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Sample records for polarized atomistic molecular

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

    PubMed Central

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

    2009-01-01

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

  2. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

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

  3. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2009-04-01

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

  5. 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

  6. 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

  7. 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

  8. Molecular cooperativity and compatibility via full atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kwan Yang, Kenny

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

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

    SciTech Connect

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

    2014-04-07

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

  10. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    SciTech Connect

    Jay A Brandes

    2009-09-23

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

  11. Molecular content of polar-ring galaxies

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    PubMed

    Sedghi, Mohammad; Piri, Mohammad; Goual, Lamia

    2016-04-12

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

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

    PubMed

    Stanzione, Francesca; Jayaraman, Arthi

    2016-05-01

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

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

    PubMed

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    PubMed

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

    2016-01-01

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

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

    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.

  18. 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

  19. Atomistic Molecular Dynamics Simulations of the Electrical Double

    NASA Astrophysics Data System (ADS)

    Li, Zifeng; Milner, Scott; Fichthorn, Kristen

    2015-03-01

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

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

    PubMed Central

    Maffeo, Christopher; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mishra, Shawn; Keten, Sinan

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  3. 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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

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

    PubMed Central

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

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

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

    PubMed

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

    2015-09-01

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

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

    PubMed

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

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

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

    PubMed

    Oakes, V; Furini, S; Domene, C

    2016-01-01

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

  10. 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

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

    PubMed Central

    Telesco, Shannon E.; Radhakrishnan, Ravi

    2009-01-01

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

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

    SciTech Connect

    Nutt, David; Smith, Jeremy C

    2008-10-01

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

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

    PubMed

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

    2016-01-19

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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed

    Sutthibutpong, Thana; Noy, Agnes; Harris, Sarah

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  17. Polarization effects in molecular mechanical force fields

    PubMed 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

  18. Polarization effects in molecular mechanical force fields.

    PubMed

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

    2009-08-19

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

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

    PubMed

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

    2010-04-15

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

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

    SciTech Connect

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

    2013-12-04

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

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

    PubMed

    Marino, Michele

    2016-02-01

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

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

    SciTech Connect

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

    2015-02-09

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

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

    DOE PAGESBeta

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

    2015-02-09

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

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

    PubMed

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

    2008-03-01

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

  5. Molecular hydrogen polarization images of OMC-1

    SciTech Connect

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

    1991-07-01

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

  6. Molecular hydrogen polarization images of OMC-1

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

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

    PubMed

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

    2014-05-19

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

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

    PubMed

    Booth, Jonathan J; Shalashilin, Dmitrii V

    2016-02-01

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

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

    SciTech Connect

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

    2015-06-16

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

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

    DOE PAGESBeta

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

    2015-06-16

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

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

    SciTech Connect

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

    2015-06-16

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

  12. Parallel Atomistic Simulations

    SciTech Connect

    HEFFELFINGER,GRANT S.

    2000-01-18

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

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

    PubMed

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

    2015-01-14

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

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

    PubMed

    Frolov, Andrey I; Kiselev, Michael G

    2014-10-01

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

  15. 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}.

  16. 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.

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

    PubMed Central

    Abriata, Luciano A.; Dal Peraro, Matteo

    2015-01-01

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

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

    SciTech Connect

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

    2015-12-28

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

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

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

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

    PubMed

    Pasi, Marco; Lavery, Richard

    2016-06-20

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

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

    NASA Astrophysics Data System (ADS)

    Eike, David M.; Maginn, Edward J.

    2006-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

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

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

    PubMed

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-04-14

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

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

    PubMed

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Ippolito, Mariella; Meloni, Simone

    2011-04-01

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

  10. 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

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

    PubMed

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

    2016-01-01

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

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

  15. Submillimeter Polarization Spectrum in the Vela C Molecular Cloud

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2013-04-01

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

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

    SciTech Connect

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

    2010-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2016-08-18

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

  20. Polarization of far-infrared radiation from molecular clouds

    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.

  1. Polarization of far-infrared radiation from molecular clouds

    SciTech Connect

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

    1989-10-01

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

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

    SciTech Connect

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

    2013-02-10

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    de Miranda, Marcelo P; Kendrick, Brian K

    2009-12-31

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

  5. Numerical tools for atomistic simulations.

    SciTech Connect

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

    2004-01-01

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

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

    PubMed

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

    2011-10-27

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

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

    NASA Astrophysics Data System (ADS)

    Stanzione, Francesca; Jayaraman, Arthi

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  9. 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

  10. 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

  11. 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

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

    PubMed

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

    2016-01-14

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

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

    NASA Astrophysics Data System (ADS)

    Kawakami, Tomonori; Shigemoto, Isamu; Matubayasi, Nobuyuki

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Lai, Wei; Guo, Chunlei

    2016-04-01

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

  15. Atomistic simulation of graphene-based polymer nanocomposites

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    SciTech Connect

    Houde, Martin

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Chockalingam, Rajalakshmi; Natarajan, Upendra

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2008-12-01

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

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

    PubMed

    Côté, Sébastien; Wei, Guanghong; Mousseau, Normand

    2014-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2013-01-01

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

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

    PubMed

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

    2016-05-11

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

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

    PubMed Central

    Parkin, Jamie; Khalid, Syma

    2014-01-01

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

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

    PubMed

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

    2007-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

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

    PubMed

    Frech, Roger; Petrowsky, Matt

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Natarajan, Upendra

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

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

    SciTech Connect

    Morgen, M M

    1997-05-01

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

  14. Visualizing molecular polar order in tissues via electromechanical coupling

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2016-05-19

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

  19. Chirp and polarization control of femtosecond molecular fragmentation

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-08-01

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

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

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-08-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2015-11-11

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2012-05-01

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

  6. General Reactive Atomistic Simulation Program

    Energy Science and Technology Software Center (ESTSC)

    2004-09-22

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

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

    PubMed Central

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

    1997-01-01

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

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2016-06-22

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

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

    SciTech Connect

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

    2015-04-01

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

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

    PubMed 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

  16. 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

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

    PubMed

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

    2010-07-26

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

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

    SciTech Connect

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

    2010-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  1. Web-based implementation of atomistic visualization

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  2. Atomistic Monte Carlo Simulation of Lipid Membranes

    PubMed Central

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

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

  3. Atomistic study on dithiolated oligo-phenylenevinylene gated device

    SciTech Connect

    Mahmoud, Ahmed Lugli, Paolo

    2014-11-28

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

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Collins, Brian; Delongchamp, Dean

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    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.

  9. 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.

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

    NASA Technical Reports Server (NTRS)

    Illing, R. M. E.

    1981-01-01

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

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

    PubMed Central

    Wang, Nan; Liang, Hongwei; Zen, Ke

    2014-01-01

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

  12. Flexoelectricity and the polarity of complex ferroelastic twin patterns

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    SciTech Connect

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

    2010-10-15

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

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

    PubMed

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

    2016-01-20

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

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

    PubMed

    Berhanu, Workalemahu M; Masunov, Artëm E

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed

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

    2007-07-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed

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

    2013-08-28

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

  2. 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.

  3. 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

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

    SciTech Connect

    Samela, Juha; Nordlund, Kai

    2008-07-11

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

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

    PubMed

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

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

    PubMed

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

    2011-06-20

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

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2015-04-28

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

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

    NASA Astrophysics Data System (ADS)

    Habasaki, Junko; Ngai, K. L.

    2015-04-01

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

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    1999-12-01

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

  16. 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.

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

    PubMed

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

    2012-05-24

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

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

    SciTech Connect

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

    2004-04-15

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2008-11-01

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

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

    SciTech Connect

    Farkas, D.

    1997-12-31

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-06-01

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

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

    PubMed

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

    2016-07-01

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

  8. Atomistic Simulation of Initiation in Hexanitrostilbene

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    DOE PAGESBeta

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

    2015-08-11

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

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

    SciTech Connect

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

    2015-08-11

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

  11. Atomistic Properties of Y Uranium

    SciTech Connect

    Benjamin Beeler; Chaitanya Deo; Mmichael Baskes; Maria Okuniewski

    2012-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    SciTech Connect

    Chakrabarti, Sudipto; Pal, Amlan J.

    2014-01-06

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

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

    PubMed

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

    2014-04-30

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

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

    PubMed Central

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Kempa, R. F.; Auld, J.

    1974-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Calame, Jeffrey

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

  18. 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.

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

    PubMed

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

    2003-01-01

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

  20. Atomistic modeling and simulation of nanopolycrystalline solids

    NASA Astrophysics Data System (ADS)

    Yang, Zidong

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

  1. 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

  2. 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

  3. Atomistic theory of amyloid fibril nucleation

    NASA Astrophysics Data System (ADS)

    Cabriolu, Raffaela; Kashchiev, Dimo; Auer, Stefan

    2010-12-01

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

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

    SciTech Connect

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

    2010-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Bakkour, Rani; Hofstetter, Thomas B.

    2014-05-01

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

  7. Biomembranes in atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Pluhackova, Kristyna; Böckmann, Rainer A.

    2015-08-01

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

  8. Atomistic k ⋅ p theory

    SciTech Connect

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

    2015-12-14

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

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

    NASA Astrophysics Data System (ADS)

    Moldawer, Adam Lyle

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  11. 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

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

    PubMed

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

    2015-07-14

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

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

    PubMed Central

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. Atomistic simulations of surfactant adsorption kinetics at interfaces

    NASA Astrophysics Data System (ADS)

    Iskrenova, Eugeniya; Patnaik, Soumya

    2014-03-01

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

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

    SciTech Connect

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

    2014-10-21

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

  17. Atomistic modeling of dropwise condensation

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Debolt, Stephen Edward

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

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

    PubMed Central

    Li, Xianfeng; Latour, Robert A.

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

    2003-12-01

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

  4. Atomistic Simulations of a Thermotropic Biaxial Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Peláez, Jorge; Wilson, Mark R.

    2006-12-01

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

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

    PubMed Central

    2012-01-01

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

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

    PubMed Central

    Remko, Milan; Remková, Anna; Broer, Ria

    2016-01-01

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

  7. 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.

  8. 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.

  9. 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

  10. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    SciTech Connect

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

    2005-12-31

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

  11. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    SciTech Connect

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

    2007-01-12

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

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

    NASA Astrophysics Data System (ADS)

    Sen, Fatih Gurcag

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    SciTech Connect

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

    2013-08-21

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    PubMed

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

    2012-03-01

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

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

    SciTech Connect

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

    2011-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2016-07-28

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

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

    PubMed

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

    2015-09-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  4. Atomistic 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. Atomistic simulations of material damping in amorphous silicon nanoresonators

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sankha; Song, Jun; Vengallatore, Srikar

    2016-06-01

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-09-01

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

  9. 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.

  10. 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.