50V mutation as one of the most significant mutations occurring in HIV-1 protease will be investigated in this study. Molecular dynamics (MD) simulation was utilized to examine the effect of I50V mutation on the binding of two PIs namely indinavir and amprenavir to HIV-1 protease. Prior to the simulations conducted, the electron density distributions of the PI and each residue in HIV-1 protease are derived by combining quantum fragmentation approach molecular fractionation with conjugate caps and Poisson-Boltzmann solvation model based on polarized protein-specific charge scheme. The atomic charges of the binding complex are subsequently fitted using delta restrained electrostatic potential (delta-RESP) method to overcome the poor charge determination of buried atom. This way, both intraprotease polarization and the polarization between protease and the PI are incorporated into partial atomic charges. Through this study, the mutation-induced affinity variations were calculated and significant agreement between experiments and MD simulations conducted was observed for both HIV-1 protease-drug complexes. In addition, the mechanism governing the decrease in the binding affinity of PI in the presence of I50V mutation was also explored to provide insights pertaining to the design of the next generation of anti-HIV drugs. PMID:26198456

  18. 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.

  19. Molecular orientation of molybdate ions adsorbed on goethite nanoparticles revealed by polarized in situ ATR-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Davantès, Athénaïs; Lefèvre, Grégory

    2016-11-01

    The speciation of species adsorbed on nanoparticles is a major concern for several fields, as environmental pollution and remediation, surface functionalization, or catalysis. Attenuated total reflectance infrared spectroscopy (ATR-IR) was amongst the rare methods able to give in situ information about the geometry of surface complexes on nanoparticles. A new possibility using this technique is illustrated here with the MoO42 -/goethite system. Using deuterated goethite to avoid spectral interferences, adsorption of molybdate ions on a spontaneous oriented film of nanoparticles has been followed using a polarized infrared beam. From the decomposition of spectra in the x, y and z directions, a monodentate surface complex on the {101} faces has been found as the most probable geometry. This result demonstrates that polarized ATR-IR allows to characterize in more details adsorption mode at the atomic scale, in comparison with usual ATR-IR spectroscopy.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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)

  5. 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.

  6. A hybrid atomistic electrodynamics-quantum mechanical approach for simulating surface-enhanced Raman scattering.

    PubMed

    Payton, John L; Morton, Seth M; Moore, Justin E; Jensen, Lasse

    2014-01-21

    Surface-enhanced Raman scattering (SERS) is a technique that has broad implications for biological and chemical sensing applications by providing the ability to simultaneously detect and identify a single molecule. The Raman scattering of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude. These enhancements stem from a twofold mechanism: an electromagnetic mechanism (EM), which is due to the enhanced local field near the metal surface, and a chemical mechanism (CM), which is due to the adsorbate specific interactions between the metal surface and the molecules. The local field near the metal surface can be significantly enhanced due to the plasmon excitation, and therefore chemists generally accept that the EM provides the majority of the enhancements. While classical electrodynamics simulations can accurately simulate the local electric field around metal nanoparticles, they offer few insights into the spectral changes that occur in SERS. First-principles simulations can directly predict the Raman spectrum but are limited to small metal clusters and therefore are often used for understanding the CM. Thus, there is a need for developing new methods that bridge the electrodynamics simulations of the metal nanoparticle and the first-principles simulations of the molecule to facilitate direct simulations of SERS spectra. In this Account, we discuss our recent work on developing a hybrid atomistic electrodynamics-quantum mechanical approach to simulate SERS. This hybrid method is called the discrete interaction model/quantum mechanics (DIM/QM) method and consists of an atomistic electrodynamics model of the metal nanoparticle and a time-dependent density functional theory (TDDFT) description of the molecule. In contrast to most previous work, the DIM/QM method enables us to retain a detailed atomistic structure of the nanoparticle and provides a natural bridge between the electronic structure methods and the macroscopic

  7. Atomistic model of the spider silk nanostructure

    NASA Astrophysics Data System (ADS)

    Keten, Sinan; Buehler, Markus J.

    2010-04-01

    Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

  8. Solvation of complex surfaces via molecular density functional theory.

    PubMed

    Levesque, Maximilien; Marry, Virginie; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel

    2012-12-14

    We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.

  9. 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

  10. 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

  11. Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    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

  12. 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.

  13. 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.

  14. Determination of Collagen Fiber Orientation in Human Tissue by Use of Polarization Measurement of Molecular Second-Harmonic-Generation Light

    NASA Astrophysics Data System (ADS)

    Yasui, Takeshi; Tohno, Yoshiyuki; Araki, Tsutomu

    2004-05-01

    Based on the reflection-type polarization measurement of second-harmonic-generation (SHG) light induced by collagen molecules, we are able to determine the collagen fiber orientation in human tissues taken from a cadaver. The resulting SHG radar graph shows the direction of the absolute orientation and the degree of organization of collagen fibers. To evaluate the probing sensitivity to the collagen orientation, we compared the proposed method with other polarimetric methods. Use of the proposed method revealed characteristic orientation differences among collagen fibers and demonstrated significant inhomogeneity with respect to the distribution of collagen orientation in human dentin. The proposed method provides a powerful research and diagnostic tool for examining the collagen orientation in human tissues.

  15. Determining the molecular origin of radiation damage/enhancement in electro-optic polymeric materials through polarized light microscopy

    NASA Astrophysics Data System (ADS)

    Perez-Moreno, Javier

    2014-09-01

    Previous studies on the radiation effects upon polymer and polymer-based photonic materials suggest that the radiation resistance of the material is heavily dependent on the choice of polymer-host and guest-chromophore. The best results to date have been achieved with electro optic polymeric materials based on CLD1 doped in APC, which has resulted in improved performance at the device level upon gamma-ray irradiation at moderate doses. Still, our understanding of the physical mechanisms behind the enhancement of the performance is unclear. In this paper, we discuss how polarized light microscopy could be used as a means to quantify the effect of the different physical parameters that influence the optical response of electro-optic polymeric thin film samples.

  16. 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.

  17. Molten salt eutectics from atomistic simulations.

    PubMed

    Jayaraman, Saivenkataraman; Thompson, Aidan P; von Lilienfeld, O Anatole

    2011-09-01

    Despite their importance for solar thermal power applications, phase-diagrams of molten salt mixture heat transfer fluids (HTFs) are not readily accessible from first principles. We present a molecular dynamics scheme general enough to identify eutectics of any HTF candidate mixture. The eutectic mixture and temperature are located using the liquid mixture free energy and the pure component solid-liquid free energy differences. The liquid mixture free energy is obtained using thermodynamic integration over particle identity transmutations sampled with molecular dynamics at a single temperature. Drawbacks of conventional phase diagram mapping methodologies are avoided by not considering solid mixtures, thereby evading expensive computations of solid phase free energies. Numerical results for binary and ternary mixtures of alkali nitrates agree well with experimental measurements.

  18. Microwave-assisted on-spot derivatization for gas chromatography-mass spectrometry based determination of polar low molecular weight compounds in dried blood spots.

    PubMed

    Sadones, Nele; Van Bever, Elien; Archer, John R H; Wood, David M; Dargan, Paul I; Van Bortel, Luc; Lambert, Willy E; Stove, Christophe P

    2016-09-23

    Dried blood spot (DBS) sampling and analysis is increasingly being applied in bioanalysis. Although the use of DBS has many advantages, it is also associated with some challenges. E.g. given the limited amount of available material, highly sensitive detection techniques are often required to attain sufficient sensitivity. In gas chromatography coupled to mass spectrometry (GC-MS), derivatization can be helpful to achieve adequate sensitivity. Because this additional sample preparation step is considered as time-consuming, we introduce a new derivatization procedure, i.e. "microwave-assisted on-spot derivatization", to minimize sample preparation of DBS. In this approach the derivatization reagents are directly applied onto the DBS and derivatization takes place in a microwave instead of via conventional heating. In this manuscript we evaluated the applicability of this new concept of derivatization for the determination of two polar low molecular weight molecules, gamma-hydroxybutyric acid (GHB) and gabapentin, in DBS using a standard GC-MS configuration. The method was successfully validated for both compounds, with imprecision and bias values within acceptance criteria (<20% at LLOQ, <15% at 3 other QC levels). Calibration lines were linear over the 10-100μg/mL and 1-30μg/mL range for GHB and gabapentin, respectively. Stability studies revealed no significant decrease of gabapentin and GHB in DBS upon storage at room temperature for at least 84 days. Furthermore, DBS-specific parameters, including hematocrit and volume spotted, were evaluated. As demonstrated by the analysis of GHB and gabapentin positive samples, "microwave-assisted on-spot derivatization" proved to be reliable, fast and applicable in routine toxicology. Moreover, other polar low molecular weight compounds of interest in clinical and/or forensic toxicology, including vigabatrin, beta-hydroxybutyric acid, propylene glycol, diethylene glycol, 1,4-butanediol and 1,2-butanediol, can also be

  19. Microwave-assisted on-spot derivatization for gas chromatography-mass spectrometry based determination of polar low molecular weight compounds in dried blood spots.

    PubMed

    Sadones, Nele; Van Bever, Elien; Archer, John R H; Wood, David M; Dargan, Paul I; Van Bortel, Luc; Lambert, Willy E; Stove, Christophe P

    2016-09-23

    Dried blood spot (DBS) sampling and analysis is increasingly being applied in bioanalysis. Although the use of DBS has many advantages, it is also associated with some challenges. E.g. given the limited amount of available material, highly sensitive detection techniques are often required to attain sufficient sensitivity. In gas chromatography coupled to mass spectrometry (GC-MS), derivatization can be helpful to achieve adequate sensitivity. Because this additional sample preparation step is considered as time-consuming, we introduce a new derivatization procedure, i.e. "microwave-assisted on-spot derivatization", to minimize sample preparation of DBS. In this approach the derivatization reagents are directly applied onto the DBS and derivatization takes place in a microwave instead of via conventional heating. In this manuscript we evaluated the applicability of this new concept of derivatization for the determination of two polar low molecular weight molecules, gamma-hydroxybutyric acid (GHB) and gabapentin, in DBS using a standard GC-MS configuration. The method was successfully validated for both compounds, with imprecision and bias values within acceptance criteria (<20% at LLOQ, <15% at 3 other QC levels). Calibration lines were linear over the 10-100μg/mL and 1-30μg/mL range for GHB and gabapentin, respectively. Stability studies revealed no significant decrease of gabapentin and GHB in DBS upon storage at room temperature for at least 84 days. Furthermore, DBS-specific parameters, including hematocrit and volume spotted, were evaluated. As demonstrated by the analysis of GHB and gabapentin positive samples, "microwave-assisted on-spot derivatization" proved to be reliable, fast and applicable in routine toxicology. Moreover, other polar low molecular weight compounds of interest in clinical and/or forensic toxicology, including vigabatrin, beta-hydroxybutyric acid, propylene glycol, diethylene glycol, 1,4-butanediol and 1,2-butanediol, can also be

  20. 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.

  1. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface

    PubMed Central

    He, Xibing; Guvench, Olgun; MacKerell, Alexander D.; Klein, Michael L.

    2010-01-01

    Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length. PMID:20614916

  2. 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.

  3. Methods and numerical aspects of nanoscopic contact area estimation in atomistic tribological simulations

    NASA Astrophysics Data System (ADS)

    Eder, S.; Vernes, A.; Betz, G.

    2014-01-01

    We show how data obtained from molecular dynamics (MD) simulations of nanoscale friction should be treated for producing constitutive system parameters with a proper error estimation. A visualisation scheme for discrete atomistic geometries based on the smooth particle method (SPM) was parametrised and validated to yield an accurate and computationally robust estimation of the contact area between two touching nanoscopic asperities. We present some thoughts on the error estimation of the contact forces occurring due to the load and the shearing motion. The variance in the friction force constitutes the main source of error for the fitting of the constitutive system parameters. The dependence of the constitutive system parameters on the number of available data points was also studied. It was shown that an equal spacing (by load) of the data points can result in better values for the system parameters than the convergence trend suggests.

  4. 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

  5. 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

  6. Atomistic modeling of carbon Cottrell atmospheres in bcc iron.

    PubMed

    Veiga, R G A; Perez, M; Becquart, C S; Domain, C

    2013-01-16

    Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

  7. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    NASA Astrophysics Data System (ADS)

    Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

    2013-01-01

    Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

  8. Molecular and morphological adaptations in compressed articular cartilage by polarized light microscopy and Fourier-transform infrared imaging.

    PubMed

    Xia, Y; Alhadlaq, H; Ramakrishnan, N; Bidthanapally, A; Badar, F; Lu, M

    2008-10-01

    Fifteen articular cartilage-bone specimens from one canine humeral joint were compressed in the strain range of 0-50%. The deformation of the extracellular matrices in cartilage was preserved and the same tissue sections were studied using polarized light microscopy (PLM) and Fourier-transform infrared imaging (FTIRI). The PLM results show that the most significant changes in the apparent zone thickness due to 'reorganization' of the collagen fibrils based on the birefringence occur between 0% and 20% strain values, where the increase in the superficial zone and decrease in the radial zone thicknesses are approximately linear with the applied strain. The FTIRI anisotropy results show that the two amide components with bond direction perpendicular to the external compression retain anisotropy (amide II in the superficial zone and amide I in the radial zone). In contrast, the measured anisotropy from the two amide components with bond direction parallel to the external compression changes their anisotropy significantly (amide I in the superficial zone and amide II in the radial zone). Statistical analysis shows that there is an excellent correlation (r=0.98) between the relative depth of the minimum retardance in PLM and the relative depth of the amide II anisotropic cross-over. The changes in amide anisotropies in different histological zones are explained by the strain-dependent tipping angle of the amide bonds. These depth-dependent adaptations to static loading in cartilage's morphological structure and chemical distribution could be useful in the future studies of the early diseased cartilage.

  9. 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

  10. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald

    PubMed Central

    Lagardère, Louis; Lipparini, Filippo; Polack, Étienne; Stamm, Benjamin; Cancès, Éric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

    2015-01-01

    In this paper, we present a scalable and efficient 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-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 for a polarizable model making 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 non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations. PMID:26512230

  11. 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.

  12. 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.

  13. 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…

  14. Finite element analysis of an atomistically derived cohesive model for brittle fracture

    NASA Astrophysics Data System (ADS)

    Lloyd, J. T.; Zimmerman, J. A.; Jones, R. E.; Zhou, X. W.; McDowell, D. L.

    2011-09-01

    In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671-86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

  15. Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-10-01

    We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

  16. Development of Direct and Optical Polarized Nuclear Magnetic Resonance (NMR) Methods for Characterization and Engineering of Mesophased Molecular Structures

    SciTech Connect

    Maxwell, R; Baumann, T; Taylor, B

    2002-01-29

    The development of NMR methods for the characterization of structure and dynamics in mesophase composite systems was originally proposed in this LDRD. Mesophase systems are organic/inorganic hybrid materials whose size and motional properties span the definition of liquids and solids, such as highly viscous gels or colloidal suspensions. They are often composite, ill defined, macromolecular structures that prove difficult to characterize. Mesophase materials are of broad scientific and programmatic interest and include composite load bearing foams, aerogels, optical coatings, silicate oligomers, porous heterogeneous catalysts, and nanostructured materials such as semiconductor quantum dot superlattices. Since mesophased materials and precursors generally lack long-range order they have proven to be difficult to characterize beyond local, shortrange order. NMR methods are optimal for such a task since NMR observables are sensitive to wide ranges of length (0-30{angstrom}) and time (10{sup -9}-10{sup 0}sec) scales. We have developed a suit of NMR methods to measure local, intermediate, and long range structure in a series of mesophase systems and have constructed correlations between NMR observables and molecular size, topology, and network structure. The goal of this research was the development of a strong LLNL capability in the characterization of mesophased materials by NMR spectroscopy that will lead to a capability in rational synthesis of such materials and a fundamental understanding of their structure-property relationships. We demonstrate our progress towards attaining this goal by presenting NMR results on four mesophased model systems.

  17. 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.

  18. 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.

  19. 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.

  20. Comparison of the Luminous Efficiencies of Ga- and N-Polar InxGa1 -xN /InyGa1 -yN Quantum Wells Grown by Plasma-Assisted Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Fernández-Garrido, Sergio; Lähnemann, Jonas; Hauswald, Christian; Korytov, Maxim; Albrecht, Martin; Chèze, Caroline; Skierbiszewski, Czesław; Brandt, Oliver

    2016-09-01

    We investigate the luminescence of Ga- and N-polar InxGa1 -xN /InyGa1 -yN quantum wells grown by plasma-assisted molecular beam epitaxy on freestanding GaN as well as 6H -SiC substrates. In striking contrast to their Ga-polar counterparts, the N-polar quantum wells prepared on freestanding GaN do not exhibit any detectable photoluminescence even at 10 K. Theoretical simulations of the band profiles combined with resonant excitation of the quantum wells allow us to rule out carrier escape and subsequent surface recombination as the reason for this absence of luminescence. To explore the hypothesis of a high concentration of nonradiative defects at the interfaces between wells and barriers, we analyze the photoluminescence of Ga- and N-polar quantum wells prepared on 6H -SiC as a function of the well width. Intense luminescence is observed for both Ga- and N-polar samples. As expected, the luminescence of the Ga-polar quantum wells quenches and redshifts with increasing well width due to the quantum confined Stark effect. In contrast, both the intensity and the energy of the luminescence from the N-polar samples are essentially independent of the well width. Transmission electron microscopy reveals that the N-polar quantum wells exhibit abrupt interfaces and homogeneous composition, excluding emission from In-rich clusters as the reason for this anomalous behavior. The microscopic origin of the luminescence in the N-polar samples is elucidated using spatially resolved cathodoluminescence spectroscopy. Regardless of well width, the luminescence is found to not originate from the N-polar quantum wells but from the semipolar facets of ∨ -pit defects. These results cast serious doubts on the potential of N-polar InxGa1 -xN /InyGa1 -yN quantum wells grown by plasma-assisted molecular beam epitaxy for the development of long-wavelength light-emitting diodes.

  1. 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.

  2. 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

  3. 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.

  4. Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability.

    PubMed

    Goldwaser, Elodie; de Courcy, Benoit; Demange, Luc; Garbay, Christiane; Raynaud, Françoise; Hadj-Slimane, Reda; Piquemal, Jean-Philip; Gresh, Nohad

    2014-11-01

    We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are all linked together by conjugated bonds. The calculations use the SIBFA polarizable molecular mechanics procedure. Prior to docking simulations, it is essential to ensure that variations in the ligand conformational energy upon rotations around its six main-chain torsional bonds are correctly represented (as compared to high-level ab initio quantum chemistry, QC). This is done in two successive calibration stages and one validation stage. In the latter, the minima identified following independent stepwise variations of each of the six main-chain torsion angles are used as starting points for energy minimization of all the torsion angles simultaneously. Single-point QC calculations of the minimized structures are then done to compare their relative energies ΔE conf to the SIBFA ones. We compare three different methods of deriving the multipoles and polarizabilities of the central, most critical moiety of the inhibitor: carboxythiourea (CTU). The representation that gives the best agreement with QC is the one that includes the effects of the mutual polarization energy E pol between the amide and thioamide moieties. This again highlights the critical role of this contribution. The implications and perspectives of these findings are discussed.

  5. Structural properties of silver nanowires from atomistic descriptions

    NASA Astrophysics Data System (ADS)

    Jia, Jianming; Shi, Daning; Zhao, Jijun; Wang, Baolin

    2007-10-01

    The structural formation process and physical properties of silver nanowires were investigated via an unbiased genetic algorithm search using empirical potential combined with density-functional theory calculations. Some unexpected structural behaviors resulting from the intrinsic properties of silver were revealed. Two kinds of atomic arrangements, i.e., normal and abnormal configurations, appear alternately during the growth of wire, from which a (111) facet-based formation mechanism was observed. The excellent agreements between theoretical results and experimental observations on the structural motif, Young’s modulus, and shell effects of Ag nanowires indicate the importance of objective and precise atomistic descriptions in the study of nanosystems.

  6. 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.

  7. 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.

  8. 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.

  9. Ion irradiation tolerance of graphene as studied by atomistic simulations

    SciTech Connect

    Ahlgren, E. H.; Lehtinen, O.; Kotakoski, J.; Krasheninnikov, A. V.

    2012-06-04

    As impermeable to gas molecules and at the same time transparent to high-energy ions, graphene has been suggested as a window material for separating a high-vacuum ion beam system from targets kept at ambient conditions. However, accumulation of irradiation-induced damage in the graphene membrane may give rise to its mechanical failure. Using atomistic simulations, we demonstrate that irradiated graphene even with a high vacancy concentration does not show signs of such instability, indicating a considerable robustness of graphene windows. We further show that upper and lower estimates for the irradiation damage in graphene can be set using a simple model.

  10. 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

  11. 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

  12. 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

  13. Atomistic simulation of ion beam patterning with crater functions

    NASA Astrophysics Data System (ADS)

    Yang, Zhangcan; Lively, Michael; Allain, Jean Paul

    2013-07-01

    In this study, an atomistic model is developed to simulate ripple pattern formation when a surface is irradiated by incident low-energy energetic ions. The model treats individual ion impacts using crater functions, which represent the average change in the surface shape due to a single-ion impact. These functions incorporate the complete redistribution of mass along the surface due to an impact, and not just that due to sputtering. While most models only treat erosion, analysis of the craters reveals that the amount of mass redistributed across the surface is an order of magnitude greater than the mass removed by sputtering. Simulations in this study are conducted for 500 eV Ar+ bombardments of Si at angles of 0° to 60° with 5° increment at temperature of 350 K. Initial simulations with this model have shown agreement with prior observations of ripple pattern formation. However, some significant departures from other models based on the Bradley-Harper theory have emerged; the key difference is that the presence of crater rims plays a key role in ripple formation, which could explain phenomena such as maximum ripple amplitudes which most models do not account for. These results show that atomistic crater functions are a viable method for modeling ion beam patterning. They indicate that mass redistribution is a key mechanism for surface patterning.

  14. 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

  15. 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.

  16. Atomistic interpretation of solid solution hardening from spectral analysis.

    PubMed

    Plendl, J N

    1971-05-01

    From analysis of a series of vibrational spectra of ir energy absorption and laser Raman, an attempt is made to interpret solid solution hardening from an atomistic point of view for the system CaF(2)/SrF(2). It is shown to be caused by the combined action of three atomic characteristics, i.e., their changes as a function of composition. They are deformation of the atomic coordination polyhedrons, overlap of the outer electron shells of the atom pairs, and the ratio of the ionic to covalent share of binding. A striking nonlinear behavior of the three characteristics, as a function of composition, gives maximum atomic bond strength to the 55/45 position of the system CaF(2)/SrF(2), in agreement with the measured data of the solid solution hardening. The curve for atomic bond strength, derived from the three characteristics, is almost identical to the curve for measured microhardness data. This result suggests that the atomistic interpretation, put forward in this paper, is correct.

  17. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

    PubMed Central

    Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

    2016-01-01

    Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

  18. A material frame approach for evaluating continuum variables in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Zimmerman, Jonathan A.; Jones, Reese E.; Templeton, Jeremy A.

    2010-03-01

    We present a material frame formulation analogous to the spatial frame formulation developed by Hardy, whereby expressions for continuum mechanical variables such as stress and heat flux are derived from atomic-scale quantities intrinsic to molecular simulation. This formulation is ideally suited for developing an atomistic-to-continuum correspondence for solid mechanics problems. We derive expressions for the first Piola-Kirchhoff (P-K) stress tensor and the material frame heat flux vector directly from the momentum and energy balances using localization functions in a reference configuration. The resulting P-K stress tensor, unlike the Cauchy expression, has no explicit kinetic contribution. The referential heat flux vector likewise lacks the kinetic contribution appearing in its spatial frame counterpart. Using a proof for a special case and molecular dynamics simulations, we show that our P-K stress expression nonetheless represents a full measure of stress that is consistent with both the system virial and the Cauchy stress expression developed by Hardy. We also present an expanded formulation to define continuum variables from micromorphic continuum theory, which is suitable for the analysis of materials represented by directional bonding at the atomic scale.

  19. Atomistic surface erosion and thin film growth modelled over realistic time scales

    NASA Astrophysics Data System (ADS)

    Scott, Chris; Blackwell, Sabrina; Vernon, Louis; Kenny, Steven; Walls, Michael; Smith, Roger

    2011-11-01

    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.

  20. Supramolecular Systems Behavior at the Air-Water Interface. Molecular Dynamic Simulation Study.

    NASA Astrophysics Data System (ADS)

    Sandoval, C.; Saavedra, M.; Gargallo, L.; Radić, D.

    2008-08-01

    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 α-cyclodextrin (CD) with poly(ethylene-oxide)(PEO), poly(ɛ-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF). The simulations were carried out for a surface area of 30Å. 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.

  1. 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.

  2. ATOMIC AND MOLECULAR PHYSICS: High order correlation-polarization potential for vibrational excitation scattering of diatomic molecules by low-energy electrons

    NASA Astrophysics Data System (ADS)

    Feng, Hao; Sun, Wei-Guo; Zeng, Yang-Yang

    2009-11-01

    This paper introduces a correlation-polarization potential with high order terms for vibrational excitation in electron-molecule scattering. The new polarization potential generalizes the two-term approximation so that it can better reflect the dependence of correlation and polarization effects on the position coordinate of the scattering electron. It applies the new potential on the vibrational excitation scattering from N2 in an energy range which includes the 2Πg shape resonance. The good agreement of theoretical resonant peaks with experiments shows that polarization potentials with high order terms are important and should be included in vibrational excitation scattering.

  3. 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.

  4. Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT1 and ETA receptor antagonists

    PubMed Central

    Singh, Khuraijam Dhanachandra; Muthusamy, Karthikeyan

    2013-01-01

    Aim: Both endothelin ETA receptor antagonists and angiotensin AT1 receptor antagonists lower blood pressure in hypertensive patients. A dual AT1 and ETA receptor antagonist may be more efficacious antihypertensive drug. In this study we identified the mode and mechanism of binding of imidazole series of compounds as dual AT1 and ETA receptor antagonists. Methods: Molecular modeling approach combining quantum-polarized ligand docking (QPLD), MM/GBSA free-energy calculation and 3D-QSAR analysis was used to evaluate 24 compounds as dual AT1 and ETA receptor antagonists and to reveal their binding modes and structural basis of the inhibitory activity. Pharmacophore-based virtual screening and docking studies were performed to identify more potent dual antagonists. Results: 3D-QSAR models of the imidazole compounds were developed from the conformer generated by QPLD, and the resulting models showed a good correlation between the predicted and experimental activity. The visualization of the 3D-QSAR model in the context of the compounds under study revealed the details of the structure-activity relationship: substitution of methoxymethyl and cyclooctanone might increase the activity against AT1 receptor, while substitution of cyclohexone and trimethylpyrrolidinone was important for the activity against ETA receptor; addition of a trimethylpyrrolidinone to compound 9 significantly reduced its activity against AT1 receptor but significantly increased its activity against ETA receptor, which was likely due to the larger size and higher intensities of the H-bond donor and acceptor regions in the active site of ETA receptor. Pharmacophore-based virtual screening followed by subsequent Glide SP, XP, QPLD and MM/GBSA calculation identified 5 potential lead compounds that might act as dual AT1 and ETA receptor antagonists. Conclusion: This study may provide some insights into the development of novel potent dual ETA and AT1 receptor antagonists. As a result, five compounds are

  5. Polarizability versus mobility: atomistic force field for ionic liquids.

    PubMed

    Chaban, Vitaly

    2011-09-21

    Based on classical molecular dynamics simulations, we discuss the impact of Coulombic interactions on a comprehensive set of properties of room temperature ionic liquids (RTILs) containing 1,3-dimethylimidazolium (MMIM(+)), N-butylpyridinium (BPY(+)), and bis(trifluoromethane sulfonyl)imide (TFSI(-)) ions. Ionic transport is found to be noticeably hindered by the excessive Coulombic energy, originating from the neglect of electronic polarization in the condensed phase of these RTILs. Starting from the models, recently suggested by Lopes and Padua, we show that realistic ionic dynamics can be achieved by the uniform scaling of electrostatic charges on all interaction sites. The original model systematically overestimates density and heat of vaporization of RTILs. Since density linearly depends on charge scaling, it is possible to use it as a convenient beacon to promptly derive a correct scaling factor. Based on the simulations of [BPY][TFSI] and [MMIM][TFSI] over a wide temperature range, we conclude that the suggested technique is feasible to greatly improve quality of the already existing non-polarizable FFs for RTILs.

  6. Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a Light Harvesting 2 complex.

    PubMed

    van der Vegte, C P; Prajapati, J D; Kleinekathöfer, U; Knoester, J; Jansen, T L C

    2015-01-29

    The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient manner. A general description of the chromophores and the interaction with their local environment is crucial to understand this highly efficient energy transport. Here we include this interaction in an atomistic way using mixed quantum-classical (molecular dynamics) simulations of spectra. In particular, we present the first atomistic simulation of nonlinear optical spectra for LH2 and use it to study the energy transport within the complex. We show that the frequency distributions of the pigments strongly depend on their positions with respect to the protein scaffold and dynamics of their local environment. Furthermore, we show that although the pigments are closely packed the transition frequencies of neighboring pigments are essentially uncorrelated. We present the simulated linear absorption spectra for the LH2 complex and provide a detailed explanation of the states responsible for the observed two-band structure. Finally, we discuss the energy transfer within the complex by analyzing population transfer calculations and 2D spectra for different waiting times. We conclude that the energy transfer from the B800 ring to the B850 ring is mediated by intermediate states that are delocalized over both rings, allowing for a stepwise downhill energy transport.

  7. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    PubMed Central

    Beauchamp, Kyle A.; Behr, Julie M.; Rustenburg, Ariën S.; Bayly, Christopher I.; Kroenlein, Kenneth; Chodera, John D.

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using the AM1-BCC charge model against experimental measurements (specifically bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive, and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge forcefields in the representation low dielectric environments such as those seen in binding cavities or biological membranes. PMID:26339862

  8. 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

  9. Elastic deformation and area per lipid of membranes: atomistic view from solid-state deuterium NMR spectroscopy.

    PubMed

    Kinnun, Jacob J; Mallikarjunaiah, K J; Petrache, Horia I; Brown, Michael F

    2015-01-01

    This article reviews the application of solid-state ²H nuclear magnetic resonance (NMR) spectroscopy for investigating the deformation of lipid bilayers at the atomistic level. For liquid-crystalline membranes, the average structure is manifested by the segmental order parameters (SCD) of the lipids. Solid-state ²H NMR yields observables directly related to the stress field of the lipid bilayer. The extent to which lipid bilayers are deformed by osmotic pressure is integral to how lipid-protein interactions affect membrane functions. Calculations of the average area per lipid and related structural properties are pertinent to bilayer remodeling and molecular dynamics (MD) simulations of membranes. To establish structural quantities, such as area per lipid and volumetric bilayer thickness, a mean-torque analysis of ²H NMR order parameters is applied. Osmotic stress is introduced by adding polymer solutions or by gravimetric dehydration, which are thermodynamically equivalent. Solid-state NMR studies of lipids under osmotic stress probe membrane interactions involving collective bilayer undulations, order-director fluctuations, and lipid molecular protrusions. Removal of water yields a reduction of the mean area per lipid, with a corresponding increase in volumetric bilayer thickness, by up to 20% in the liquid-crystalline state. Hydrophobic mismatch can shift protein states involving mechanosensation, transport, and molecular recognition by G-protein-coupled receptors. Measurements of the order parameters versus osmotic pressure yield the elastic area compressibility modulus and the corresponding bilayer thickness at an atomistic level. Solid-state ²H NMR thus reveals how membrane deformation can affect protein conformational changes within the stress field of the lipid bilayer.

  10. 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.

  11. 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.

  12. Emergence of linear elasticity from the atomistic description of matter.

    PubMed

    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. PMID:27497565

  13. 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.

  14. Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

    SciTech Connect

    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.

  15. Numerical algorithms for the atomistic dopant profiling of semiconductor materials

    NASA Astrophysics Data System (ADS)

    Aghaei Anvigh, Samira

    In this dissertation, we investigate the possibility to use scanning microscopy such as scanning capacitance microscopy (SCM) and scanning spreading resistance microscopy (SSRM) for the "atomistic" dopant profiling of semiconductor materials. For this purpose, we first analyze the discrete effects of random dopant fluctuations (RDF) on SCM and SSRM measurements with nanoscale probes and show that RDF significantly affects the differential capacitance and spreading resistance of the SCM and SSRM measurements if the dimension of the probe is below 50 nm. Then, we develop a mathematical algorithm to compute the spatial coordinates of the ionized impurities in the depletion region using a set of scanning microscopy measurements. The proposed numerical algorithm is then applied to extract the (x, y, z) coordinates of ionized impurities in the depletion region in the case of a few semiconductor materials with different doping configuration. The numerical algorithm developed to solve the above inverse problem is based on the evaluation of doping sensitivity functions of the differential capacitance, which show how sensitive the differential capacitance is to doping variations at different locations. To develop the numerical algorithm we first express the doping sensitivity functions in terms of the Gâteaux derivative of the differential capacitance, use Riesz representation theorem, and then apply a gradient optimization approach to compute the locations of the dopants. The algorithm is verified numerically using 2-D simulations, in which the C-V curves are measured at 3 different locations on the surface of the semiconductor. Although the cases studied in this dissertation are much idealized and, in reality, the C-V measurements are subject to noise and other experimental errors, it is shown that if the differential capacitance is measured precisely, SCM measurements can be potentially used for the "atomistic" profiling of ionized impurities in doped semiconductors.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Circularly Polarized MHOHG with Bichromatic Circularly Polarized Laser Pulses

    NASA Astrophysics Data System (ADS)

    Bandrauk, Andre D.; Mauger, Francois; Uzer, Turgay

    2016-05-01

    Circularly polarized MHOHG-Molecular High Order Harmonic Generation is shown to occur efficiently with intense ultrashort bichromatic circularly polarized pulses due to frequent electron-parent -ion recollision with co-or counter-rotating incident circular pulses as predicted in 1995. We show in this context that molecules offer a very robust and efficient frameworkfor the production of circularly polarized harmonics for the generation of single circularly polarized ``attosecond'' pulses. The efficiency of such new MHOHG is shown to depend on the compatibility of the symmetry of the molecular medium with the net electric field generated by the combination of the laser pulses.Using a time-dependent symmetry analysis with concrete examples such as H 2 + vs H 3 + we show how all the features(harmonic order and ∧ polarization) of MHOHG can be explained and predicted.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide

    NASA Astrophysics Data System (ADS)

    Erhart, Paul; Albe, Karsten

    2005-01-01

    We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work [Phys. Rev. B 65, 195124 (2002)] and is built on three independently fitted potentials for SiSi , CC , and SiC interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space.

  13. Structure and properties of composites based chitosan and carbon nanostructures: atomistic and coarse-grained simulation

    NASA Astrophysics Data System (ADS)

    Glukhova, O. E.; Kolesnikova, A. S.; Grishina, O. A.; Slepchenkov, M. M.

    2015-03-01

    At the present time actual task of the modern materials is the creation of biodegradable biocompatible composite materials possessing high strength properties for medical purposes. One of the most promising biomaterials from a position of creation on their basis super strong nanofibres is chitosan. The aim of this work is a theoretical study of the structural features and physico-mechanical properties of biocomposite materials based on chitosan and carbon nanostructures. As matrix nanocomposite we considered various carbon nano-objects, namely carbon nanotubes and graphene. Using the developed original software complex KVAZAR we built atomistic and coarse-grained models of the biocomposite material. To identify regularities of influence of the configuration of the carbon matrix on the mechanical and electronic properties of biocomposite we carried out a series of numerical experiments using a classical algorithm of molecular dynamics and semi-empirical methods. The obtained results allow us to suggest that the generated biocomposite based on chitosan and carbon nanostructures has high stability and strength characteristics. Such materials can be used in biomedicine as a base material for creating of artificial limbs.

  14. Continuum and atomistic modeling of ion partitioning into a peptide nanotube.

    PubMed Central

    Asthagiri, D; Bashford, D

    2002-01-01

    Continuum and atomistic descriptions of the partitioning of ions into a self-assembled (D,L)-octapeptide nanotube, cyclo[-(L-Ala-D-Ala)(4)-], are presented. Perturbation free energy calculations, including Ewald electrostatics, are used to estimate the electrostatic component of the excess free energy of charging Li(+), Na(+), Rb(+), and Cl(minus sign) ions inside the nanotube. The radial density and orientational distribution of water around the ion is calculated for the ion at two different positions inside the tube; it is seen that the calculated distributions are sensitive to the location of the ions. Two different continuum electrostatic models are formulated to describe the ion solvation inside the nanotube. When enhanced orientational structuring of water dipoles is evidenced, explicitly including the first solvation shell as part of the low dielectric nanotube environment provides good agreement with molecular dynamics simulations. When water orientational structuring is as in the reference bulk solvent, we find that treating the first shell water explicitly or as a high dielectric continuum leads to similar results. These results are discussed, and their importance for continuum electrostatic modeling of ion channels are highlighted. PMID:11867436

  15. 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).

  16. 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.

  17. 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.

  18. Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria.

    PubMed

    Huh, Joonsuk; Saikin, Semion K; Brookes, Jennifer C; Valleau, Stéphanie; Fujita, Takatoshi; Aspuru-Guzik, Alán

    2014-02-01

    Phototrophic organisms such as plants, photosynthetic bacteria, and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have several functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be among the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria, the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level, we introduce an atomistic model that mimics a complete light-harvesting apparatus of green sulfur bacteria. The model contains approximately 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate, and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the transfer between collective excited states of pigments can result in robust energy funneling to the initial excitation conditions and temperature changes. Moreover, the same mechanism describes the coexistence of multiple time scales of excitation dynamics frequently observed in ultrafast optical experiments. While our findings support the hypothesis of supertransfer, the model reveals energy transport through multiple channels on different length scales.

  19. Stapled BH3 Peptides against MCL-1: Mechanism and Design Using Atomistic Simulations

    PubMed Central

    Joseph, Thomas L.; Lane, David P.; Verma, Chandra S.

    2012-01-01

    Atomistic simulations of a set of stapled alpha helical peptides derived from the BH3 helix of MCL-1 (Stewart et al. (2010) Nat Chem Biol 6: 595–601) complexed to a fragment (residues 172–320) of MCL-1 revealed that the highest affinity is achieved when the staples engage the surface of MCL-1 as has also been demonstrated for p53-MDM2 (Joseph et al. (2010) Cell Cycle 9: 4560–4568; Baek et al. (2012) J Am Chem Soc 134: 103–106). Affinity is also modulated by the ability of the staples to pre-organize the peptides as helices. Molecular dynamics simulations of these stapled BH3 peptides were carried out followed by determination of the energies of interactions using MM/GBSA methods. These show that the location of the staple is a key determinant of a good binding stapled peptide from a bad binder. The good binder derives binding affinity from interactions between the hydrophobic staple and a hydrophobic patch on MCL-1. The position of the staple was varied, guiding the design of new stapled peptides with higher affinities. PMID:22952838

  20. 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.

  1. 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.

  2. Atomistic Simulations of Hydrated Nafion and Temperature Effects on Hydronium Ion Mobility

    SciTech Connect

    Venkatnathan, Arun; Devanathan, Ram; Dupuis, Michel

    2007-04-06

    The effects of level of hydration and temperature on the nanostructure of an atomistic model of a NafionTM (Du Pont) membrane and the vehicular transport of hydronium ions and water molecules were examined using classical molecular dynamics simulations. Through the determination and analysis of structural and dynamical parameters such as density, radial distribution functions, coordination numbers, means square deviations, and diffusion coefficients, we identify that hydronium ions themselves play a role in modifying the interfacial structure in the membrane at the sulfonate pendants. In the regime of low level of hydration, short hydrogen bonded linkages made of water molecules and also hydronium ions give a more constrained structure to the sulfonate pendants. The diffusion coefficient for water was found to be in good accord with experimental data. The diffusion coefficient for hydronium ions was determined to be much smaller (6 to 10 times) than for water. Temperature was found to have a significant effect on the absolute value of the diffusion coefficients for both water and hydroniums.

  3. 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.

  4. Computational Study of Atomistic Strain Relaxation Mechanisms in Biaxially Strained Ultra-Thin Metallic Films

    NASA Astrophysics Data System (ADS)

    Gungor, M. Rauf; Maroudas, Dimitrios

    2005-03-01

    Understanding the mechanical response under certain loading conditions of nanometer-scale-thick metallic films is fundamentally and technologically important. In this presentation, we report a comprehensive computational analysis on the atomistic mechanisms of strain relaxation under a wide range of applied biaxial tensile strain in free-standing ultra-thin Cu films based on multi-million-atom molecular-dynamics simulations. Our analysis reveals that after an elastic response at low strain (< 2%), plastic deformation occurs accompanied by dislocation emission from the void surface, void surface morphological transition, dislocation jogging, vacancy generation and migration along dislocation cores, as well as formation and propagation of threading dislocation loops from the film's surfaces. At higher (> 6%) strain levels, a transition to a new plastic deformation regime gives rise to a practically uniform distribution of dislocations in the metallic thin film. Under such conditions, dislocations are emitted from the thin film's surfaces and inhibit void growth due to their interactions with the dislocations emitted from the void surface and the resulting pinning of the latter defects.

  5. Atomistic finite element model for axial buckling and vibration analysis of single-layered graphene sheets

    NASA Astrophysics Data System (ADS)

    Rouhi, S.; Ansari, R.

    2012-01-01

    In this article, an atomistic model is developed to study the buckling and vibration characteristics of single-layered graphene sheets (SLGSs). By treating SLGSs as space-frame structures, in which the discrete nature of graphene sheets is preserved, they are modeled using three-dimensional elastic beam elements for the bonds. The elastic moduli of the beam elements are determined via a linkage between molecular mechanics and structural mechanics. Based on this model, the critical compressive forces and fundamental natural frequencies of single-layered graphene sheets with different boundary conditions and geometries are obtained and then compared. It is indicated that the compressive buckling force decreases when the graphene sheet aspect ratio increases. At low aspect ratios, the increase of aspect ratios will result in a significant decrease in the critical buckling load. It is also indicated that increasing aspect ratio at a given side length results in the convergence of buckling envelops associated with armchair and zigzag graphene sheets. The influence of boundary conditions will be studied for different geometries. It will be shown that the influence of boundary conditions is not significant for sufficiently large SLGSs.

  6. 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).

  7. 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

  8. Atomistic modelling and prediction of glass forming ability in bulk metallic glasses

    NASA Astrophysics Data System (ADS)

    Sedighi, Sina

    Atomistic modeling (via molecular dynamics with EAM interaction potentials) was conducted for the detailed investigation of kinetics, thermodynamics, structure, and bonding in Ni-Al and Cu-Zr metallic glasses. This work correlates GFA with the nature of atomic-level bonding and vibrational properties, with results potentially extensible to the Transition Metal -- Transition Metal and Transition Metal -- Metalloid alloy classes in general. As a first step in the development of a liquid-only GFA tuning approach, an automated tool has also been created for the broad compositional sampling of liquid and glassy phase properties in multicomponent (binary, ternary, quaternary) alloy systems. Its application to the Cu-Zr alloy system shows promising results, including the successful identification of the two highest GFA compositions, Cu50Zr50 and Cu64Zr 36. Combined, the findings of this work highlight the critical importance of incorporating more complex alloy-specific information regarding the nature of bonding and ordering at the atomic level into such an approach.

  9. 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

  10. 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

  11. Direct correlation between the internal quantum efficiency and photoluminescence lifetime in undoped ZnO epilayers grown on Zn-polar ZnO substrates by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Takamizu, D.; Nishimoto, Y.; Akasaka, S.; Yuji, H.; Tamura, K.; Nakahara, K.; Onuma, T.; Tanabe, T.; Takasu, H.; Kawasaki, M.; Chichibu, S. F.

    2008-03-01

    The equivalent internal quantum efficiency (ηinteq) at 300K of the near-band-edge excitonic photoluminescence (PL) peak in ZnO epilayers grown by plasma-assisted molecular beam epitaxy on Zn-polar ZnO substrates was directly correlated with the PL lifetime (τPL) for the first time. This relation seems to be universal for O-polar ZnO films grown by other methods. Present homoepitaxial ZnO epilayers grown above 800°C exhibited atomically flat surfaces, and the best full-width-at-half-maximum value of (0002) ZnO x-ray diffraction ω-rocking curves was 17.6arcsec. The high-temperature growth also led to a long τPL of 1.2ns at 300K. As a result, a record high ηinteq value (9.6%) was eventually obtained under an excitation density of 5W/cm2 (He-Cd, 325.0nm). The homoepitaxial Zn-polar ZnO films grown by molecular beam epitaxy are coming to be used for p-n junction devices.

  12. 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.

  13. 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.

  14. Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

    NASA Astrophysics Data System (ADS)

    Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

    2016-09-01

    The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

  15. 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.

  16. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

    PubMed

    Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J

    2011-06-14

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein

  17. Polar Bear

    USGS Publications Warehouse

    Amstrup, S.D.; ,; Lentfer, J.W.

    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.

  18. 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

  19. 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

  20. 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.

  1. Polarization control at spin-driven ferroelectric domain walls.

    PubMed

    Leo, Naëmi; Bergman, Anders; Cano, Andres; Poudel, Narayan; Lorenz, Bernd; Fiebig, Manfred; Meier, Dennis

    2015-04-14

    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.

  2. Molecular modeling and simulation of atactic polystyrene/amorphous silica nanocomposites

    NASA Astrophysics Data System (ADS)

    Mathioudakis, I.; Vogiatzis, G. G.; Tzoumanekas, C.; Theodorou, D. N.

    2016-08-01

    The local structure, segmental dynamics, topological analysis of entanglement networks and mechanical properties of atactic polystyrene - amorphous silica nanocomposites are studied via molecular simulations using two interconnected levels of representation: (a) A coarse - grained level. Equilibration at all length scales at this level is achieved via connectivity - altering Monte Carlo simulations. (b) An atomistic level. Initial configurations for atomistic Molecular Dynamics (MD) simulations are obtained by reverse mapping well- equilibrated coarse-grained configurations. By analyzing atomistic MD trajectories, the polymer density profile is found to exhibit layering in the vicinity of the nanoparticle surface. The dynamics of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm. Atomistic simulation results for the mechanical properties are compared to the experimental measurements and other computational works.

  3. 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.

  4. 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

  5. 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

  6. Atomistic models of general anesthetics for use in in silico biological studies.

    PubMed

    Arcario, Mark J; Mayne, Christopher G; Tajkhorshid, Emad

    2014-10-23

    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.

  7. 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

  8. 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.

  9. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. II. Adsorption and diffusion

    NASA Astrophysics Data System (ADS)

    Kim, Nayong; Harale, Aadesh; Tsotsis, Theodore T.; Sahimi, Muhammad

    2007-12-01

    Nanoporous layered double hydroxide (LDH) materials have wide applications, ranging from being good adsorbents for gases (particularly CO2) and liquid ions to membranes and catalysts. They also have applications in medicine, environmental remediation, and electrochemistry. Their general chemical composition is [M1-xIIMxIII(OH-)2]x+[Xn/mm -•nH2O], where M represents a metallic cation (of valence II or III), and Xn/mm - is an m-valence inorganic, or heteropolyacid, or organic anion. We study diffusion and adsorption of CO2 in a particular LDH with MII=Mg, MIII=Al, and x ≃0.71, using an atomistic model developed based on energy minimization and molecular dynamics simulations, together with a modified form of the consistent-valence force field. The adsorption isotherms and self-diffusivity of CO2 in the material are computed over a range of temperature, using molecular simulations. The computed diffusivities are within one order of magnitude of the measured ones at lower temperatures, while agreeing well with the data at high temperatures. The measured and computed adsorption isotherms agree at low loadings, but differ by about 25% at high loadings. Possible reasons for the differences between the computed properties and the experimental data are discussed, and a model for improving the accuracy of the computed properties is suggested. Also studied are the material's hydration and swelling properties. As water molecules are added to the pore space, the LDH material swells to some extent, with the hydration energy exhibiting interesting variations with the number of the water molecules added. The implications of the results are discussed.

  10. Multiscale coupling of molecular dynamics and peridynamics

    NASA Astrophysics Data System (ADS)

    Tong, Qi; Li, Shaofan

    2016-10-01

    We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.

  11. 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

  12. 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.

    PubMed

    Lefort, Ronan; Bordat, Patrice; Cesaro, Attilio; Descamps, Marc

    2007-01-01

    This paper uses chemical shift surfaces to simulate experimental (13)C 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 (13)C nuclear magnetic resonance measurements. Implications of these findings for the fragility of trehalose glass and bioprotectant action are discussed. PMID:17212504

  13. 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.

  14. Transistor roadmap projection using predictive full-band atomistic modeling

    SciTech Connect

    Salmani-Jelodar, M. Klimeck, G.; Kim, S.; Ng, K.

    2014-08-25

    In this letter, a full band atomistic quantum transport tool is used to predict the performance of double gate metal-oxide-semiconductor field-effect transistors (MOSFETs) over the next 15 years for International Technology Roadmap for Semiconductors (ITRS). As MOSFET channel lengths scale below 20 nm, the number of atoms in the device cross-sections becomes finite. At this scale, quantum mechanical effects play an important role in determining the device characteristics. These quantum effects can be captured with the quantum transport tool. Critical results show the ON-current degradation as a result of geometry scaling, which is in contrast to previous ITRS compact model calculations. Geometric scaling has significant effects on the ON-current by increasing source-to-drain (S/D) tunneling and altering the electronic band structure. By shortening the device gate length from 20 nm to 5.1 nm, the ratio of S/D tunneling current to the overall subthreshold OFF-current increases from 18% to 98%. Despite this ON-current degradation by scaling, the intrinsic device speed is projected to increase at a rate of at least 8% per year as a result of the reduction of the quantum capacitance.

  15. 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.

  16. Atomistic simulation of the differences between calcite and dolomite surfaces

    SciTech Connect

    Titiloye, J.O.; Leeuw, N.H. de; Parker, S.C.

    1998-08-01

    Atomistic simulation methods have been used to calculate and compare the surface structures and energies of the {l_brace}10{bar 1}4{r_brace}, {l_brace}0001{r_brace}, {l_brace}10{bar 1}0{r_brace}, {l_brace}11{bar 2}0{r_brace} and {l_brace}10{bar 1}1{r_brace} surfaces of calcite and dolomite and to evaluate their equilibrium morphologies. The calcite {l_brace}10{bar 1}4{r_brace} and the dolomite {l_brace}10{bar 1}0{r_brace} and {l_brace}11{bar 2}0{r_brace} surfaces are the most stable crystal planes. Investigation of the segregation of Mg and Ca ions in the dolomite crystal shows a clear preference for Ca{sup 2+} ions at the surface sites and for Mg{sup 2+} ions in the bulk sites and hence growth onto dolomite results in calcium carbonate or high magnesian calcite crystals which helps explain the difficulty in crystallizing dolomite vs. calcite under laboratory conditions.

  17. Coarse-Grained and Atomistic Modeling of Polyimides

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Hinkley, Jeffrey A.

    2004-01-01

    A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

  18. Atomistic mechanisms for bilayer growth of graphene on metal substrates

    SciTech Connect

    Chen, Wei; Cui, Ping; Zhu, Wenguang; Kaxiras, Efthimios; Gao, Yanfei; Zhang, Zhenyu

    2015-01-08

    Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast, the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse "Ehrlich-Schwoebel barrier" effect, becoming smaller for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. Lastly, these findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.

  19. Atomistic mechanisms for bilayer growth of graphene on metal substrates

    DOE PAGESBeta

    Chen, Wei; Cui, Ping; Zhu, Wenguang; Kaxiras, Efthimios; Gao, Yanfei; Zhang, Zhenyu

    2015-01-08

    Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast,more » the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse "Ehrlich-Schwoebel barrier" effect, becoming smaller for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. Lastly, these findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.« less

  20. Equilibrium at the edge and atomistic mechanisms of graphene growth

    PubMed Central

    Artyukhov, Vasilii I.; Liu, Yuanyue; Yakobson, Boris I.

    2012-01-01

    The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene. PMID:22949702

  1. Atomistic modeling of phonon transport in turbostratic graphitic structures

    NASA Astrophysics Data System (ADS)

    Mao, Rui; Chen, Yifeng; Kim, Ki Wook

    2016-05-01

    Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated at the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10-10 K m2/W to 116 × 10-10 K m2/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.

  2. Seawater Pervaporation through Zeolitic Imidazolate Framework Membranes: Atomistic Simulation Study.

    PubMed

    Gupta, Krishna M; Qiao, Zhiwei; Zhang, Kang; Jiang, Jianwen

    2016-06-01

    An atomistic simulation study is reported for seawater pervaporation through five zeolitic imidazolate framework (ZIF) membranes including ZIF-8, -93, -95, -97, and -100. Salt rejection in the five ZIFs is predicted to be 100%. With the largest aperture, ZIF-100 possesses the highest water permeability of 5 × 10(-4) kg m/(m(2) h bar), which is substantially higher compared to commercial reverse osmosis membranes, as well as zeolite and graphene oxide pervaporation membranes. In ZIF-8, -93, -95, and -97 with similar aperture size, water flux is governed by framework hydrophobicity/hydrophilicity; in hydrophobic ZIF-8 and -95, water flux is higher than in hydrophilic ZIF-93 and -97. Furthermore, water molecules in ZIF-93 move slowly and remain in the membrane for a long time but undergo to-and-fro motion in ZIF-100. The lifetime of hydrogen bonds in ZIF-93 is found to be longer than in ZIF-100. This simulation study quantitatively elucidates the dynamic and structural properties of water in ZIF membranes, identifies the key governing factors (aperture size and framework hydrophobicity/hydrophilicity), and suggests that ZIF-100 is an intriguing membrane for seawater pervaporation. PMID:27195441

  3. Atomistic Simulations of Poly(N-isopropylacrylamide) Surfactants in Water

    NASA Astrophysics Data System (ADS)

    Abbott, Lauren J.; Stevens, Mark J.

    2015-03-01

    The amphiphilic polymer poly(N-isopropylacrylamide) (PNIPAM) displays a sharp phase transition at its LCST around 32 °C, which results from competing interactions of the hydrophobic and hydrophilic groups with water. This thermoresponsive behavior can be exploited in more complex architectures, such as block copolymers or surfactants, to provide responsive PNIPAM head groups. In these systems, however, changes to the hydrophobic/hydrophilic balance can alter the transition behavior. In this work, we perform atomistic simulations of PNIPAM-alkyl surfactants to study the temperature dependence of their structures. A single chain of the surfactant does not show temperature-responsive behavior. Instead, below and above the LCST of PNIPAM, the surfactant folds to bring the hydrophobic alkyl tail in contact with the PNIPAM backbone, shielding it from water. In addition to single chains, we explore the self-assembly of multiple surfactants into micelles and how the temperature-dependent behavior is changed. 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. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  4. Quantifying grain boundary damage tolerance with atomistic simulations

    NASA Astrophysics Data System (ADS)

    Foley, Daniel; Tucker, Garritt J.

    2016-10-01

    Grain boundaries play a pivotal role in defect evolution and accommodation within materials. Irradiated metals have been observed to form defect denuded zones in the vicinity of grain boundaries. This is especially apparent in nanocrystalline metals, which have an increased grain boundary concentration, as compared to their polycrystalline counterparts. Importantly, the effect of individual grain boundaries on microstructural damage tolerance is related to the character or structural state of the grain boundary. In this work, the damage accommodation behavior of a variety of copper grain boundaries is studied using atomistic simulations. Damage accumulation behavior is found to reach a saturation point where both the free volume and energy of a grain boundary fluctuate within an elliptical manifold, which varies in size for different boundary characters. Analysis of the grain boundaries shows that extrinsic damage accommodation occurs due to localized atomic shuffling accompanied by free volume rearrangement within the boundary. Continuous damage accumulation leads to altered atomic structural states that oscillate around a mean non-equilibrium state, that is energetically metastable. Our results suggest that variation of grain boundary behavior, both from equilibrium and under saturation, is directly related to grain boundary equilibrium energy and some boundaries have a greater propensity to continually accommodate damage, as compared to others.

  5. Equilibrium at the edge and atomistic mechanisms of graphene growth.

    PubMed

    Artyukhov, Vasilii I; Liu, Yuanyue; Yakobson, Boris I

    2012-09-18

    The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene. PMID:22949702

  6. 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

  7. A spacetime, balance-law formulation of coupled atomistic and continuum dynamics for solids

    NASA Astrophysics Data System (ADS)

    Kraczek, Brent

    Coupled dynamic atomistic and continuum computational methods for solids have received much interest recently, because many problems are not addressed well by either model alone. In most coupled methods more emphasis has been placed on damping spurious reflections than on balancing momentum and energy. I present a new method for concurrent coupling of dynamic atomistic and continuum simulations of solids that enforces these balance laws on the atom/element level while minimizing spurious reflections. The coupled formulation is composed of the continuum spacetime discontinuous Galerkin (SDG) method and the mathematically consistent, time finite element, atomistic discontinuous Galerkin (ADG) method. On the continuum side I develop a two- and three-field SDG formulations for linearized elastodynamics to illuminate the mathematical structure of the original one-field SDG formulation and to assist in making connections to the atomistic formulation. On the atomistic side I examine connections between the SDG and ADG methods, and then extend this to relationships with the Velocity Verlet integrator. The component SDG and ADG methods are coupled using the same Godunov flux solution as is used by the SDG method, to enforce weakly the jump conditions on momentum balance and kinematic compatibility. To obtain compatible fluxes on the atomistic side of the coupling boundary I define a boundary atomistic trace that can be optimized to minimize boundary reflections. The coupled SDG--ADG formulation preserves the characteristic structure of the hyperbolic problem, guarantees element/atom-wise momentum balance to machine precision and yields energy error that is small, dissipative and controllable. The flux-based coupling can also be used with the Velocity Verlet method in place of the ADG, although the SDG--VV method suffers from uncontrolled energy error for long-time simulations due to the mismatch in the mathematical models. I present the formulations in spacetime, with one

  8. Polarization and polarization fatigue in ferroelectrics

    NASA Astrophysics Data System (ADS)

    Du, Xiaofeng

    This thesis addresses some fundamental issues in ferroelectricity and its applications through a computational and experimental effort. It focuses on a variety of perovskite-type ferroelectric oxides and investigates the physical basis for spontaneous polarization, domain wall dynamics, and texture development in thin film applications. The dipole-dipole interactions between ionic species in perovskite-type materials have been calculated to determine the local field and the lattice instability. Different ferroelectric and anti-ferroelectric polarization transitions can be realized by taking into account the structure distortion of the parent perovskites. We find the local field is enhanced by short range disorder and its nature varies from disorder to disorder, causing polarization transitions in non-(100) directions. The molecular field theory has also been extended to layered perovskites, which favors in-plane polarization over c-polarization. These theoretical predictions are in agreement with the experimental observations of various perovskites and layered perovskites in both single crystal and thin film forms. Domain switching in PZT has been studied by probing the frequency dependency of polarization hysteresis. A picture of thermally activated domain wall movement is established from the frequency spectra of coercive field. The field dependence of domain wall bulging and the nature of the binding between pinning obstacles and the walls are inferred from such a study. Consistent with this picture, polarization fatigue can be defined as a process of increasing the resistance from pinning defects to domain wall motion. The chemical species that act as pinning defects have been identified through model experiments that control carrier injection, electrode interfaces, and film compositions. Based on these observations, a methodology is proposed to evaluate and predict the fatigue damage of both PZT and layered perovskite thin films. Processing of layered

  9. An atomistic approach to conduction between nanoelectrodes through a single molecule.

    PubMed

    Reimers, Jeffrey R; Shapley, Warwick A; Lambropoulos, Nicholas; Hush, Noel S

    2002-04-01

    Capacitance and other properties of nanoelectrodes, finite-size metal clusters envisaged for use in complex molecular-electronic devices, are discussed. The applicability of classical electrostatics (Coulomb's and Gauss' law, Poisson's equation, etc.) to atomistic systems is investigated and the self-energy necessary to store a finite charge on an atom is found to be of central importance. In particular, the neglect of electron exchange is found to introduce severe limitations, with quantum calculations predicting fundamentally different electronic structures. Also, the well-known poor representation of the atomic self-energy inherent to modern DFT is discussed, along with its implications for molecular electronics calculations. An INDO/S method is introduced with new parameters for gold. This is the simplest approximate computational scheme that correctly includes quantum electrostatic, resonance, and spin effects, and is capable of describing arbitrary excited electronic states. Encouraging results are obtained for some trial problems. In particular, voltage differential between the electrodes in electrode-molecule-electrode conduction is obtained, not through an a priori prescription but rather by moving whole electrons between the electrodes and analyzing the response. The voltage drops across the molecule-electrode junctions and the central molecular region are then deduced. This alternative to the current Landauer-based 1-particle transmission equations for electrode-molecule-electrode conduction is discussed in terms of the use of the electronic states of the system. It provides a proper description not only of conduction via electrode-to-molecule charge or hole transfer but also of conduction via simultaneous charge and hole transfer via low-lying excited molecular electronic states, including the ability to account for electroluminescence and other chemical effects. In addition, various aspects of our research on the quantitative prediction of the I

  10. 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.

  11. Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation

    NASA Astrophysics Data System (ADS)

    LeBard, David N.; Matyushov, Dmitry V.

    2008-04-01

    We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

  12. Atomistic Insight into Tetraalkylphosphonium-Bis(oxalato)borate Ionic Liquid/Water Mixtures. I. Local Microscopic Structure.

    PubMed

    Wang, Yong-Lei; Sarman, Sten; Glavatskih, Sergei; Antzutkin, Oleg N; Rutland, Mark W; Laaksonen, Aatto

    2015-04-23

    Atomistic simulations have been performed to investigate the microscopic structural organization of aqueous solutions of trihexyltetradecylphosphonium bis(oxalato)borate ([P6,6,6,14][BOB]) ionic liquid (IL). The evolution of the microscopic liquid structure and the local ionic organization of IL/water mixtures as a function of the water concentration is visualized and systematically analyzed via radial and spatial distribution functions, coordination numbers, hydrogen bond network, and water clustering analysis. The microscopic liquid structure in neat IL is characterized by a connected apolar network composed of the alkyl chains of [P6,6,6,14] cations and isolated polar domains consisting of the central segments of [P6,6,6,14] cations and [BOB] anions, and the corresponding local ionic environment is described by direct contact ion pairs. In IL/water mixtures with lower water mole fractions, the added water molecules are dispersed and embedded in cavities between neighboring ionic species and the local ionic structure is characterized by solvent-shared ion pairs through cation-water-anion triple complexes. With a gradual increase in the water concentration in IL/water mixtures, the added water molecules tend to aggregate and form small clusters, intermediate chain-like structures, large aggregates, and eventually a water network in water concentrated simulation systems. A further progressive dilution of IL/water mixtures leads to the formation of self-organized micelle-like aggregates characterized by a hydrophobic core and hydrophilic shell consisting of the central polar segments in [P6,6,6,14] cations and [BOB] anions in a highly branched water network. The striking structural evolution of the [P6,6,6,14][BOB] IL/water mixtures is rationalized by the competition between favorable hydrogen bonded interactions and strong electrostatic interactions between the polar segments in ionic species and the dispersion interactions between the hydrophobic alkyl chains in

  13. A framework for solving atomistic phonon-structure scattering problems in the frequency domain using perfectly matched layer boundaries

    SciTech Connect

    Kakodkar, Rohit R.; Feser, Joseph P.

    2015-09-07

    We present a numerical approach to the solution of elastic phonon-interface and phonon-nanostructure scattering problems based on a frequency-domain decomposition of the atomistic equations of motion and the use of perfectly matched layer (PML) boundaries. Unlike molecular dynamic wavepacket analysis, the current approach provides the ability to simulate scattering from individual phonon modes, including wavevectors in highly dispersive regimes. Like the atomistic Green's function method, the technique reduces scattering problems to a system of linear algebraic equations via a sparse, tightly banded matrix regardless of dimensionality. However, the use of PML boundaries enables rapid absorption of scattered wave energies at the boundaries and provides a simple and inexpensive interpretation of the scattered phonon energy flux calculated from the energy dissipation rate in the PML. The accuracy of the method is demonstrated on connected monoatomic chains, for which an analytic solution is known. The parameters defining the PML are found to affect the performance and guidelines for selecting optimal parameters are given. The method is used to study the energy transmission coefficient for connected diatomic chains over all available wavevectors for both optical and longitudinal phonons; it is found that when there is discontinuity between sublattices, even connected chains of equivalent acoustic impedance have near-zero transmission coefficient for short wavelengths. The phonon scattering cross section of an embedded nanocylinder is calculated in 2D for a wide range of frequencies to demonstrate the extension of the method to high dimensions. The calculations match continuum theory for long-wavelength phonons and large cylinder radii, but otherwise show complex physics associated with discreteness of the lattice. Examples include Mie oscillations which terminate when incident phonon frequencies exceed the maximum available frequency in the embedded nanocylinder, and

  14. Dislocation modeling in bcc lithium: A comparison between continuum and atomistic predictions in the modified embedded atoms method

    NASA Astrophysics Data System (ADS)

    Alam, Masud; Groh, Sébastien

    2015-07-01

    In this study, the modified embedded-atom method (MEAM) was applied to compare the predictions of dislocation core properties obtained by molecular statics with the continuum predictions obtained in the framework of the simplified 1D-Peierls-Nabarro model. To this end, a set of four fictive Li potentials in the MEAM framework was proposed with the condition that all four potentials reproduce the same elastic constants, the same transition energies between bcc and fcc crystal structures, and between bcc and hcp crystal structures, while the unstable stacking fault energy on the plane {110} in the direction <111> was varied around the value predicted by first-principles. Within these potentials, direct atomistic calculations were performed to evaluate dislocation core properties such as dislocation half width and Peierls stress and the results were compared with continuum predictions. We found that the trends predicted by the Peierls-Nabarro model, i.e. (i) a decrease of the dislocation half width with increasing unstable stacking fault energy, and (ii) an increase of the Peierls stress with increasing the magnitude of the unstable stacking fault energy, were recovered using atomic calculations in the MEAM framework. Moreover, the magnitude of the dislocation half width and the Peierls stress calculated in the MEAM framework are in good agreement with the Peierls-Nabarro predictions when the dislocation half width is determined using a generic strategy. Specifically, the dislocation half width is defined as the distance for which the disregistery is included between b/4 and 3b/4. It was, therefore, demonstrated herein that the set of fictive potentials could be parameterized in the MEAM framework to validate or to disprove the continuum theory using atomistic methods.

  15. 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.

  16. The atomistic mechanism of carbon nanotube cutting catalyzed by nickel under an electron beam

    NASA Astrophysics Data System (ADS)

    Lebedeva, Irina V.; Chamberlain, Thomas W.; Popov, Andrey M.; Knizhnik, Andrey A.; Zoberbier, Thilo; Biskupek, Johannes; Kaiser, Ute; Khlobystov, Andrei N.

    2014-11-01

    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.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

  17. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    NASA Astrophysics Data System (ADS)

    Jones, J. L.

    2003-03-01