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Sample records for polarized atomistic molecular

  1. Atomistic molecular dynamics simulations of shock compressed quartz

    NASA Astrophysics Data System (ADS)

    Farrow, M. R.; Probert, M. I. J.

    2011-07-01

    Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)], 10.1103/PhysRevB.43.5068 to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa.

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

    PubMed

    Rapaport, D C

    2009-04-01

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

  3. Aromatic Polyamide Reverse-Osmosis Membrane: An Atomistic Molecular Dynamics Simulation.

    PubMed

    Wei, Tao; Zhang, Lin; Zhao, Haiyang; Ma, Heng; Sajib, Md Symon Jahan; Jiang, Hua; Murad, Sohail

    2016-10-06

    Polyamide (PA) membrane-based reverse-osmosis (RO) serves as one of the most important techniques for water desalination and purification. Fundamental understanding of PA RO membranes at the atomistic level is critical to enhance their separation capabilities, leading to significant societal and commercial benefits. In this paper, a fully atomistic molecular dynamics simulation was performed to investigate PA membrane. Our simulated cross-linked membrane exhibits structural properties similar to those reported in experiments. Our results also reveal the presence of small local two-layer slip structures in PA membrane with 70% cross-linking, primarily due to short-range anisotropic interactions among aromatic benzene rings. Inside the inhomogeneous polymeric structure of the membrane, water molecules show heterogeneous diffusivities and converge adjacent to polar groups. Increased diffusion of water molecules is observed through the less cross-linked pathways. The existence of the fast pathways for water permeation has no effect on membrane's salt rejections.

  4. Atomistic molecular dynamics simulations of model C36 fullerite

    NASA Astrophysics Data System (ADS)

    Abramo, Maria C.; Caccamo, C.

    2008-02-01

    We report atomistic molecular dynamics investigations of a model C36 fullerite in which the fullerene molecules are modeled as rigid cages over which the carbon atoms occupy fixed interaction sites, distributed in space according to the experimentally known atomic positions in the molecule. Carbon sites belonging to different molecules are assumed to interact via a 12-6 Lennard-Jones-type potential; the parameters of the latter are employed in the framework of a molecular dynamics fitting procedure, through which the ambient condition physical quantities characterizing the hcp structure of solid C36 are eventually reproduced. We discuss applications of the adopted modelization to the C36 phases in a temperature range spanning from 300to1500K, and compare the obtained results to the available data for C36 and other fullerenes, and to the predictions of the well known Girifalco central potential modelization of interactions in fullerenes, as applied to the C36 case.

  5. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    NASA Astrophysics Data System (ADS)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

  6. Molecular cooperativity and compatibility via full atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kwan Yang, Kenny

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

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

    SciTech Connect

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

    2014-04-07

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

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

    PubMed

    Sedghi, Mohammad; Piri, Mohammad; Goual, Lamia

    2016-04-12

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

  9. State Representation Approach for Atomistic Time-Dependent Transport Calculations in Molecular Junctions.

    PubMed

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  10. Atomistic modeling of IR action spectra under circularly polarized electromagnetic fields: toward action VCD spectra.

    PubMed

    Calvo, Florent

    2015-03-01

    The nonlinear response and dissociation propensity of an isolated chiral molecule, camphor, to a circularly polarized infrared laser pulse was simulated by molecular dynamics as a function of the excitation wavelength. The results indicate similarities with linear absorption spectra, but also differences that are ascribable to dynamical anharmonic effects. Comparing the responses between left- and right-circularly polarized pulses in terms of dissociation probabilities, or equivalently between R- and S-camphor to a similarly polarized pulse, we find significant differences for the fingerprint C = O amide mode, with a sensitivity that could be sufficient to possibly enable vibrational circular dichroism as an action technique for probing molecular chirality and absolute conformations in the gas phase.

  11. Molecular recognition effects in atomistic models of imprinted polymers.

    PubMed

    Dourado, Eduardo M A; Herdes, Carmelo; van Tassel, Paul R; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  12. 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

  13. 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.

  14. Unravelling Mg2+-RNA binding with atomistic molecular dynamics.

    PubMed

    Cunha, Richard A; Bussi, Giovanni

    2017-02-01

    Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg(2+) on a RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg(2+) affinity due to ion competition and hybridization respectively, and predict that RNA flexibility has a site dependent effect. This suggests a non trivial interplay between RNA conformational entropy and divalent cation binding.

  15. Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.

    PubMed

    Sutthibutpong, Thana; Harris, Sarah A; Noy, Agnes

    2015-06-09

    DNA molecular center-lines designed from atomistic-resolution structures are compared for the evaluation of the writhe in supercoiled DNA using molecular dynamics simulations of two sets of minicircles with 260 and 336 base pairs. We present a new method called WrLINE that systematically filters out local (i.e., subhelical turn) irregularities using a sliding-window averaged over a single DNA turn and that provides a measure of DNA writhe that is suitable for comparing atomistic resolution data with those obtained from measurements of the global molecular shape. In contrast, the contour traced by the base-pair origins defined by the 3DNA program largely overestimates writhe due to the helical periodicity of DNA. Nonetheless, this local modulation of the molecular axis emerges as an internal mechanism for the DNA to confront superhelical stress, where the adjustment between low and high twist is coupled to a high and low local periodicity, respectively, mimicking the different base-stacking conformational space of A and B canonical DNA forms.

  16. 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

  17. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

    PubMed

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

    2017-03-07

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

  18. 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.

  19. 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

  20. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    NASA Astrophysics Data System (ADS)

    Seppä, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti

    2017-03-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.

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

    PubMed

    Papaleo, Elena

    2015-01-01

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

  2. 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.

  3. 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

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

    PubMed

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

    2011-04-12

    The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10-15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F(233). Analysis indicates that the local electric field within the VSD is focused near the F(233) residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments.

  5. Asymmetry of lipid bilayers induced by monovalent salt: Atomistic molecular-dynamics study

    NASA Astrophysics Data System (ADS)

    Gurtovenko, Andrey A.

    2005-06-01

    Interactions between salt ions and lipid components of biological membranes are essential for the structure, stability, and functions of the membranes. The specific ionic composition of aqueous buffers inside and outside of the cell is known to differ considerably. To model such a situation we perform atomistic molecular-dynamics (MD) simulations of a single-component phosphatidylcholine lipid bilayer which separates two aqueous reservoirs with and without NaCl salt. To implement the difference in electrolyte composition near two membrane sides, a double bilayer setup (i.e., two bilayers in a simulation box) is employed. It turns out that monovalent salt, being in contact with one leaflet only, induces a pronounced asymmetry in the structural, electrostatic, and dynamical properties of bilayer leaflets after 50ns of MD simulations. Binding of sodium ions to the carbonyl region of the leaflet which is in contact with salt results in the formation of "Na-lipids" complexes and, correspondingly, reduces mobility of lipids of this leaflet. In turn, attractive interactions of chloride ions (mainly located in the aqueous phase close to the water-lipid interface) with choline lipid groups lead to a substantial (more vertical) reorientation of postphatidylcholine headgroups of the leaflet adjoined to salt. The difference in headgroup orientation on two sides of a bilayer, being coupled with salt-induced reorientation of water dipoles, leads to a notable asymmetry in the charge-density profiles and electrostatic potentials of bilayer constitutes of the two leaflets. Although the overall charge density of the bilayer is found to be almost insensitive to the presence of salt, a slight asymmetry in the charge distribution between the two bilayer leaflets results in a nonzero potential difference of about 85mV between the two water phases. Thus, a transmembrane potential of the order of the membrane potential in a cell can arise without ionic charge imbalance between two aqueous

  6. 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

  7. A Novel Monte Carlo Scheme for the Rapid Equilibration of Atomistic Model Polymer Systems of Precisely Defined Molecular Architecture

    NASA Astrophysics Data System (ADS)

    Karayiannis, Nikos Ch.; Mavrantzas, Vlasis G.; Theodorou, Doros N.

    2002-03-01

    Two novel connectivity-altering atomistic Monte Carlo moves are presented for the fast equilibration of condensed phases of long-chain systems with a variety of chain architectures. With the new moves, isotropic or oriented melts of linear or long-chain branched polymers, dense brushes of terminally grafted macromolecules, and cyclic peptides can be simulated. Results concerning the structural, conformational, and volumetric properties of linear, monodisperse polyethylene melts, simulated with a new united-atom molecular model, are in excellent agreement with experimental data.

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

  9. 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

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

    DOE PAGES

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; ...

    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

  11. 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.

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

    PubMed

    Tvaroška, Igor

    2015-02-11

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

  13. 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

    2008-03-04

    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.

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

    NASA Astrophysics Data System (ADS)

    Schubert, Thomas; Schneck, Emanuel; Tanaka, Motomu

    2011-08-01

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

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

    PubMed

    Schubert, Thomas; Schneck, Emanuel; Tanaka, Motomu

    2011-08-07

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

  16. 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.

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

    DOE PAGES

    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

  18. 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.

  19. Atomistic understanding of diffusion kinetics in nanocrystals from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Yun-Jiang; Gao, Guo-Jie J.; Ogata, Shigenobu

    2013-09-01

    Understanding the grain size effect on diffusion in nanocrystals has been hampered by the difficulty of measuring diffusion directly in experiments. Here large-scale atomistic modeling is applied to understand the diffusion kinetics in nanocrystals. Enhanced short-circuit diffusivity is revealed to be controlled by the rule of mixtures for grain-boundary diffusion and lattice diffusion, which can be accurately described by the Maxwell-Garnett equation instead of the commonly thought Hart equation, and the thermodynamics of pure grain-boundary self-diffusion is not remarkably affected by varying grain size. Experimentally comparable Arrhenius parameters with atomic detail validate our results. We also propose a free-volume diffusion mechanism considering negative activation entropy and small activation volume. These help provide a fundamental understanding of how the activation parameters depend on size and the structure-property relationship of nanostructured materials from a physical viewpoint.

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

    PubMed

    Vargiu, Attilio V; Magistrato, Alessandra

    2014-09-01

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

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

    PubMed Central

    Reif, Maria M; Oostenbrink, Chris

    2014-01-01

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker–Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry

  2. 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}.

  3. 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.

  4. Molecular dynamics study of coagulation in silica-nanocolloid-water-NaCl systems based on the atomistic model.

    PubMed

    Habasaki, Junko; Ishikawa, Masamichi

    2014-11-21

    In the present work, large scale molecular dynamics (MD) simulations of nanocolloidal silica in aqueous NaCl solutions were performed using a fully atomistic model to study the microscopic structures and dynamics of the systems that lead to aggregation or gelation. Our attention is focused on the self-organizations that occur in the structures of the colloidal silica and water for various concentrations of NaCl. As the salt concentration increased, coagulation developed through the direct bonding of SiO4 units. The trend was explained by the systematic changes in the pair correlation functions related to the barrier height in the potential of mean force [J. G. Kirkwood, J. Chem. Phys., 1935, 3, 300]. Network structures of silica were visualised, and their fractal dimensions were examined by computing the running coordination numbers of Si-Si pairs and also by the analysis of two dimensional images. The calculated dimension by the former method was comparable to the experimental observations for the aggregation of silica colloids, and at longer length scales, super-aggregation was evident in the gelation process. The result from the 2D images is found to be insensitive to the differences in the structure. Clear changes in both the structure and mobility of the water were observed as the NaCl concentration increased, suggesting the importance of the solvent structures to these processes, although such a feature is lacking in the conventional models and most simulations of colloids.

  5. 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.

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

    PubMed Central

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

    2014-01-01

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

  7. 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

  8. 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

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

    PubMed Central

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

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

  10. Early structural development in melt-quenched polymer PTT from atomistic molecular dynamic simulations

    NASA Astrophysics Data System (ADS)

    Hsieh, Min-Kang; Lin, Shiang-Tai

    2009-12-01

    Molecular dynamics simulations are performed to study the initial structural development in poly(trimethylene terephthalate) (PTT) when quenched below its melting point. The development of local ordering has been observed in our simulations. The thermal properties, such as the glass transition temperature (Tg) and the melting temperature (Tm), determined from our simulations are in reasonable agreement with experimental values. It is found that, between these two temperatures, the number of local structures quickly increases during the thermal relaxation period soon after the system is quenched and starts to fluctuate afterwards. The formation and development of local structures is found to be driven mainly by the torsional and van der Waals forces and follows the classical nucleation-growth mechanism. The variation of local structures' fraction with temperature exhibits a maximum between Tg and Tm, resembling the temperature dependence of the crystallization rate for most polymers. In addition, the backbone torsion distribution for segments within the local structures preferentially reorganizes to the trans-gauche-gauche-trans (t-g-g-t) conformation, the same as that in the crystalline state. As a consequence, we believe that such local structural ordering could be the baby nuclei that have been suggested to form in the early stage of polymer crystallization.

  11. Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Gao, N.; Yang, L.; Gao, F.; Kurtz, R. J.; West, D.; Zhang, S.

    2017-04-01

    A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic-scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state configuration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly different time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial-assisted mechanism is first explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.

  12. Atomistic Molecular Dynamics Simulation of the Surface Properties of P3HT Films

    NASA Astrophysics Data System (ADS)

    Yimer, Yeneneh; Mofakham, Sima; Dhinojwala, Ali; Tsige, Mesfin

    2011-03-01

    In recent years P3HT has attracted much interest mainly because of its potential applications in solar cells, light emitting diodes and field effect transistors. The performance of these devices is strongly dependent on the structural packing, morphology and interfacial properties of the P3HT. In order to improve the devices efficiency, understanding the structural and dynamical properties of P3HT at the atomic level is important. Most studies on P3HT have mainly focused on understanding its bulk properties. However, the orientation of P3HT chains at the polymer/air interface has not been well investigated. Using molecular dynamics simulations we have studied the interfacial properties of free-standing P3HT films. The simulation results show that at the air/polymer interface the alkane side groups of the P3HT chains orient mainly to the interface in qualitatively good agreement with SFG experimental results. The surface tension of P3HT in its melt state shows strong dependence on temperature and chain length and is directly related to the roughness of the P3HT surface. This work is supported by the NSF (DMR0847580).

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  14. Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method.

    PubMed

    Gao, N; Yang, L; Gao, F; Kurtz, R J; West, D; Zhang, S

    2017-04-12

    A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic-scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state configuration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly different time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial-assisted mechanism is first explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.

  15. 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

  16. 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.

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

    PubMed Central

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

    2016-01-01

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

  18. Molecular photoelectron holography with circularly polarized laser pulses.

    PubMed

    Yang, Weifeng; Sheng, Zhihao; Feng, Xingpan; Wu, Miaoli; Chen, Zhangjin; Song, Xiaohong

    2014-02-10

    We investigate the photoelectron momentum distribution of molecular-ion H2+driven by ultrashort intense circularly polarized laser pulses. Both numerical solutions of the time-dependent Schrödinger equation (TDSE) and a quasiclassical model indicate that the photoelectron holography (PH) with circularly polarized pulses can occur in molecule. It is demonstrated that the interference between the direct electron wave and rescattered electron wave from one core to its neighboring core induces the PH. Moreover, the results of the TDSE predict that there is a tilt angle between the interference pattern of the PH and the direction perpendicular to the molecular axis. Furthermore, the tilt angle is sensitively dependent on the wavelength of the driven circularly polarized pulse, which is confirmed by the quasiclassical calculations. The PH induced by circularly polarized laser pulses provides a tool to resolve the electron dynamics and explore the spatial information of molecular structures.

  19. 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

    2013-04-04

    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

  20. Coupling atomistic and continuum length scales in heteroepitaxial systems: Multiscale molecular-dynamics/finite-element simulations of strain relaxation in Si/ Si3 N4 nanopixels

    NASA Astrophysics Data System (ADS)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2005-09-01

    A hybrid atomistic-continuum simulation approach has been implemented to study strain relaxation in lattice-mismatched Si/Si3N4 nanopixels on a Si(111) substrate. We couple the molecular-dynamics (MD) and finite-element simulation approaches to provide an atomistic description near the interface and a continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are validated against full multimillion-atom MD simulations. We find that strain relaxation in Si/Si3N4 nanopixels may occur through the formation of a network of interfacial domain boundaries reminiscent of interfacial misfit dislocations. They result from the nucleation of domains of different interfacial bonding at the free edges and corners of the nanopixel, and subsequent to their creation they propagate inwards. We follow the motion of the domain boundaries and estimate a propagation speed of about ˜2.5×103m/s . The effects of temperature, nanopixel architecture, and film structure on strain relaxation are also investigated. We find: (i) elevated temperature increases the interfacial domain nucleation rates; (ii) a thin compliant Si layer between the film and the substrate plays a beneficial role in partially suppressing strain relaxation; and (iii) additional control over the interface morphology may be achieved by varying the film structure.

  1. Extending classical molecular theory with polarization.

    PubMed

    Keyes, Tom; Napoleon, Raeanne L

    2011-01-27

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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Magnetic Field Structure in Molecular Clouds by Polarization Measurements

    NASA Astrophysics Data System (ADS)

    Chen, W. P.; Su, B. H.; Eswaraiah, C.; Pandey, A. K.; Wang, C. W.; Lai, S. P.; Tamura, M.; Sato, S.

    2015-03-01

    We report on a program to delineate magnetic field structure inside molecular clouds by optical and infrared polarization observations. An ordered magnetic field inside a dense cloud may efficiently align the spinning dust grains to cause a detectable level of optical and near-infrared polarization of otherwise unpolarized background starlight due to dichroic extinction. The near-infrared polarization data were taken by SIRPOL mounted on IRSF in SAAO. Here we present the SIRPOL results in RCW 57, for which the magnetic field is oriented along the cloud filaments, and in Carina Nebula, for which no intrinsic polarization is detected in the turbulent environment. We further describe TRIPOL, a compact and efficient polarimer to acquire polarized images simultaneously at g', r', and i' bands, which is recently developed at Nagoya University for adaption to small-aperture telescopes. We show how optical observations probe the translucent outer parts of a cloud, and when combining with infrared observations probing the dense parts, and with millimeter and submillimeter observations to sutdy the central embedded protostar, if there is one, would yield the magnetic field structure on different length scales in the star-formation process.

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

    PubMed

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

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

  8. 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.

  9. 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

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

    PubMed

    Chen, Shuang; Zeng, Xiao Cheng

    2014-04-30

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

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

    PubMed Central

    Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

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

  12. 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.

  13. Atomistic Molecular Dynamics Simulations of Carbon Dioxide Diffusivity in n-Hexane, n-Decane, n-Hexadecane, Cyclohexane, and Squalane.

    PubMed

    Moultos, Othonas A; Tsimpanogiannis, Ioannis N; Panagiotopoulos, Athanassios Z; Trusler, J P Martin; Economou, Ioannis G

    2016-12-22

    Atomistic molecular dynamics simulations were carried out to obtain the diffusion coefficients of CO2 in n-hexane, n-decane, n-hexadecane, cyclohexane, and squalane at temperatures up to 423.15 K and pressures up to 65 MPa. Three popular models were used for the representation of hydrocarbons: the united atom TraPPE (TraPPE-UA), the all-atom OPLS, and an optimized version of OPLS, namely, L-OPLS. All models qualitatively reproduce the pressure dependence of the diffusion coefficient of CO2 in hydrocarbons measured recently, and L-OPLS was found to be the most accurate. Specifically for n-alkanes, L-OPLS also reproduced the measured viscosities and densities much more accurately than the original OPLS and TraPPE-UA models, indicating that the optimization of the torsional potential is crucial for the accurate description of transport properties of long chain molecules. The three force fields predict different microscopic properties such as the mean square radius of gyration for the n-alkane molecules and pair correlation functions for the CO2-n-alkane interactions. CO2 diffusion coefficients in all hydrocarbons studied are shown to deviate significantly from the Stokes-Einstein behavior.

  14. Laser Polarization Effect on Molecular Harmonic and Elliptically Polarized Attosecond Pulse Generation

    NASA Astrophysics Data System (ADS)

    Feng, Li-Qiang; Li, Wen-Liang; Liu, Hang

    2017-01-01

    Molecular harmonic spectra of {{{H}}}2+ driven by the linearly polarized laser pulses with different polarized angles have been theoretically investigated through solving the two-dimensional time-dependent Schrödinger equation. (i) Below-threshold harmonic spectra show a visible enhanced peak around the 7th harmonic (H7), which produces a red-shift phenomenon as the internuclear distance increased. Theoretical analyses show the red-shift enhanced peak is caused by the laser-induced electron transfer between the ground state and the 1st excited state of {{{H}}}2+. (ii) Due to the two-centre interference phenomenon, the above-threshold harmonic spectra exhibit many maxima and minima. (iii) With the introduction of the polarized angle, the anomalous elliptically polarized harmonics can be found. But, with the introduction of the spatial inhomogeneous effect, not only the ellipticities of the harmonics are equal to a stable value of \\varepsilon ∼ 0.1–0.3, but also the harmonic cutoffs are extended. As a result, four super-bandwidths of 407 eV, 310 eV, 389 eV, and 581 eV can be obtained. Time profiles of the harmonic generations have been shown to explain the harmonic characteristics. Finally, a series of elliptically polarized (\\varepsilon ∼ 0.1–0.3) attosecond X-ray pulses with durations from 18as to 25as can be directly produced through Fourier transformation of the spectral continuum. Supported by National Natural Science Foundation of China under Grant No. 11504151, Doctoral Scientific Research Foundation of Liaoning Province under Grant No. 201501123 and Scientific Research Fund of Liaoning Provincial Education Department under Grant No. L2014242

  15. Membrane negative curvature induced by a hybrid peptide from pediocin PA-1 and plantaricin 149 as revealed by atomistic molecular dynamics simulations.

    PubMed

    da Hora, G C A; Archilha, N L; Lopes, J L S; Müller, D M; Coutinho, K; Itri, R; Soares, T A

    2016-11-04

    Antimicrobial peptides (AMPs) are cationic peptides that kill bacteria with a broad spectrum of action, low toxicity to mammalian cells and exceptionally low rates of bacterial resistance. These features have led to considerable efforts in developing AMPs as an alternative antibacterial therapy. In vitro studies have shown that AMPs interfere with membrane bilayer integrity via several possible mechanisms, which are not entirely understood. We have performed the synthesis, membrane lysis measurements, and biophysical characterization of a novel hybrid peptide. These measurements show that PA-Pln149 does not form nanopores, but instead promotes membrane rupture. It causes fast rupture of the bacterial model membrane (POPG-rich) at concentrations 100-fold lower than that required for the disruption of mammalian model membranes (POPC-rich). Atomistic molecular dynamics (MD) simulations were performed for single and multiple copies of PA-Pln149 in the presence of mixed and pure POPC/POPG bilayers to investigate the concentration-dependent membrane disruption by the hybrid peptide. These simulations reproduced the experimental trend and provided a potential mechanism of action for PA-Pln149. It shows that the PA-Pln149 does not form nanopores, but instead promotes membrane destabilization through peptide aggregation and induction of membrane negative curvature with the collapse of the lamellar arrangement. The sequence of events depicted for PA-Pln149 may offer insights into the mechanism of action of AMPs previously shown to induce negative deformation of membrane curvature and often associated with peptide translocation via non-bilayer intermediate structures.

  16. Collective alignment of polar filaments by molecular motors.

    PubMed

    Ziebert, F; Vershinin, M; Gross, S P; Aranson, I S

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors' stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

  17. 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.

  18. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis.

    PubMed

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2017-03-08

    Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

  19. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

    PubMed Central

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2017-01-01

    Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations. PMID:28272553

  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.

  1. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

    NASA Astrophysics Data System (ADS)

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2017-03-01

    Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

  2. Spin-polarized electron transport through helicene molecular junctions

    NASA Astrophysics Data System (ADS)

    Pan, Ting-Rui; Guo, Ai-Min; Sun, Qing-Feng

    2016-12-01

    Recently, the spin-selectivity effect of chiral molecules has been attracting extensive and growing interest among the scientific communities. Here, we propose a model Hamiltonian to study spin-dependent electron transport through helicene molecules which are connected by two semi-infinite graphene nanoribbons and try to elucidate a recent experiment of the spin-selectivity effect observed in the helicene molecules. The results indicate that the helicene molecules can present a significant spin-filtering effect in the case of extremely weak spin-orbit coupling, which is three orders of magnitude smaller than the hopping integral. The underlying physics is attributed to intrinsic chiral symmetry of the helicene molecules. When the chirality is switched from the right-handed species to the left-handed species, the spin polarization is reversed exactly. These results are consistent with a recent experiment [V. Kiran et al., Adv. Mater. 28, 1957 (2016), 10.1002/adma.201504725]. In addition, the spin-filtering effect of the helicene molecules is robust against molecular lengths, dephasing strengths, and space position disorder. This theoretical work may motivate further studies on chiral-induced spin selectivity in molecular systems.

  3. 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

  4. Atomistics of friction

    NASA Astrophysics Data System (ADS)

    Hirano, M.

    2006-03-01

    When two solid bodies contact and slide against each other, a frictional phenomenon occurs. There have been two models for the origin of the friction forces: the surface roughness model and Tomlinson's model. The surface roughness model explains the origin of the static friction force; contacting solid surfaces are so rough that surface asperities are mechanically locked against the gravitational force. From an atomistic point of view, Tomlinson explained a mechanism of the energy dissipation for the origin of the dynamic friction force. The atomistic mechanisms are described for the origin of the static and the dynamic friction forces, based on the theoretical conclusion that Tomlinson's mechanism is unlikely to occur in realistic frictional systems. The mechanism for the origin of the static friction force resembles the mechanical locking mechanism in a surface roughness model. The origin of the dynamic friction force is formulated as a problem of how the given translational kinetic energy dissipates into the internal relative motions of constituent atoms of bodies during sliding. From studying the available phase space volume of the translational motion becomes negligibly small for a large system size, compared with that of the internal motions, it is concluded that the energy dissipation occurs irreversibly from the translational motion to the internal motions. The comparison of the atomistic mechanisms with the surface roughness model and Tomlinson's model is discussed. A phenomenon of superlubricity, where two solid bodies move relatively with no resistance, is discussed.

  5. 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 A. R.; Angilè, Francesco E.; Ashton, Peter; Benton, Steven J.; Devlin, Mark J.; Dober, Bradley; Fissel, Laura M.; 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; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Diego Soler, Juan; Thomas, Nicholas E.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

    2017-03-01

    We present a large-scale combination of near-infrared (near-IR) interstellar polarization data from background starlight with polarized emission data at submillimeter wavelengths for the Vela C molecular cloud. The near-IR data consist of more than 6700 detections probing a range of visual extinctions between 2 and 20 {mag} in and around the cloud. The submillimeter data were collected in Antarctica by the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry. This is the first direct combination of near-IR and submillimeter polarization data for a molecular cloud aimed at measuring the “polarization efficiency ratio” ({R}{eff}), a quantity that is expected to depend only on grain-intrinsic physical properties. It is defined as {p}500/({p}I/{τ }V), where p 500 and p I are polarization fractions at 500 μ {{m}} and the I band, respectively, and {τ }V is the optical depth. To ensure that the same column density of material is producing both polarization from emission and from extinction, we conducted a careful selection of near-background stars using 2MASS, Herschel, and Planck data. This selection excludes objects contaminated by the Galactic diffuse background material as well as objects located in the foreground. Accounting for statistical and systematic uncertainties, we estimate an average {R}{eff} value of 2.4 ± 0.8, which can be used to test the predictions of dust grain models designed for molecular clouds when such predictions become available. The ratio {R}{eff} appears to be relatively flat as a function of the cloud depth for the range of visual extinctions probed.

  6. Molecular mechanisms of membrane polarity in renal epithelial cells.

    PubMed

    Campo, C; Mason, A; Maouyo, D; Olsen, O; Yoo, D; Welling, P A

    2005-01-01

    Exciting discoveries in the last decade have cast light onto the fundamental mechanisms that underlie polarized trafficking in epithelial cells. It is now clear that epithelial cell membrane asymmetry is achieved by a combination of intracellular sorting operations, vectorial delivery mechanisms and plasmalemma-specific fusion and retention processes. Several well-defined signals that specify polarized segregation, sorting, or retention processes have, now, been described in a number of proteins. The intracellular machineries that decode and act on these signals are beginning to be described. In addition, the nature of the molecules that associate with intracellular trafficking vesicles to coordinate polarized delivery, tethering, docking, and fusion are also becoming understood. Combined with direct visualization of polarized sorting processes with new technologies in live-cell fluorescent microscopy, new and surprising insights into these once-elusive trafficking processes are emerging. Here we provide a review of these recent advances within an historically relevant context.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  8. Identification of the Molecular Determinants of Breast Epithelial Cell Polarity

    DTIC Science & Technology

    2004-10-01

    most apical part of lateral membranes, indicating that apico-basal polarity is established even in malignant T4 cells. In 3D lrBM culture, desmosomes ...and hemidesmosomes are highly visible in lateral and basal domains of S I cells, respectively. On the other hand, desmosomes and hemidesmosomes are...restored distinct localizations of desmosomes and hemidesmosomes and thus established basal polarity. TJs are difficult to identify in Fig. 3B as they are

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

    SciTech Connect

    Morgen, Michael Mark

    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.

  10. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters.

    PubMed

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia; Skotland, Tore; Sylvänne, Tuulia; Kauhanen, Dimple; Ekroos, Kim; Sandvig, Kirsten; Vattulainen, Ilpo

    2016-06-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3].

  11. 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.

  12. Chirp and polarization control of femtosecond molecular fragmentation

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    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.

  13. Chirp and polarization control of femtosecond molecular fragmentation.

    PubMed

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

    2012-03-01

    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.

  14. 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.

  15. Solid phase extraction cleanup for non-polar and moderately polar molecular markers of PM 2.5 sources

    NASA Astrophysics Data System (ADS)

    Turlington, John M.; McDow, Stephen R.

    2010-06-01

    A solid phase extraction cleanup step substantially improved analytical efficiency and data quality for measurements of non-polar and moderately polar organic molecular marker concentrations in airborne particulate matter. Rapid gas chromatography column deterioration was evident after very few samples in the absence of a cleanup step, resulting in the need for frequent recalibration. High molecular weight polycyclic aromatic hydrocarbons, were among the species most strongly impacted by the deterioration, exhibiting deviations as high as 30-40% from expected calibration verification standard values after only a few injections. Column deterioration and calibration verification failure were eliminated by introducing a solid phase extraction step prior to analysis and a total of 58 samples were analyzed with no unacceptable deviation of calibration verification standards from target values

  16. Molecular dynamics analysis of the effect of electronic polarization on the structure and single-particle dynamics of mixtures of ionic liquids and lithium salts

    NASA Astrophysics Data System (ADS)

    Lesch, Volker; Montes-Campos, Hadrián; Méndez-Morales, Trinidad; Gallego, Luis Javier; Heuer, Andreas; Schröder, Christian; Varela, Luis M.

    2016-11-01

    We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field. Specifically, the mean-squared displacements are larger for the polarizable potentials at identical time intervals and the intermediate subdiffusive plateaus are greatly reduced, so the transition to the diffusive regime takes place much earlier than in the non-polarizable media. Moreover, the correlations of the added cations inside their cages are weakened out earlier and their vibrational densities of states are slightly red-shifted, reflecting the weakening effect of the electronic polarization on the Coulomb coupling in these dense ionic media. The comparison of OPLS-AA with non-polarizable APPLE&P indicates that adding polarization to OPLS-AA is not sufficient to achieve results close to experiments.

  17. Molecular dynamics analysis of the effect of electronic polarization on the structure and single-particle dynamics of mixtures of ionic liquids and lithium salts.

    PubMed

    Lesch, Volker; Montes-Campos, Hadrián; Méndez-Morales, Trinidad; Gallego, Luis Javier; Heuer, Andreas; Schröder, Christian; Varela, Luis M

    2016-11-28

    We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field. Specifically, the mean-squared displacements are larger for the polarizable potentials at identical time intervals and the intermediate subdiffusive plateaus are greatly reduced, so the transition to the diffusive regime takes place much earlier than in the non-polarizable media. Moreover, the correlations of the added cations inside their cages are weakened out earlier and their vibrational densities of states are slightly red-shifted, reflecting the weakening effect of the electronic polarization on the Coulomb coupling in these dense ionic media. The comparison of OPLS-AA with non-polarizable APPLE&P indicates that adding polarization to OPLS-AA is not sufficient to achieve results close to experiments.

  18. Atomistic deformation mechanisms in twinned copper nanospheres.

    PubMed

    Bian, Jianjun; Niu, Xinrui; Zhang, Hao; Wang, Gangfeng

    2014-01-01

    In the present study, we perform molecular dynamic simulations to investigate the compression response and atomistic deformation mechanisms of twinned nanospheres. The relationship between load and compression depth is calculated for various twin spacing and loading directions. Then, the overall elastic properties and the underlying plastic deformation mechanisms are illuminated. Twin boundaries (TBs) act as obstacles to dislocation motion and lead to strengthening. As the loading direction varies, the plastic deformation transfers from dislocations intersecting with TBs, slipping parallel to TBs, and then to being restrained by TBs. The strengthening of TBs depends strongly on the twin spacing.

  19. Polar solvation dynamics in water and methanol: search for molecularity.

    PubMed

    Sajadi, Mohsen; Weinberger, Michael; Wagenknecht, Hans-Achim; Ernsting, Nikolaus P

    2011-10-21

    Time-dependent Stokes shifts (TDSS) were measured for diverse polarity probes in water, heavy water, methanol, and benzonitrile, by broadband fluorescence up-conversion with 85 fs time resolution. In water the spectral dynamics is solute-independent and quantitatively described by simple dielectric continuum theory of solvation. In methanol the slower part of the TDSS is solute-dependent. A correlation with anisotropy decay suggests that methanol solvation dynamics is modulated by orientational solute diffusion. An empirical power law which links the solvation relaxation function of a mobile solute to that of an immobile solute is experimentally verified. Activation energies for the average relaxation rate are also given. Solvation dynamics in H(2)O and D(2)O are identical at and above 20 °C but diverge below.

  20. Ultrafast Polarization Switching in a Biaxial Molecular Ferroelectric Thin Film: [Hdabco]ClO4.

    PubMed

    Tang, Yuan-Yuan; Zhang, Wan-Ying; Li, Peng-Fei; Ye, Heng-Yun; You, Yu-Meng; Xiong, Ren-Gen

    2016-12-07

    Molecular ferroelectrics are attracting much attention as valuable complements to conventional ceramic ferroelectrics owing to their solution processability and nontoxicity. Encouragingly, the recent discovery of a multiaxial molecular ferroelectric, tetraethylammonium perchlorate, is expected to be able to solve the problem that in the technologically relevant thin-film form uniaxial molecular ferroelectrics have been found to perform considerably more poorly than in bulk. However, it can show good polarization-electric field (P-E) hysteresis loops only at very low frequency, severely hampering practical applications such as ferroelectric random access memory. Here, we present a biaxial molecular ferroelectric thin film of [Hdabco]ClO4 (dabco = 1,4-diazabicyclo[2.2.2]octane) (1), where a perfect ferroelectric hysteresis loop can be observed even at 10 kHz. It is the first example of a molecular ferroelectric thin film whose polarization can be switched at such a high frequency. Moreover, using piezoresponse force microscopy, we clearly observed the coexistence of 180° and non-180° ferroelectric domains and provided direct experimental proof that 180° ferroelectric switching and non-180° ferroelastic switching are both realized; that is, a flexible alteration of the polarization axis direction can occur in the thin film by applying an electric field. These results open a new avenue for applications of molecular ferroelectrics and will inspire further exploration of high-performance multiaxial molecular ferroelectric thin films.

  1. An innovative approach to molecularly imprinted capillaries for polar templates by grafting polymerization.

    PubMed

    Giovannoli, Cristina; Passini, Cinzia; Baravalle, Patrizia; Anfossi, Laura; Giraudi, Gianfranco; Baggiani, Claudio

    2012-06-01

    Molecularly imprinted polymers have been successfully used as selective stationary phases in capillary electrophoresis. Notwithstanding, this technique suffers from several drawbacks as the loss of molecular recognition properties in aqueous media and the lack of feasibility for imprinted systems directed towards highly polar templates soluble in aqueous environments only. Thus, the preparation of imprinted polymers for highly polar, water-soluble analytes, represents a challenge. In this work, we present an innovative approach to overcome these drawbacks. It is based on a surface molecular imprinting technique that uses preformed macromonomers as both functional recognition elements and cross-linking agents. A poly-2-hydroxyethyl-co-methacrylic acid linear polymer was grafted from the surface of silica capillaries. The grafted polymer was exhaustively esterified with methacrylic anhydride to obtain polyethylendimethacrylate-co-methacrylic acid linear chains. Then, as a proof of concept, an adequate amount of a very polar template like penicillin V was added in a hydro-organic mixture, and a thin layer of imprinted polymer was obtained by cross-linking the polymer linear chains. The binding behaviour of the imprinted and non-imprinted capillaries was evaluated in different separation conditions in order to assess the presence of template selectivity and molecular recognition effects. The experimental results clearly show that this innovative kind of imprinted material can be easily obtained in very polar polymerization environments and that it is characterized by enhanced molecular recognition properties in aqueous buffers and good selectivity towards the template and strictly related molecules.

  2. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  3. 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

  4. Molecular and epigenetic basis of macrophage polarized activation.

    PubMed

    Porta, Chiara; Riboldi, Elena; Ippolito, Alessandro; Sica, Antonio

    2015-08-01

    Macrophages are unique cells for origin, heterogeneity and plasticity. At steady state most of macrophages are derived from fetal sources and maintained in adulthood through self-renewing. Despite sharing common progenitors, a remarkable heterogeneity characterized tissue-resident macrophages indicating that local signals educate them to express organ-specific functions. Macrophages are extremely plastic: chromatin landscape and transcriptional programs can be dynamically re-shaped in response to microenvironmental changes. Owing to their ductility, macrophages are crucial orchestrators of both initiation and resolution of immune responses and key supporters of tissue development and functions in homeostatic and pathological conditions. Herein, we describe current understanding of heterogeneity and plasticity of macrophages using the M1-M2 dichotomy as operationally useful simplification of polarized activation. We focused on the complex network of signaling cascades, metabolic pathways, transcription factors, and epigenetic changes that control macrophage activation. In particular, this network was addressed in sepsis, as a paradigm of a pathological condition determining dynamic macrophage reprogramming.

  5. Atomistic k ṡ p theory

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Pseudopotentials, tight-binding models, and k ṡ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ṡ p theory. In its usual formulation, k ṡ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ṡ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp3 tight-binding model. We can thus directly derive the parameters in the sp3 tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III-V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ṡ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ṡ p models to be combined in the same system.

  6. Analytical Control of Molecular Excitations Including Strong Field Polarization Effects

    NASA Astrophysics Data System (ADS)

    Zou, Shiyang; Ren, Qinghua; Balint-Kurti, Gabriel G.; Manby, Frederick R.

    2006-06-01

    An analytical scheme is presented for designing a laser pulse to excite H2 from one specified vibrational-rotational state to another. The scheme is based on an adiabatic two-state approximation in a Floquet picture. By continuously and smoothly changing the laser frequency, we explicitly harness the dynamic Stark shifts and maintain resonance between the dressed diabatic states during laser-molecule interaction. The explicit time-dependent solution of the Schrödinger equation confirms the validity and efficacy of the analytically designed laser pulses. The scheme depends on the molecular polarizability to achieve its control objectives.

  7. Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

    SciTech Connect

    Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander; Lasne, Jérôme; Jørgensen, Jakob H.; Glavic, Artur; Lauter, Valeria; Iversen, Bo B.; McCoustra, Martin R. S.; Field, David

    2016-10-02

    It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 108 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.

  8. Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

    DOE PAGES

    Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander; ...

    2016-10-02

    It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 108 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of amore » representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.« less

  9. The First Observation of the Submillimeter Polarization Spectrum in a Low-AV Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Campbell Ashton, Peter; Ade, Peter; Angilè, Francesco E.; 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; Santos, Fabio P.; Savini, Giorgio; Scott, Douglas; Shariff, Jamil; Soler, Juan D.; Thomas, Nicholas; tucker, carole; Tucker, Gregory S.; Ward-Thompson, Derek; BLASTPol

    2017-01-01

    Polarized emission from aligned interstellar dust is both a crucial tool for studies of magnetism in the interstellar medium and a troublesome contaminant in studies of the polarized cosmic microwave background. In each case, an understanding of the significance of the dust polarization signal requires well-calibrated models that accurately describe dust grains’ physical properties and interactions with their environment. Despite decades of progress in both theory and observation, polarized dust emission models remain largely underconstrained. During its 2012 flight, BLASTPol (the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry) obtained simultaneous broad-band polarimetric maps at 250, 350, and 500 μm of a several degree-scale region containing several low-AV molecular clouds. Combining these data with polarimetric observations from the Planck 850 μm band, we have produced a submillimeter polarization spectrum for one of these objects for the first time. We find the polarization degree to be largely constant across the four submillimeter bands. This result introduces a new observable with the potential to place strong empirical constraints on polarized dust models of the ISM in a density regime that has not been accessible to previous experiments. Comparing with the work of Draine & Fraisse (2009), our result is inconsistent with two of their four models. In particular, the two models for which all polarization arises from the aligned silicate component yield submillimeter polarization spectra that rise steeply with wavelength, in disagreement with our observations. This line of investigation will continue in the near future, as new experiments like The Next-Generation BLAST Polarimeter (BLAST-TNG) use their enhanced sensitivities to characterize polarized dust emission in even more diffuse environments.

  10. Atomistic simulation of Voronoi-based coated nanoporous metals

    NASA Astrophysics Data System (ADS)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

    In this study, a new method developed for the generation of periodic atomistic models of coated and uncoated nanoporous metals (NPMs) is presented by examining the thermodynamic stability of coated nanoporous structures. The proposed method is mainly based on the Voronoi tessellation technique, which provides the ability to control cross-sectional dimension and slenderness of ligaments as well as the thickness of coating. By the utilization of the method, molecular dynamic (MD) simulations of randomly structured NPMs with coating can be performed efficiently in order to investigate their physical characteristics. In this context, for the purpose of demonstrating the functionality of the method, sample atomistic models of Au/Pt NPMs are generated and the effects of coating and porosity on the thermodynamic stability are investigated by using MD simulations. In addition to that, uniaxial tensile loading simulations are performed via MD technique to validate the nanoporous models by comparing the effective Young’s modulus values with the results from literature. Based on the results, while it is demonstrated that coating the nanoporous structures slightly decreases the structural stability causing atomistic configurational changes, it is also shown that the stability of the atomistic models is higher at lower porosities. Furthermore, adaptive common neighbour analysis is also performed to identify the stabilized atomistic structure after the coating process, which provides direct foresights for the mechanical behaviour of coated nanoporous structures.

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

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

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

  12. 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.

  13. 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

  14. Polarized Molecular Orbital Model Chemistry. II. The PMO Method

    PubMed Central

    Zhang, Peng; Fiedler, Luke; Leverentz, Hannah R.; Truhlar, Donald G.; Gao, Jiali

    2012-01-01

    We present a new semiempirical molecular orbital method based on neglect of diatomic differential overlap. This method differs from previous NDDO-based methods in that we include p orbitals on hydrogen atoms to provide a more realistic modeling of polarizability. As in AM1-D and PM3-D, we also include damped dispersion. The formalism is based on the original MNDO one, but in the process of parameterization we make some specific changes to some of the functional forms. The present article is a demonstration of the capability of the new approach, and it presents a successful parametrization for compounds composed only of hydrogen and oxygen atoms, including the important case of water clusters. PMID:23378824

  15. 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

  16. 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.

  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.

  18. 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

  19. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    DTIC Science & Technology

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  20. Molecular-level comparison of alkylsilane and polar-embedded reversed-phase liquid chromatography systems.

    PubMed

    Rafferty, Jake L; Siepmann, J Ilja; Schure, Mark R

    2008-08-15

    Stationary phases with embedded polar groups possess several advantages over conventional alkylsilane phases, such as reduced peak tailing, enhanced selectivity for specific functional groups, and the ability to use a highly aqueous mobile phase. To gain a deeper understanding of the retentive properties of these reversed-phase packings, molecular simulations were carried out for three different stationary phases in contact with mobile phases of various water/methanol ratios. Two polar-embedded phases were modeled, namely, amide and ether containing, and compared to a conventional octadecylsilane phase. The simulations show that, due to specific hydrogen bond interactions, the polar-embedded phases take up significantly more solvent and are more ordered than their alkyl counterparts. Alkane and alcohol probe solutes indicate that the polar-embedded phases are less retentive than alkyl phases for nonpolar species, whereas polar species are more retained by them due to hydrogen bonding with the embedded groups and the increased amount of solvent within the stationary phase. This leads to a significant reduction of the free-energy barrier for the transfer of polar species from the mobile phase to residual silanols, and this reduced barrier provides a possible explanation for reduced peak tailing.

  1. Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.

    PubMed

    Shityakov, Sergey; Neuhaus, Winfried; Dandekar, Thomas; Förster, Carola

    2013-01-01

    Molecular polar surface (PS) descriptors are very useful parameters in prediction of drug transport properties. They could be also used to investigate the blood-brain barrier (BBB) permeation rate for various chemical compounds. In this study, a dataset of drugs (n = 19) from various pharmacological groups was studied to estimate their potential properties to permeate across the BBB. Experimental logBB data were available as steady-state distribution values of the in vivo rat model for these molecules. Including accurate calculation of the electrostatic potential maps, polar surface descriptors, such as a two-dimensional polar surface area (2D-PSA), topological polar surface area (TPSA) and three-dimensional polar surface area or polar area (3D-PSA; PA) were measured and analysed. We report the strong correlation of these descriptors with logBB values for the prediction of BBB permeation using the linear partial least squares (PLS) fitting technique. The 3D-PSA descriptor showed the best fit to logBB values with R² = 0.92 and RMSD = 0.29 (p-value < 0.0001). The obtained results demonstrate that all descriptors bear high predictive powers and could provide an efficient strategy to envisage the pharmacokinetic properties of chemical compounds to permeate across the BBB at an early stage of the drug development process.

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

    PubMed

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

    2013-01-08

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

  3. 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.

  4. Circularly Polarized X Rays: Another Probe of Ultrafast Molecular Decay Dynamics

    SciTech Connect

    Travnikova, Oksana; Lindblad, Andreas; Nicolas, Christophe; Soederstroem, Johan; Kimberg, Victor; Miron, Catalin; Liu Jicai; Gel'mukhanov, Faris

    2010-12-03

    Dissociative nuclear motion in core-excited molecular states leads to a splitting of the fragment Auger lines: the Auger-Doppler effect. We present here for the first time experimental evidence for an Auger-Doppler effect following F1s{yields}a{sub 1g}* inner-shell excitation by circularly polarized x rays in SF{sub 6}. In spite of a uniform distribution of the dissociating S-F bonds near the polarization plane of the light, the intersection between the subpopulation of molecules selected by the core excitation with the cone of dissociation induces a strong anisotropy in the distribution of the S-F bonds that contributes to the scattering profile measured in the polarization plane.

  5. Structural features of binary mixtures of supercritical CO2 with polar entrainers by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Gurina, D. L.; Antipova, M. L.; Petrenko, V. E.

    2013-10-01

    Computer simulations of supercritical carbon dioxide and its mixtures with polar cosolvents: water, methanol, and ethanol (concentration, 0.125 mole fractions) at T = 318 K and ρ = 0.7 g/cm3 are performed. Atom-atom radial distribution functions are calculated by classical molecular dynamics, while the probability distributions of relative orientation of CO2 molecules in the first and second coordination spheres describing the geometry of the nearest environment of CO2 molecules and the trajectories of cosolvent molecules are found using Car-Parrinello molecular dynamics. Based on the latter, the conclusions regarding structure and interactions of polar entrainers in their mixtures with supercritical CO2 are made. It is shown that the microstructure of carbon dioxide varies only slightly upon the introduction of cosolvents.

  6. Characterization of polar molecular species adsorbed on LiNbO3 surfaces

    NASA Astrophysics Data System (ADS)

    Bharath, Satyaveda; Pearl, Thomas

    2008-10-01

    In order to explore the mechanisms of adsorption on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3: LN), `Z-cut'; along the (0001) plane, has been prepared and characterized and subsequently exposed to a polar molecule. 4-n-octyl-4'-cyanobiphenyl (8CB) liquid crystal was chosen as our model system. Low-energy electron diffraction, atomic force microscopy, surface contact angle measurement, and X-ray photoelectron spectroscopy were used to characterize the surface of LN as well as the nature of the films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Preferential attachment for positive domains was observed indicating an interaction between the polar end group of the molecule and the surface charge of the surface. Understanding anchoring mechanisms for polarizable molecules on uniformly poled surfaces allows for a fuller appreciation of how ferroelectric surfaces can be used for controlling molecular organization.

  7. Characterization of molecularly imprinted polymers using a new polar solvent titration method.

    PubMed

    Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

    2014-07-01

    A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs.

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

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

  9. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

    NASA Astrophysics Data System (ADS)

    Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V.; Carloni, Paolo

    2006-04-01

    Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases.

  10. Atomistic insights into the lung cancer-associated L755P mutation in HER2 resistance to lapatinib: a molecular dynamics study.

    PubMed

    Yang, Bei; Zhang, Haiping; Wang, Hao

    2015-02-01

    HER2, a member of the human ErbB protein family belonging to receptor tyrosine kinases, plays important roles in regulating crucial cellular processes, including cell migration, proliferation, and differentiation. A missense mutation, L755P, in the HER2 kinase domain has been involved in lung cancer in humans and exhibits reduced response to lapatinib therapy. However, the detailed mechanism of how the HER2 L755P mutation causes drug resistance to lapatinib remains elusive. Here, molecular docking, molecular dynamics (MD) simulations, binding free energy calculations [molecular mechanics and generalized Born/surface area (MM-GBSA)] were performed to reveal the mechanism of drug resistance due to the HER2 L755P mutation. MD simulations revealed that the L755P mutation caused structural changes in the regions of helix αC, the glycine-rich loop, and the activation loop, thereby leading to the loss of interactions between the solubilizing group of lapatinib and HER2. Moreover, MM-GBSA calculations suggested that hydrophobic interactions between lapatinib and HER2 contribute most to the binding affinity, and that the L755P mutation could result in a less energetically favorable HER2/lapatinib complex. This may weaken the binding of lapatinib to the mutated HER2, thereby leading to the emergence of drug resistance. This study offers a structural explanation for the effect of the L755P mutation on the HER2/lapatinib complex.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. 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.

  13. Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

    PubMed Central

    Tse, Amanda; Verkhivker, Gennady M.

    2016-01-01

    The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may

  14. PolCat: Modelling submillimetre polarization of molecular cloud cores using successive parametrized coordinate transformations

    NASA Astrophysics Data System (ADS)

    Franzmann, E. L.; Fiege, J. D.

    2016-12-01

    We introduce a software package called PolCat for modelling magnetized molecular cloud cores using submillimetre linear polarization and continuum intensity maps from thermal dust emission. Our PolCat modelling software builds a three-dimensional triaxial core model via the use of consecutive parametrized coordinate transformations, and produces simulated polarization maps to fit to observational datasets. We utilize a multi-objective evolutionary optimizer to search the parameter space to simultaneously minimize χ2 for the intensity and polarization position angle maps. The aim of this paper is to test PolCat by applying it to several artificial data sets, characterizing the capabilities and performance of the code using approximately 400 test runs. We find that PolCat is able to distinguish between polarization maps of twisted and non-twisted field geometries and identify the symmetry of the twist when one exists in the data. PolCat generally obtains the correct shapes of cores when fit to models with the correct field geometry. We characterized the degeneracy of our models due to orientation, finding that there are at least eight degenerate core orientations that produce identical polarization maps for the case of triaxial cores. The degeneracy increases with core symmetry. We expect PolCat to be a useful tool for modelling observational polarization data sets. Our tests demonstrate that the code can often eliminate incorrect field configurations, while finding a range or potential models that can explain the data. Physical considerations can often further reduce the set of allowed models, resulting in reasonable constraints on field geometry.

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

    PubMed Central

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

    2016-01-01

    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

  16. 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.

  17. 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.

  18. 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.

  19. The atomistic mechanism of hcp-to-bcc martensitic transformation in the Ti-Nb system revealed by molecular dynamics simulations.

    PubMed

    Li, Yang; Li, JiaHao; Liu, BaiXin

    2015-02-14

    Applying the constructed Ti-Nb potentials, molecular dynamics simulations were conducted to investigate the martensitic transformation of Ti100-xNbx alloys (x = 5, 10…25) from the α' phase (hcp) to the β phase (bcc). It is found that the transformation involved four phases, i.e. α', α'', fco (face-centered orthorhombic), and β phases. The structures of the obtained phases exhibit consistency with experimental data, verifying the validity of atomic simulations. The simulations not only revealed the processes of atomic displacements during the transformation, but also elucidated the underlying mechanism of the martensitic transformation at the atomic level. The martensitic transformation incorporates three types of coinstantaneous deformations i.e. slide, shear as well as extension, and the subsequent lattice constant relaxation. Furthermore, according to the proposed mechanism, the crystallographic correlation between the initial α' phase and the final β phase has been deduced. The simulation results provide a clear landscape on the martensitic transformation mechanism, facilitating our comprehensive understanding on the phase transition in the Ti-Nb system.

  20. The Molecular Behavior of a Single β-Amyloid inside a Dipalmitoylphosphatidylcholine Bilayer at Three Different Temperatures: An Atomistic Simulation Study.

    PubMed

    Kargar, Faezeh; Emadi, Saeed; Fazli, Hossein

    2017-03-25

    The behavior of a single Aβ40 molecule within a dipalmitoylphosphatidylcholine (DPPC) bilayer was studied by all-atom molecular dynamics simulations. The effect of membrane structure was investigated on Aβ40 behavior, secondary structure and insertion depth. Simulations were performed at three temperatures (323, 310 and 300 K) to probe three different bilayer fluidities. Results show that at all above temperatures the peptide contains two short helices, coil, bend and turn structures. At 300 K, the peptide contains a region with β structure in C-terminal region. Our results also show that Aβ decreases the bilayer thickness and the order of lipids in its vicinity which leads to water insertion into the bilayer and concomitant increase in the local fluidity. The peptide remains embedded in the bilayer at all temperatures, and become inserted into the bilayer up to several residues at 323 and 310 K. At 310 and 300 K, the dominant interaction energy between Aβ and bilayer changes from electrostatic to van der Waals. It can be proposed that at higher temperatures (e.g., 323 K) Lys28 and the C-terminal region of the peptide play the role of two anchors that keep Aβ inside the top leaflet. This study demonstrates that Aβ molecule can perturb the integrity of cellular membranes. This article is protected by copyright. All rights reserved.

  1. 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

    2013-11-07

    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.

  2. Influence of specific intermolecular interactions on the thermal and dielectric properties of bulk polymers: atomistic molecular dynamics simulations of Nylon 6.

    PubMed

    Lukasheva, N V; Tolmachev, D A; Nazarychev, V M; Kenny, J M; Lyulin, S V

    2017-01-04

    Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges. The simulations allowed the study of the thermal and dielectric properties in a wide range of temperatures and cooling rates. The feasibility of the use of the three methods for the estimation of the glass transition temperature not only from the temperature dependence of structural characteristics such as density, but also by using the electrostatic energy and dielectric constant is demonstrated. The values of glass transition temperatures obtained at different cooling rates are practically the same for the three methods. By proper accounting for partial charges in the simulations, a reasonable agreement between the results of our simulations and experimental data for the density, thermal expansion coefficient, static dielectric constant and activation energy of γ and β relaxations is obtained demonstrating the validity of the modeling approach reported.

  3. Atomistic simulation of nanostructured materials

    NASA Astrophysics Data System (ADS)

    Zhu, Ronghua

    Atomistic based computer modeling and simulation of nanostructured materials has become an important subfield of materials research. Based on the multiresolution method, which combines the continuum mechanics, kinetic Monte Carlo method and molecular dynamics method, we study the nanostructured materials grown by quantum-dot self-assembly, mechanical properties of strained semiconductors, and mechanical properties of carbon nanotube reinforced composites. This thesis covers the following three main contributions. 1. Self-organization of semiconductors InAs/GaAs in Stranski-Krastanov growth mode is studied using kinetic Monte Carlo simulations method coupled with the Green's function solution for the elastic strain energy distribution. The relevant growth parameters such as growth temperature, surface coverage, flux rate, and growth interruption time are investigated. It is shown clearly that when the long-range strain energy is included in the simulation, ordered uniform size distribution can be achieved. To address the effect of material anisotropy, the anisotropic substrates of GaAs with different growth orientations (001), (111), and (113) and an isotropic substrate Iso (001), reduced from cubic GaAs, are also investigated. Simulation results show that at selected growth parameters for temperature, coverage, and growth interruption time, strain energy field in the substrate is the key factor that controls the pattern of island distribution. Furthermore, layer-by-layer growth of quantum dots is also simulated briefly, and vertical alignment is observed that could lead to progressively uniform island sizes and spatial ordering. 2. Since the misfit strain will be induced during the quantum dots epitaxial growth, the mechanical property of the grown semiconductors will be influenced. In this thesis, utilizing the basic continuum mechanics, we present a molecular dynamic prediction for the elastic stiffness C11, C12 and C 44 in strained silicon and InAs as functions

  4. Molecular density functional theory: application to solvation and electron-transfer thermodynamics in polar solvents.

    PubMed

    Borgis, Daniel; Gendre, Lionel; Ramirez, Rosa

    2012-03-01

    A molecular density functional theory of solvation is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position- and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, the unknown excess term of the functional can be approximated by the angular-dependent direct correlation function of the pure solvent. This function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation. The corresponding functional can then be minimized on a three-dimensional cubic grid for positions and a Gauss-Legendre angular grid for orientations to provide the solvation free energy of embedded molecules at the same time as the solvent three-dimensional microscopic structure. This functional minimization procedure is much more efficient than direct molecular dynamics simulations combined with thermodynamic integration schemes. The approach is shown to be also pertinent to the molecular-level determination of electron-transfer properties such as reaction free energy and reorganization energy. It is illustrated for molecular solvation and photochemical electron-transfer reactions in acetonitrile, a prototypical polar aprotic solvent.

  5. Quantitative analysis of molecular orientation in chlorophyll a Langmuir monolayer: a polarized visible reflection spectroscopic study.

    PubMed Central

    Okamura, E; Hasegawa, T; Umemura, J

    1995-01-01

    Polarized visible reflection spectra of a chlorophyll a (Chl.a) Langmuir monolayer have been measured in situ at various surface pressures. By applying Hansen's optics to the three-phase plane-bounded system (air/Chl.a monolayer/water), the negative reflection absorbances observed were reproduced satisfactorily by the theoretical calculation. Molecular orientation of Chl.a in the monolayer was evaluated quantitatively as a function of surface pressure, from the reflection absorbance of p- and s-polarized spectra of the red (Qy) band. It has been proven that Chl.a molecules in the monolayer form aggregates (islands) even in the low surface pressure region and that during the monolayer compression the molecules are gradually reorganized from inhomogeneous islands to ordered structures, with the chromophores oriented on the average vertically to the water surface. Images FIGURE 1 PMID:8519968

  6. Enhanced Raman scattering at dielectric surfaces. 2. Molecular orientations from polarized surface Raman scattering

    SciTech Connect

    Walls, D.J.; Bohn, P.W. )

    1990-03-08

    The ability to obtain polarized Raman scattering for monolayer adsorbates deposited on oxide covered noble-metal island film structures has been closely examined. The relationship of the relative intensities of the in-plane enhanced electric field components to the depolarization ratios of the totally symmetric Raman vibrational modes of p-nitrobenzoic acid and phthalazine was found to indicate a constant depolarization of the in-plane electric field components induced by the island film particles themselves. With this information and with polarized Raman scattering information from nontotally symmetric phthalazine vibrations, we report a quantitative determination of the average surface molecular orientation of phthalazine monolayers at sputtered SiO{sub 2} surfaces.

  7. 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.

  8. Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K.

    PubMed

    Cheng, Tao; Xiao, Hai; Goddard, William A

    2017-02-21

    A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of -0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than -0.6 V (RHE) ethylene, the major product, is produced via the Eley-Rideal (ER) mechanism using H2O + e(-) The rate-determining step (RDS) is C-C coupling of two CO, with ΔG(‡) = 0.69 eV. For an applied potential less than -0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than -0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4 These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface.

  9. A concurrent atomistic-continuum methodolody and its applications

    NASA Astrophysics Data System (ADS)

    Xiong, Liming

    The objective of my dissertation research is to develop a concurrent atomistic-continuum (CAC) modeling and simulation tool for crystalline solids. The theoretical foundation of the methodology is a newly developed atomistic field theory (AFT). In this work, finite element method (FEM) is implemented to pursue the numerical solutions of the governing equations in AFT, where atomistic information has been naturally built in. Since those governing equations are constructed in terms of local densities, in the finite element implementations, different meshes can be used in the regions of different concerns. When the finest mesh is used, there is a finite element node corresponding to each lattice point embedded with multiple atoms, the computational model becomes identical to a fully atomistic model. When a coarse mesh is used, that is, the size of the finite element is much larger than lattice spacing, the majority of the degrees of freedom are eliminated and the computational cost can be largely reduced, the resulting model is a coarse grained (CG) model. When the coarse mesh and finest mesh are concurrently implemented within one computational model, that is, the finest mesh is used within the critical regions and the coarser mesh is used away from the critical regions. The resulting model is naturally a CAC model governed by one single theoretical framework. With much less computational resources requested than that by fully atomistic simulations, the simulation packages developed in this work has been applied to model and simulate critical phenomena such as dislocations, phase transformations and fracture in various crystalline materials including ceramics such as MgO, silicon and silicon carbide and also metals such as copper under mechanical loading. All of the simulations conducted in this work are verified through the direct comparisons with that from the corresponding full molecular dynamics (MD) simulations. In addition, the limitations, potential

  10. Molecular hydraulic properties of montmorillonite: a polarized fourier transform infrared spectroscopic study.

    PubMed

    Amarasinghe, Priyanthi M; Katti, Kalpana S; Katti, Dinesh R

    2008-12-01

    Understanding the rates at which fluid flows into clay interlayers at the molecular level is fundamental to designing an effective clay barrier system. In this work, molecular interactions at the Na-montmorillonite (MMT)-water interface, emphasizing the flow properties of the clay interlayer, have been studied at the molecular and nanoscale level using polarized Fourier transform infrared (FT-IR) spectroscopic and X-ray diffraction (XRD) techniques. Clay-water slurries were smeared on inert gold-coated metal substrates for FT-IR experiments and slurries were smeared on quartz plates for XRD experiments. By analyzing the O-H stretching and H-O-H bending vibrations in clay slurries, it was concluded that the molecular behavior of interlayer water is significantly different from the molecular behavior of bulk water. With increasing clay-water interaction time, it was also seen that the Si-O stretching bands of clay are being significantly altered by the water molecules in the interlayer. Using these spectroscopic techniques we have estimated the time required for water to flow into the clay interlayer. Further, by analyzing the particle size of the clay using atomic force microscopy (AFM) imaging, we were able to estimate the flow velocity of the water in the clay interlayer. This velocity is found to be 3.23 x 10(-9) cm/s. This flow velocity was found to be of the same order of magnitude as the hydraulic conductivity of smectite-type clay reported elsewhere. Also described in this work is the correct positioning of the Si-O out-of-plane vibration band of MMT at the two-layer saturation level in the interlayer. This band was only observed in p-polarized spectra at 1211 cm(-1). Thus, we attribute this band to the Si-O out-of-plane vibration band.

  11. Impact on interface spin polarization of molecular bonding to metallic surfaces.

    PubMed

    Javaid, S; Bowen, M; Boukari, S; Joly, L; Beaufrand, J-B; Chen, Xi; Dappe, Y J; Scheurer, F; Kappler, J-P; Arabski, J; Wulfhekel, W; Alouani, M; Beaurepaire, E

    2010-08-13

    We have studied the repercussion of the molecular adsorption mechanism on the electronic properties of the interface between model nonmagnetic or magnetic metallic surfaces and metallo-organic phthalocyanines molecules (Pcs). Our intertwined x-ray absorption spectroscopy experiments and computational studies reveal that manganese Pc (MnPc) is physisorbed onto a Cu(001) surface and retains the electronic properties of a free molecule. On the other hand, MnPc is chemisorbed onto Co(001), leading to a dominant direct exchange interaction between the Mn molecular site and the Co substrate. By promoting an interfacial spin-polarized conduction state on the molecule, these interactions reveal an important lever to tailor the spintronic properties of hybrid organic-metallic interfaces.

  12. 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.

  13. 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.

  14. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field.

    PubMed

    Yao, Xue X; Ji, Chang G; Xie, Dai Q; Zhang, John Z H

    2013-05-15

    The DNA binding domain of transposon Tn916 integrase (INT-DBD) binds to DNA target site by positioning the face of a three-stranded antiparallel β-sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT-DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein-DNA binding complex. In the current work, the combined use of quantum-based polarized protein-specific charge (PPC) for protein and polarized nucleic acid-specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT-DBD and DNA. Our study shows that the protein-DNA structure is stabilized by polarization and the calculated protein-DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein-DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA.

  15. 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

  16. 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

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

    PubMed

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

    2004-05-18

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    PubMed

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

    2012-10-01

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

  20. 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.

  1. The notion of a plastic material spin in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

    2016-12-01

    A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

  2. 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

    2016-09-07

    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.

  3. 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.

  4. Atomistic properties of γ uranium.

    PubMed

    Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

    2012-02-22

    The properties of the body-centered cubic γ 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 (γ) 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 γ 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 calculation of γ U properties above 0 K with interatomic potentials.

  5. Atomistic Modeling of Mechanical Loss in Amorphous Oxides

    NASA Astrophysics Data System (ADS)

    Hamdan, Rashid; Trinastic, Jonathan; Cheng, Hai-Ping

    2013-03-01

    The mechanical and optical loss in amorphous solids, described by the internal friction and light scattering susceptibility are investigated using classical, atomistic molecular dynamics simulation. We implemented the trajectory bisection method and the non-local ridge method in DL-POLY molecular dynamics simulation software. These methods were used to locate the different local potential energy minima that a system visits through an MD trajectory and the transition state between any two consecutive minima. From the distributions of the barrier height and asymmetry, and the relaxation time of the different transition states we calculated the internal friction of pure amorphous silica and mixed oxides. Acknowledgment: NSF/PHYS

  6. 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.

  7. 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.

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

    DOE PAGES

    Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.; ...

    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

  9. 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.

  10. Insulin adsorption on crystalline SiO2: Comparison between polar and nonpolar surfaces using accelerated molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nejad, Marjan A.; Mücksch, Christian; Urbassek, Herbert M.

    2017-02-01

    Adsorption of insulin on polar and nonpolar surfaces of crystalline SiO2 (cristobalite and α -quartz) is studied using molecular dynamics simulation. Acceleration techniques are used in order to sample adsorption phase space efficiently and to identify realistic adsorption conformations. We find major differences between the polar and nonpolar surfaces. Electrostatic interactions govern the adsorption on polar surfaces and can be described by the alignment of the protein dipole with the surface dipole; hence spreading of the protein on the surface is irrelevant. On nonpolar surfaces, on the other hand, van-der-Waals interaction dominates, inducing surface spreading of the protein.

  11. AN IMPRINT OF MOLECULAR CLOUD MAGNETIZATION IN THE MORPHOLOGY OF THE DUST POLARIZED EMISSION

    SciTech Connect

    Soler, J. D.; Netterfield, C. B.; Fissel, L. M.; Hennebelle, P.; Martin, P. G.; Miville-Deschenes, M.-A.

    2013-09-10

    We describe a morphological imprint of magnetization found when considering the relative orientation of the magnetic field direction with respect to the density structures in simulated turbulent molecular clouds. This imprint was found using the Histogram of Relative Orientations (HRO), a new technique that utilizes the gradient to characterize the directionality of density and column density structures on multiple scales. We present results of the HRO analysis in three models of molecular clouds in which the initial magnetic field strength is varied, but an identical initial turbulent velocity field is introduced, which subsequently decays. The HRO analysis was applied to the simulated data cubes and mock-observations of the simulations produced by integrating the data cube along particular lines of sight. In the three-dimensional analysis we describe the relative orientation of the magnetic field B with respect to the density structures, showing that: (1) the magnetic field shows a preferential orientation parallel to most of the density structures in the three simulated cubes, (2) the relative orientation changes from parallel to perpendicular in regions with density over a critical density n{sub T} in the highest magnetization case, and (3) the change of relative orientation is largest for the highest magnetization and decreases in lower magnetization cases. This change in the relative orientation is also present in the projected maps. In conjunction with simulations, HROs can be used to establish a link between the observed morphology in polarization maps and the physics included in simulations of molecular clouds.

  12. Concentration measurements in molecular gas mixtures with a two-pump pulse femtosecond polarization spectroscopy technique

    NASA Astrophysics Data System (ADS)

    Hertz, E.; Chaux, R.; Faucher, O.; Lavorel, B.

    2001-08-01

    Recently, we have demonstrated the ability of the Raman-induced polarization spectroscopy (RIPS) technique to accurately determine concentration or polarizability anisotropy ratio in low-pressure binary molecular mixtures [E. Hertz, B. Lavorel, O. Faucher, and R. Chaux, J. Chem. Phys. 113, 6629 (2000)]. It has been also pointed out that macroscopic interference, occurring when two revivals associated to different molecules time overlap, can be used to achieve measurements with picosecond time resolution. The applicability of the technique is intrinsically limited to a concentration range where the signals of both molecules are of the same magnitude. In this paper, a two-pump pulse sequence with different intensities is used to overcome this limitation. The relative molecular responses are weighted by the relative laser pump intensities to give comparable signals. Furthermore, by tuning the time delay between the two-pump pulses, macroscopic interference can be produced regardless of the accidental coincidences between the two molecular temporal responses. The study is performed in a CO2-N2O gas mixture and the concentration is measured with and without macroscopic interference. Applications of the method in the field of noninvasive diagnostics of combustion media are envisaged.

  13. The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups.

    PubMed

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

    2017-05-04

    The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green's function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

  14. 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

  15. Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents

    NASA Astrophysics Data System (ADS)

    Leontyev, I. V.; Tovmash, A. V.; Vener, M. V.; Rostov, I. V.; Basilevsky, M. V.

    2005-12-01

    Outersphere reorganization energies ( λ) for intramolecular electron transfer (ET) and hole transfer are studied in anion- and cation-radical forms of complex organic substrates (biphenylyl-spacer-naphtyl) in polar solvents simulated by means of the nonpolarizable models of water and 1,2-dichloroethane. The earlier elaborated molecular/continuum approach (the MD/FRCM, J. Chem. Phys., 119 (2003) 8024) is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses within a nonpolarizable MD simulation (the SPC water model). Quantum-chemical calculations of solute charge distributions were performed with semiempirical (AM1) and second ab initio (HF/6-31G(d,p)) approximations. Ab initio charges give lower λ-values and are preferable, probably, because of including the effect of the SCRF polarization of the diabatic ET states. Standard Lennard-Jones and charge parameters implemented in MD runs were not specially fitted for reproducing ET effects. The difference in values for a cation and an anion originating from the same parent structure was specially investigated. As shown earlier, this effect, nonlinear in its nature, proved to be extremely large when a model dipolar two-site system was studied. For the present ET structures representing real chemical substrates it has reduced to a plausible value of 6-8 kcal/mol. The study of the temperature dependence of λ comprises a first MD simulation of this problem and its slope was found to be in accord with an experimental observation for an anionic species. Calculations of absolute λ-values for the hole transfer in 1,2-dichloroethane are the first MD simulations of reorganization energies in experimentally studied reactions. Computed values of λ-s are higher than the experimental data. The effect of this magnitude could be eliminated by proper tuning the solvent parameters.

  16. 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

  17. Structure and polarization properties of water: molecular dynamics with a nonadditive intermolecular potential.

    PubMed

    Shvab, I; Sadus, Richard J

    2012-05-01

    The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.

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

    NASA Astrophysics Data System (ADS)

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

    2001-10-01

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

  19. 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.

  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. 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.

  2. NiTi superelasticity via atomistic simulations

    NASA Astrophysics Data System (ADS)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

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

  3. Polarization-resolved photoluminescence study of individual GaN nanowires grown by catalyst-free molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Schlager, John B.; Sanford, Norman A.; Bertness, Kris A.; Barker, Joy M.; Roshko, Alexana; Blanchard, Paul T.

    2006-05-01

    Polarization- and temperature-dependent photoluminescence (PL) measurements were performed on individual GaN nanowires. These were grown by catalyst-free molecular beam epitaxy on Si(111) substrates, ultrasonically removed, and subsequently dispersed on sapphire substrates. The wires were typically 5-10μm in length, c-axis oriented, and 30-100nm in diameter. Single wires produced sufficient emission intensity to enable high signal-to-noise PL data. Polarized PL spectra differed for the σ and π polarization cases, illustrating the polarization anisotropy of the exciton emission associated with high-quality wurtzite GaN. This anisotropy in PL emission persisted even up to room temperature (4-296K). Additionally, the nanowire PL varied with excitation intensity and with (325nm) pump exposure time.

  4. Connecting Atomistic and Continuous Models of Elastodynamics

    NASA Astrophysics Data System (ADS)

    Braun, Julian

    2017-02-01

    We prove the long-time existence of solutions for the equations of atomistic elastodynamics on a bounded domain with time-dependent boundary values as well as their convergence to a solution of continuum nonlinear elastodynamics as the interatomic distances tend to zero. Here, the continuum energy density is given by the Cauchy-Born rule. The models considered allow for general finite range interactions. To control the stability of large deformations we also prove a new atomistic Gårding inequality.

  5. 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

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

    PubMed

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

    2013-06-28

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

  7. Atomistic simulations of grain and interphase boundary mobility

    NASA Astrophysics Data System (ADS)

    Hoyt, J. J.

    2014-04-01

    In recent years, atomistic simulations have provided valuable insights into the thermodynamic and kinetic properties of grain and interphase boundaries. In this work, we provide a brief overview of kinetic processes occurring at migrating interfaces and survey various molecular dynamics techniques for extracting grain boundary mobilities. The advantages and disadvantages of fluctuation and applied driving force methods will be discussed. In addition, we review recent examples of simulations that have identified structural phase transformations at grain boundaries. Finally, simulations that have investigated the mobility and atomic mechanisms of growth of an fcc-bcc interphase boundary are summarized.

  8. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

    PubMed Central

    2015-01-01

    The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported. PMID:25202918

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  10. Determination of 3D molecular orientation by concurrent polarization analysis of multiple Raman modes in broadband CARS spectroscopy

    PubMed Central

    2016-01-01

    A theoretical description is presented about a new analysis method to determine three-dimensional (3D) molecular orientation by concurrently analyzing multiple Raman polarization profiles. Conventional approaches to polarization Raman spectroscopy are based on single peaks, and their 2D-projected polarization profiles are limited in providing 3D orientational information. Our new method analyzes multiple Raman profiles acquired by a single polarization scanning measurement of broadband coherent anti-Stokes Raman scattering (BCARS). Because the analysis uses only dimensionless quantities, such as intensity ratios and phase difference between multiple profiles, the results are not affected by sample concentration and the system response function. We describe how to determine the 3D molecular orientation with the dimensionless observables by using two simplified model cases. In addition, we discuss the effect of orientational broadening on the polarization profiles in the two model cases. We find that in the presence of broadening we can still determine the mean 3D orientation angles and, furthermore, the degree of orientational broadening. PMID:26561197

  11. 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.

  12. Using molecular simulation to predict solute solvation and partition coefficients in solvents of different polarity.

    PubMed

    Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Macedo, Eugénia A; Economou, Ioannis G

    2011-05-28

    A methodology is proposed for the prediction of the Gibbs energy of solvation (Δ(Solv)G) based on MD simulations. The methodology is then used to predict Δ(Solv)G of four solutes (namely propane, benzene, ethanol and acetone) in several solvents of different polarities (including n-hexane, n-hexadecane, ethylbenzene, 1-octanol, acetone and water) while testing the validity of the TraPPE force field parameters. Excellent agreement with experimental data is obtained, with average deviations of 0.2, 1.1, 0.8 and 1.2 kJ mol(-1), for the four solutes respectively. Subsequently, partition coefficients (log P) for forty different solute/solvent systems are predicted. The a priori knowledge of partition coefficient values is of high importance in chemical and pharmaceutical separation process design or as a measure of the increasingly important environmental fate. Here again, the agreement between experimental data and simulation predictions is excellent, with an absolute average deviation of 0.28 log P units. However, this deviation can be decreased down to 0.14 log P units, just by optimizing partial atomic charges of acetone in the water phase. Consequently, molecular simulation is proven to be a tool with strong physical basis able to predict log P with competitive accuracy when compared to the popular statistical methods with weak physical basis.

  13. Relationship between Passive Permeability and Molecular Polarity Using Block Relevance Analysis.

    PubMed

    Goetz, Gilles H; Shalaeva, Marina; Caron, Giulia; Ermondi, Giuseppe; Philippe, Laurence

    2017-02-06

    EPSA is an experimental descriptor of molecular polarity obtained from chromatographic retention in supercritical fluid chromatography (SFC) systems, previously shown by Goetz et al. to correlate with passive permeability of cyclic peptides. The present study focuses on EPSA in relation to passive permeability of small molecules. We applied block relevance (BR) analysis to interpret the relative significance of mechanistic forces prevailing in EPSA. The BR analysis is a computational tool that allows the interpretation of the balance of intermolecular interactions governing systems such as the aforementioned chromatographic retention in EPSA. EPSA and passive permeability determined by Ralph Russ canine kidney cells (RRCK) or low efflux Madin Darby canine kidney cells (MDCK-LE) and human epithelial colorectal adenocarcinoma cells (Caco-2), studied on a data set of commercial drugs, indicated that EPSA is relevant in describing permeability of hydrophilic drugs (CLogP < 1). We then verified, on a data set of 1699 Rule of 5 compliant Pfizer compounds, that when CLogP < 1, a value of EPSA < 100 significantly increases the likelihood of high permeability.

  14. 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.

  15. 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.

  16. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling.

    PubMed

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  17. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling

    NASA Astrophysics Data System (ADS)

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T.; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  18. 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

  19. Terahertz-Field-Induced Large Macroscopic Polarization and Domain-Wall Dynamics in an Organic Molecular Dielectric

    NASA Astrophysics Data System (ADS)

    Morimoto, T.; Miyamoto, T.; Yamakawa, H.; Terashige, T.; Ono, T.; Kida, N.; Okamoto, H.

    2017-03-01

    A rapid polarization control in paraelectric materials is important for an ultrafast optical switching useful in the future optical communication. In this study, we applied terahertz-pump second-harmonic-generation-probe and optical-reflectivity-probe spectroscopies to the paraelectric neutral phase of an organic molecular dielectric, tetrathiafulvalene-p -chloranil and revealed that a terahertz pulse with the electric-field amplitude of ˜400 kV /cm produces in the subpicosecond time scale a large macroscopic polarization whose magnitude reaches ˜20 % of that in the ferroelectric ionic phase. Such a large polarization generation is attributed to the intermolecular charge transfers and breathing motions of domain walls between microscopic neutral and ionic domains induced by the terahertz electric field.

  20. The early history of the polarizing region: from classical embryology to molecular biology.

    PubMed

    Tickle, Cheryll

    2002-01-01

    The polarizing region of the developing limb bud is one of the best known examples of a cell-cell signalling centre that mediates patterning in vertebrate embryos. This article traces some highlights in the history of the polarizing region from its discovery by John Saunders and early work that defined polarizing activity through a period in which modelling was pre-eminent, right up to the discovery of defined molecules with polarizing activity. There is a particular focus on the discovery that retinoic acid could mimic signalling of the polarizing activity and this finding is then set in the context of more recent work which implicates Shh and BMPs in mediating polarizing activity.

  1. Mechanism of ligand binding to alpha 1-acid glycoprotein (orosomucoid): correlated thermodynamic factors and molecular parameters of polarity.

    PubMed Central

    Urien, S; Giroud, Y; Tsai, R S; Carrupt, P A; Brée, F; Testa, B; Tillement, J P

    1995-01-01

    Eight ligands were used in this study, four basic, three neutral and one acidic. Their binding to serum alpha 1-acid glycoprotein (orosomucoid) was measured at several temperatures, and the data were analysed together by a general model with three unknowns, number of binding sites, delta H0 and delta S0. The partition coefficients of the ligands were measured in octanol/water and heptane/water systems (log Poct. and log Phep.), and their molecular volumes were calculated by molecular modelling techniques. These structural properties allow determination of polarity parameters (delta log Poct.-hep., lambda oct. and lambda hep.) which encode in different proportions the various polar interactions between the solute and the aqueous and organic phases, i.e. hydrogen-bonding capacity and dipolarity/polarizability. This study shows that good correlations exist between delta H0 or delta S0 and polarity parameters, such that the enthalpic contribution to binding increases with increasing polarity of the ligands, mainly hydrogen-bond-donor acidity, whereas their entropic contribution to binding decreases. PMID:7887909

  2. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

    NASA Astrophysics Data System (ADS)

    Zhang, Liyun; Li, Yuzhi; Yuan, Yuan; Jiang, Yuanyuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

    2016-11-01

    In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.

  3. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

    PubMed Central

    Zhang, Liyun; Li, Yuzhi; Yuan, Yuan; Jiang, Yuanyuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

    2016-01-01

    In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification. PMID:27874101

  4. 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

  5. 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

  6. 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.

  7. Linearly and circularly polarized laser photoinduced molecular order in azo dye doped polymer films

    NASA Astrophysics Data System (ADS)

    Saad, Bendaoud

    2017-03-01

    Photo-induced behavior of Azo Disperse one (AZD1) doped Poly(Methyl MethAcrylate) (PMMA) using both linear and circular polarized light is studied. The anisotropy is not erased by the circular polarization light. The circular polarization light combined with relatively long lifetime of the cis state in azo dye doped polymers activate all transverse directions of the angular hole burning through the spot in the film inducing anisotropy. Under circular polarized light, there is no orientation perpendicularly to the helex described by the rotating electric field vector, trans molecules reorients in the propagation direction of the pump beam. The polarization state of the probe beam after propagation through the pumped spot depends strongly on the angle of incidence of both pump and probe beams on the input face. In the case where circular polarized pump and probe beams are under the same angle of incidence, the probe beam "sees" anisotropic film as if it is isotropic. Results of this work shows the possibility to reorient azobenzene-type molecules in two orthogonal directions using alternately linearly and circularly polarized beams.

  8. Concurrent atomistic-continuum simulation of polycrystalline strontium titanate

    NASA Astrophysics Data System (ADS)

    Yang, Shengfeng; Zhang, Ning; Chen, Youping

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  10. Shape-controlled growth of metal nanoparticles: an atomistic view.

    PubMed

    Konuk, Mine; Durukanoğlu, Sondan

    2016-01-21

    Recent developments in shape-controlled synthesis of metallic nano-particles present a promising path for precisely tuning chemical activity, selectivity, and stability of nano-materials. While previous studies have highlighted the macroscopic description of synthesis processes, there is less understanding as to whether individual atomic-scale processes possess any significant role in controlling the growth of nano-products. The presented molecular static and dynamic simulations are the first simulations to understand the underlying atomistic mechanisms of the experimentally determined growth modes of metal nano-clusters. Our simulations on Ag nano-cubes confirm that metal nano-seeds enclosed by {100} facets can be directed to grow into octopods, concave, truncated cubes, and cuboctahedra when the relative surface diffusion and deposition rates are finely tuned. Here we further showed that atomic level processes play a significant role in controllably fine tuning the two competing rates: surface diffusion and deposition. We also found that regardless of temperature and the initial shape of the nano-seeds, the exchange of the deposited atom with an edge atom of the seed is by far the governing diffusion mechanism between the neighboring facets, and thus is the leading atomistic process determining the conditions for fine tuning of macroscopic processes.

  11. Investigation of solvent polarity effect on molecular structure and vibrational spectrum of xanthine with the aid of quantum chemical computations.

    PubMed

    Polat, Turgay; Yıldırım, Gurcan

    2014-04-05

    The main scope of this study is to determine the effects of 8 solvents on the geometric structure and vibrational spectra of the title compound, xanthine, by means of the DFT/B3LYP level of theory in the combination with the polarizable conductor continuum model (CPCM) for the first time. After determination of the most-steady state (favored structure) of the xanthine molecule, the role of the solvent polarity on the SCF energy (for the molecule stability), atomic charges (for charge distribution) and dipole moments (for molecular charge transfer) belonging to tautomer is discussed in detail. The results obtained indicate not only the presence of the hydrogen bonding and strong intra-molecular charge transfer (ICT) in the compound but the increment of the molecule stability with the solvent polarity, as well. Moreover, it is noted that the optimized geometric parameters and the theoretical vibrational frequencies are in good agreement with the available experimental results found in the literature. In fact, the correlations between the experimental and theoretical findings for the molecular structures improve with the enhancement of the solvent polarity. At the same time, the dimer forms of the xanthine compound are simulated to describe the effect of intermolecular hydrogen bonding on the molecular geometry and vibrational frequencies. It is found that the CO and NH stretching vibrations shift regularly to lower frequency value with higher IR intensity as the dielectric medium enhances systematically due to the intermolecular NH⋯O hydrogen bonds. Theoretical vibrational spectra are also assigned based on the potential energy distribution (PED) using the VEDA 4 program.

  12. 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.

  13. Angle-dependent molecular above-threshold ionization with ultrashort intense linearly and circularly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-07-01

    We present molecular above-threshold ionization (MATI) spectra generated by ultrashort intense linearly and circularly polarized laser pulses from nonperturbative numerical solutions of the corresponding time-dependent Schrödinger equation in the molecular-ion H2+. It is found that high-order MATI spectra with maximum kinetic energy 32Up, where Up=I0/4meω02 is the ponderomotive energy at intensity I0 and frequency ω0, can be obtained in H2+ at great internuclear distances R for both linear and circular polarizations. Quasiclassical laser-induced collision models confirm that such high-order MATIs mainly result from a collision with neighboring ions of the ionized electron. Interference patterns in the high-order MATI spectra are critically sensitive to both the internuclear distance R of the molecules and the polarizations of the driving laser pulses. Moreover, with few-cycle laser pulses, the carrier-envelope phase sensitivity of MATI angular distributions is also investigated for varying internuclear distances R. At critical internuclear distances for charge-resonance-enhanced ionization, we also find that enhanced interference patterns occur.

  14. Angle-dependent molecular above-threshold ionization with ultrashort intense linearly and circularly polarized laser pulses

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-07-15

    We present molecular above-threshold ionization (MATI) spectra generated by ultrashort intense linearly and circularly polarized laser pulses from nonperturbative numerical solutions of the corresponding time-dependent Schroedinger equation in the molecular-ion H{sub 2}{sup +}. It is found that high-order MATI spectra with maximum kinetic energy 32U{sub p}, where U{sub p}=I{sub 0}/4m{sub e}{omega}{sub 0}{sup 2} is the ponderomotive energy at intensity I{sub 0} and frequency {omega}{sub 0}, can be obtained in H{sub 2}{sup +} at great internuclear distances R for both linear and circular polarizations. Quasiclassical laser-induced collision models confirm that such high-order MATIs mainly result from a collision with neighboring ions of the ionized electron. Interference patterns in the high-order MATI spectra are critically sensitive to both the internuclear distance R of the molecules and the polarizations of the driving laser pulses. Moreover, with few-cycle laser pulses, the carrier-envelope phase sensitivity of MATI angular distributions is also investigated for varying internuclear distances R. At critical internuclear distances for charge-resonance-enhanced ionization, we also find that enhanced interference patterns occur.

  15. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

    PubMed Central

    Duan, Li L.; Zhu, T.; Li, Yu C.; Zhang, Qing G.; Zhang, John Z. H.

    2017-01-01

    Molecular dynamics simulations in explicit water are carried out to study the binding of six inhibitors to HIV-1 protease (PR) for up to 700 ns using the standard AMBER force field and polarized protein-specific charge (PPC). PPC is derived from quantum mechanical calculation for protein in solution and therefore it includes electronic polarization effect. Our results show that in all six systems, the bridging water W301 drifts away from the binding pocket in AMBER simulation. However, it is very stable in all six complexes systems using PPC. Especially, intra-protease, protease-inhibitor hydrogen bonds are dynamic stabilized in MD simulation. The computed binding free energies of six complexes have a significantly linear correlation with those experiment values and the correlation coefficient is found to be 0.91 in PPC simulation. However, the result from AMBER simulation shows a weaker correlation with the correlation coefficient of −0.51 due to the lack of polarization effect. Detailed binding interactions of W301, inhibitors with PR are further analyzed and discussed. The present study provides important information to quantitative understanding the interaction mechanism of PR-inhibitor and PR-W301 and these data also emphasizes the importance of both the electronic polarization and the bridging water molecule in predicting precisely binding affinities. PMID:28155907

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

    SciTech Connect

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

    2014-10-16

    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. Here, 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.

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

    DOE PAGES

    Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

    2014-10-16

    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 completelymore » avoided at each configuration. Here, 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.« less

  18. The effect of natural organic matter polarity and molecular weight on NDMA formation from two antibiotics containing dimethylamine functional groups.

    PubMed

    Leavey-Roback, Shannon L; Krasner, Stuart W; Suffet, Irwin H Mel

    2016-12-01

    N-nitrosodimethylamine (NDMA) is a disinfection byproduct preferentially formed in chloraminated water. NDMA may be formed from certain chemicals containing dimethylamine (DMA) functional groups. This reaction may be slowed by the presence of natural organic matter (NOM). In this study, NOM fractionated by size or polarity was tested for its ability to slow or impede the formation of NDMA from two DMA-containing precursors, the antibiotics tetracycline and spiramycin. The high molecular weight NOM fractions (>10KDa) were shown to be the most effective in reducing the amount of NDMA formed from the precursor chemicals. The filtrate of a C-18 non-polar cartridge was also effective at reducing NDMA formation from tetracycline (spyramycin not tested). Therefore, polar and charged NOM components may be responsible for the reduction in NDMA formation. A possible mechanism for the reduction of NDMA formation from tetracycline is complexation due to the hydrogen bonding of the DMA functional group on tetracycline to polar phenolic functional groups in the NOM.

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

    NASA Astrophysics Data System (ADS)

    McCash, Kevin

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

  20. 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.

  1. 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".

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

    PubMed Central

    2013-01-01

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

  3. 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

  4. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

    DOE PAGES

    Huang, Jing; Mei, Ye; König, Gerhard; ...

    2017-01-24

    Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

  5. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    PubMed

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R(2) value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R(2) values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  6. Nuclear magnetic resonance and molecular modeling study of exocyclic carbon-carbon double bond polarization in benzylidene barbiturates

    NASA Astrophysics Data System (ADS)

    Figueroa-Villar, J. Daniel; Vieira, Andreia A.

    2013-02-01

    Benzylidene barbiturates are important materials for the synthesis of heterocyclic compounds with potential for the development of new drugs. The reactivity of benzylidene barbiturates is mainly controlled by their exocyclic carbon-carbon double bond. In this work, the exocyclic double bond polarization was estimated experimentally by NMR and correlated with the Hammett σ values of the aromatic ring substituents and the molecular modeling calculated atomic charge difference. It is demonstrated that carbon chemical shift differences and NBO charge differences can be used to predict their reactivity.

  7. Photoelectron angular distributions in molecular above threshold ionization by two colour circularly polarized ultrashort UV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2013-10-01

    Photoionization of an aligned molecular ion H? has been investigated with two colour circularly polarized ultrashort UV laser pulses by numerically solving the corresponding time dependent Schrödinger equation. Photoelectron angular distributions (PADs) in molecular above threshold ionization (MATI) exhibit: (i) asymmetry resulting from interference of coherent electron wave packets from multiple pathway ionization, which depends critically on the relative carrier envelope phase (CEP) ? between the two colour laser pulses and photoelectron kinetic energies; (ii) rotation with respect to the molecular symmetry axes due to effects of the nonspherical two center Coulomb potential. Such features are described by multi-photon perturbative theoretical ionization models. The ionization probability is functions of both the CEP ? and the angle ? between the electron emission and the molecular axis. The influence of pulse intensity and ellipticity on PADs in MATI is also investigated. It is found that the asymmetry depends on the pulse intensity whereas the rotation angle is shown to be sensitive to the pulse ellipticity, both reflecting the orientation dependence of molecular ionization probabilities.

  8. 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.

  9. Impacts of atomistic coating on thermal conductivity of germanium nanowires.

    PubMed

    Chen, Jie; Zhang, Gang; Li, Baowen

    2012-06-13

    By using nonequilibrium molecular dynamics simulations, we demonstrated that thermal conductivity of germanium nanowires can be reduced more than 25% at room temperature by atomistic coating. There is a critical coating thickness beyond which thermal conductivity of the coated nanowire is larger than that of the host nanowire. The diameter-dependent critical coating thickness and minimum thermal conductivity are explored. Moreover, we found that interface roughness can induce further reduction of thermal conductivity in coated nanowires. From the vibrational eigenmode analysis, it is found that coating induces localization for low-frequency phonons, while interface roughness localizes the high-frequency phonons. Our results provide an available approach to tune thermal conductivity of nanowires by atomic layer coating.

  10. Atomistic modeling of ion implantation technologies in silicon

    NASA Astrophysics Data System (ADS)

    Marqués, Luis A.; Santos, Iván; Pelaz, Lourdes; López, Pedro; Aboy, María

    2015-06-01

    Requirements for the manufacturing of electronic devices at the nanometric scale are becoming more and more demanding on each new technology node, driving the need for the fabrication of ultra-shallow junctions and finFET structures. Main implantation strategies, cluster and cold implants, are aimed to reduce the amount of end-of-range defects through substrate amorphization. During finFET doping the device body gets amorphized, and its regrowth is more problematic than in the case of conventional planar devices. Consequently, there is a renewed interest on the modeling of amorphization and recrystallization in the front-end processing of Si. We present multi-scale simulation schemes to model amorphization and recrystallization in Si from an atomistic perspective. Models are able to correctly predict damage formation, accumulation and regrowth, both in the ballistic and thermal-spike regimes, in very good agreement with conventional molecular dynamics techniques but at a much lower computational cost.

  11. 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.

  12. Seamless elastic boundaries for atomistic calculations

    NASA Astrophysics Data System (ADS)

    Pastewka, Lars; Sharp, Tristan A.; Robbins, Mark O.

    2012-08-01

    Modeling interfacial phenomena often requires both a detailed atomistic description of surface interactions and accurate calculations of long-range deformations in the substrate. The latter can be efficiently obtained using an elastic Green's function if substrate deformations are small. We present a general formulation for rapidly computing the Green's function for a planar surface given the interatomic interactions, and then coupling the Green's function to explicit atoms. The approach is fast, avoids ghost forces, and is not limited to nearest-neighbor interactions. The full system comprising explicit interfacial atoms and an elastic substrate is described by a single Hamiltonian and interactions in the substrate are treated exactly up to harmonic order. This concurrent multiscale coupling provides simple, seamless elastic boundary conditions for atomistic simulations where near-surface deformations occur, such as nanoindentation, contact, friction, or fracture. Applications to surface relaxation and contact are used to test and illustrate the approach.

  13. Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

    NASA Astrophysics Data System (ADS)

    Buerkle, Marius; Asai, Yoshihiro

    2017-02-01

    The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations.

  14. Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

    PubMed Central

    Buerkle, Marius; Asai, Yoshihiro

    2017-01-01

    The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations. PMID:28150738

  15. 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

  16. Solvatochromic shift of donor-acceptor substituted bithiophene in solvents of different polarity: quantum chemical and molecular dynamics simulations.

    PubMed

    Meng, Suci; Ma, Jing

    2008-04-10

    The dependence of excitation energies of the solvatochromic dye, 5-dimethylamino-5'-nitro-2,2'-bithiophene (Me(2)N-2T-NO(2)) on the solvent polarity is demonstrated by time-dependent density functional theory (TD-DFT) calculations in combination with molecular dynamics (MD) simulations. Three kinds of solvation models, namely, the continuum dielectric model, the discrete approach, and the combined discrete/continuum strategy, are employed to calculate the lowest dipole-allowed excitation energies of Me(2)N-2T-NO(2) in seven solvents with the dielectric constant, epsilon, ranging from 2.23 to 111.00. Our calculations demonstrate the limitations of the continuum dielectric model in predicting the solvatochromic shift of Me(2)N-2T-NO(2) in very polar solvents with epsilon > 35. The accuracy of the explicit solvent model is largely limited by the size of supermolecular cluster. The combined discrete/continuum solvent model gives a satisfactory description of the bathochromic shift of Me(2)N-2T-NO(2) with increasing solvent polarity, in agreement with the experimental observations.

  17. Coupling-of-length-scale approach for multiscale atomistic-continuum simulations: Atomistically-induced stress distributions in Si/Si_3N4 nanopixels

    NASA Astrophysics Data System (ADS)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George; Madhukar, Anupam

    2001-03-01

    A hybrid molecular-dynamics and finite-element simulation approach has been used to investigate stress distributions in Si(111) nanopixels covered with both crystalline and amorphous Si_3N4 thin films. Surfaces, lattice-mismatched interfaces, edges, and corners create stress fields on the order of 1 GPa inside the Si substrate with patterns that cannot be reproduced by a continuum approach alone. For these atomistically-induced inhomogeneouse stresses, the hybrid simulation approach provides an excellent agreement with the standard molecular dynamics, with considerably less computational costs.

  18. Charged dendrimers under the action of AC electric fields: Breathing characteristics of molecular size, polarizations, and ion distributions

    NASA Astrophysics Data System (ADS)

    Das, Ashok K.; Hsiao, Pai-Yi

    2015-02-01

    Langevin dynamics simulations are performed to study the response of charged dendrimers in alternating current electric fields in 3:1 salt solutions. Time evolutions of molecular size show breathing characteristics which take saw-tooth-like patterns in square-wave electric fields and undulated sine-function ones in sine-wave fields. Detailed study reveals how the dendrimer and condensed ions oscillate in the electric fields, which result in polarization of the molecule. To effect a significant deformation of the dendrimer, the applied field amplitude must be larger than some critical strength Ecrit and the field frequency smaller than a threshold fcrit. The response behavior is characterized by two relaxation times in square-wave fields, both of which decrease linearly with the strong field strength larger than Ecrit. In sine-wave fields, the molecular size exhibits interesting hysteretic behavior in plotting the curves with the field variation. A Maxwell-Wagner type polarization theory is derived and proved by simulations, which connects fcrit with the strength of the applied electric field.

  19. Effect of metallation, substituents and inter/intra-molecular polarization on electronic couplings for hole transport in stacked porphyrin dyads.

    PubMed

    Hernández-Fernández, F; Pavanello, M; Visscher, L

    2016-08-03

    We carried out a systematic study of the hole transport properties for a series of symmetrically stacked porphyrin dimers. In the first part of this study, we evaluated the sensitivity of electronic couplings to orbital relaxation due to molecular ionization and intermolecular interactions for a series of halogenated porphyrins. The effect of polarization was estimated by comparing electronic couplings from fragment orbital density functional theory (FODFT) and frozen density embedding electron transfer (FDE-CT). For the dimers considered, the effect of polarization was estimated to be less than 20%, in line with previous studies on different molecular dimers. Thus, we decided to employ a computationally cheaper FODFT method to continue our study of the effect of metals and substituents on the electronic couplings for hole transfer. We find that, compared to the non-metallated porphyrins, Ni, Fe and Pt significantly reduce the coupling, while Zn, Ti, Cd and Pd increase it. The effect of substituents was studied on a series of meso-substituted porphyrins (meso-tetrapyridineporphyrin, meso-tetraphenylporphyrin and derivatives) for which we could relate a reduction of the coupling to steric effects that reduce the overlap between the frontier orbitals of the monomers.

  20. 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.

  1. Spin-polarized Inelastic Electron Tunneling Spectroscopy of Molecular Magnetic Tunnel Junctions

    SciTech Connect

    Wang Wenyong; Richter, Curt A.

    2007-09-26

    In this study, we fabricate molecular magnetic tunnel junctions and demonstrate that inelastic electron tunneling spectroscopy technique can be utilized to inspect such junctions to investigate the existence of desired molecular species in the device area. Tunneling magnetoresistance measurements have been carried out and spin-dependent tunneling transport has been observed. Bias-dependence of the tunneling resistance has also been detected. IETS measurements at different magnetic field suggested that the TMR bias-dependence was likely caused by the inelastic scattering due to the molecular vibrations.

  2. First Principles Atomistic Model for Carbon-Doped Boron Suboxide

    DTIC Science & Technology

    2014-09-01

    First Principles Atomistic Model for Carbon-Doped Boron Suboxide by Amol B Rahane, Jennifer S Dunn, and Vijay Kumar ARL-TR-7106...2014 First Principles Atomistic Model for Carbon-Doped Boron Suboxide Amol B Rahane Dr Vijay Kumar Foundation 1969 Sector 4 Gurgaon...Final 3. DATES COVERED (From - To) October 2013–July 2014 4. TITLE AND SUBTITLE First Principles Atomistic Model for Carbon-Doped Boron Suboxide

  3. Edge energies : atomistic calculations of a continuum quantity.

    SciTech Connect

    Hamilton, John C.

    2005-06-01

    Controlling the properties of self-assembled nanostructures requires controlling their shape. Size-dependent shape transitions, frequently observed at nanolength scales, are commonly attributed to edge energy effects. To rigorously test such theories against experiment, quantitative atomistic calculations of edge energies are essential, yet none exist. I describe a fundamental ambiguity in the atomistic definition of edge energies, propose a definition based on equimolar dividing surfaces, and present an atomistic calculation of edge energies for Pd clusters.

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

    SciTech Connect

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

    2015-01-29

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

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

    DOE PAGES

    Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

    2015-01-29

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

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

    NASA Astrophysics Data System (ADS)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

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

  7. 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.

  8. 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.

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

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2010-09-01

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

  11. 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.

  12. The tunneling magnetoresistance and spin-polarized optoelectronic properties of graphyne-based molecular magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Yang, Zhi; Ouyang, Bin; Lan, Guoqing; Xu, Li-Chun; Liu, Ruiping; Liu, Xuguang

    2017-02-01

    Using density functional theory and the non-equilibrium Green’s function method, we investigate the spin-dependent transport and optoelectronic properties of the graphyne-based molecular magnetic tunnel junctions (MMTJs). We find that these MMTJs exhibit an outstanding tunneling magnetoresistance (TMR) effect. The TMR value is as high as 106%. When the magnetization directions of two electrodes are antiparallel under positive or negative bias voltages, two kinds of pure spin currents can be obtained in the systems. Furthermore, under the irradiation of infrared, visible or ultraviolet light, spin-polarized photocurrents can be generated in the MMTJs, but the corresponding microscopic mechanisms are different. More importantly, if the magnetization directions of two electrodes are antiparallel, the photocurrents with different spins are spatially separated, appearing at different electrodes. This phenomenon provides a new way to simultaneously generate two spin currents.

  13. 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.

  14. Polarization dependence of Raman scattering from a thin film involving optical anisotropy theorized for molecular orientation analysis.

    PubMed

    Itoh, Yuki; Hasegawa, Takeshi

    2012-06-14

    Polarized Raman scattering from a thin film involving uniaxial optical anisotropy deposited on a dielectric substrate has analytically been theorized. The analyte film is modeled as a three-phase system (air/film/substrate) to calculate the electromagnetic fields of the incident and scattered light propagating across the system with an aid of the transfer matrix method to exactly take the optical anisotropy of the film into account. On the new theory, a methodology for molecular orientation analysis of an extended polymethylene chain in the film is proposed, which is employed for determination of the tilt angles of the chains in single- and five-monolayer Langmuir-Blodgett (LB) films of cadmium stearate deposited on a glass plate. The results agree well with those obtained by infrared spectroscopy, which confirms reliability of the present method.

  15. Plasma-assisted Molecular Beam Epitaxy of N-polar InAlN-barrier High-electron-mobility Transistors.

    PubMed

    Hardy, Matthew T; Storm, David F; Katzer, D Scott; Downey, Brian P; Nepal, Neeraj; Meyer, David J

    2016-11-24

    Plasma-assisted molecular beam epitaxy is well suited for the epitaxial growth of III-nitride thin films and heterostructures with smooth, abrupt interfaces required for high-quality high-electron-mobility transistors (HEMTs). A procedure is presented for the growth of N-polar InAlN HEMTs, including wafer preparation and growth of buffer layers, the InAlN barrier layer, AlN and GaN interlayers and the GaN channel. Critical issues at each step of the process are identified, such as avoiding Ga accumulation in the GaN buffer, the role of temperature on InAlN compositional homogeneity, and the use of Ga flux during the AlN interlayer and the interrupt prior to GaN channel growth. Compositionally homogeneous N-polar InAlN thin films are demonstrated with surface root-mean-squared roughness as low as 0.19 nm and InAlN-based HEMT structures are reported having mobility as high as 1,750 cm(2)/V∙sec for devices with a sheet charge density of 1.7 x 10(13) cm(-2).

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

    PubMed

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

    2016-05-17

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

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

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

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

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

    SciTech Connect

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

    2014-08-21

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

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

    SciTech Connect

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

    2004-09-01

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

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

    DOE PAGES

    Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell; ...

    2014-08-21

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

  1. Atomistic simulations of nanoscale electrokinetic transport

    NASA Astrophysics Data System (ADS)

    Liu, Jin; Wang, Moran; Chen, Shiyi; Robbins, Mark

    2011-11-01

    An efficient and accurate algorithm for atomistic simulations of nanoscale electrokinetic transport will be described. The long-range interactions between charged molecules are treated using the Particle-Particle Particle-Mesh method and the Poisson equation for the electric potential is solved using an efficient multi-grid method in physical space. Using this method, we investigate two important applications in electrokinetic transport: electroosmotic flow in rough channels and electowetting on dielectric (EWOD). Simulations of electroosmotic and pressure driven flow in exactly the same geometries show that surface roughness has a much more pronounced effect on electroosmotic flow. Analysis of local quantities shows that this is because the driving force in electroosmotic flow is localized near the wall where the charge density is high. In atomistic simulations of EWOD, we find the contact angle follows the continuum theory at low voltages and always saturates at high voltages. Based on our results, a new mechanism for saturation is identified and possible techniques for controlling saturation are proposed. This work is supported by the National Science Foundation under Grant No. CMMI 0709187.

  2. Atomistic to continuum modeling of solidification microstructures

    SciTech Connect

    Karma, Alain; Tourret, Damien

    2015-09-26

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

  3. Atomistic to continuum modeling of solidification microstructures

    DOE PAGES

    Karma, Alain; Tourret, Damien

    2015-09-26

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

  4. Coupling length scales for multiscale atomistics-continuum simulations: atomistically induced stress distributions in Si/Si3N4 nanopixels.

    PubMed

    Lidorikis, E; Bachlechner, M E; Kalia, R K; Nakano, A; Vashishta, P; Voyiadjis, G Z

    2001-08-20

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  5. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si3N4 Nanopixels

    NASA Astrophysics Data System (ADS)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-01

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  6. Methods for atomistic abrasion simulations of laterally periodic polycrystalline substrates with fractal surfaces

    NASA Astrophysics Data System (ADS)

    Eder, S. J.; Bianchi, D.; Cihak-Bayr, U.; Gkagkas, K.

    2017-03-01

    In this work we discuss a method to generate laterally periodic polycrystalline samples with fractal surfaces for use in molecular dynamics simulations of abrasion. We also describe a workflow that allows us to produce random lateral distributions of simple but realistically shaped hard abrasive particles with Gaussian size distribution and random particle orientations. We evaluate some on-the-fly analysis and visualization possibilities that may be applied during a molecular dynamics simulation to considerably reduce the post-processing effort. Finally, we elaborate on a parallelizable post-processing approach to evaluating and visualizing the surface topography, the grain structure and orientation, as well as the temperature distribution in large atomistic systems.

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

    SciTech Connect

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

    2000-08-01

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

  8. Molecular motors are differentially distributed on Golgi membranes from polarized epithelial cells

    PubMed Central

    1994-01-01

    Microtubules (MT) are required for the efficient transport of membranes from the trans-Golgi and for transcytosis of vesicles from the basolateral membrane to the apical cytoplasm in polarized epithelia. MTs in these cells are primarily oriented with their plus ends basally near the Golgi and their minus-ends in the apical cytoplasm. Here we report that isolated Golgi and Golgi-enriched membranes from intestinal epithelial cells possess the actin based motor myosin-I, the MT minus- end-directed motor cytoplasmic dynein and its in vitro motility activator dynactin (p150/Glued). The Golgi can be separated into stacks, possessing features of the Golgi cisternae, and small membranes enriched in the trans-Golgi network marker TGN 38/41. Whereas myosin-I is present on all membranes in the Golgi fraction, dynein is present only on the small membrane fraction. Dynein, like myosin-I, is associated with membranes as a cytoplasmic peripheral membrane protein. Dynein and myosin-I coassociate with membranes that bind to MTs and cross-link actin filaments and MTs in a nucleotide-dependent manner. We propose that cytoplasmic dynein moves Golgi membranes along MTs to the cell cortex where myosin-I provides local delivery through the actin- rich cytoskeleton to the apical membrane. PMID:8045931

  9. Circularly polarized molecular high-order harmonic generation in H{sub 2}{sup +} with intense laser pulses and static fields

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-06-15

    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 Schroedinger equation (TDSE) for the H{sub 2}{sup +} 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 I{sub p} + 9.05U{sub p}, where I{sub p} is the ionization potential and U{sub p}=E{sub 0}{sup 2}/4m{sub e{omega}0}{sup 2} is the ponderomotive energy at amplitude E{sub 0} and frequency {omega}{sub 0} 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 H{sub 2}{sup +} 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.

  10. Molecular-Beam Epitaxial Growth and Device Potential of Polar/Nonpolar Semiconductor Heterostructures.

    DTIC Science & Technology

    2014-09-26

    SECURITY CLASSIFICATION OF THIS PAGE(Wlam Doa ntered) ?0. ABSTRACT "echniques for the molecular beam epitaxial growth of GaP and GaAs substrates were...of both GaAs and GaP was found to be the problem of avoiding antiphase domains (APDs) in the growing film, that is, of random domains containing...even better properties. Lattice-mismatched (4%) growth of GaAs on Si was achieved, using the clean Si surface technology and the (211) orientation

  11. Physically representative atomistic modeling of atomic-scale friction

    NASA Astrophysics Data System (ADS)

    Dong, Yalin

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

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

    PubMed Central

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

    2016-01-01

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

  13. Growth of high quality N-polar AlN(0001xAF) on Si(111) by plasma assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Dasgupta, Sansaptak; Wu, F.; Speck, J. S.; Mishra, U. K.

    2009-04-01

    High quality N-polar AlN epilayers were grown and characterized on Si(111) substrates by plasma assisted molecular beam epitaxy as a first step toward growth of N-polar nitrides on Si(111). Polarity inversion to N-face by an optimized predeposition of Al adatoms on the reconstructed 7×7 Si(111) surface was investigated. Al adatoms can saturate the dangling bonds of Si atoms, resulting in growth of AlN in (0001¯) direction on subsequent exposure to N2 plasma. N-polarity was confirmed by observing strong 3×3 and 6×6 reflection high-energy electron diffraction reconstructions, convergent beam electron diffraction imaging and KOH etching studies. The structural properties were investigated by x-ray diffraction measurements, cross section and plan-view TEM studies.

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

    SciTech Connect

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

    2010-10-11

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

  15. Molecular Origin and Self-Assembly of Fluorescent Carbon Nanodots in Polar Solvents.

    PubMed

    Sharma, Arjun; Gadly, Trilochan; Neogy, Suman; Ghosh, Sunil Kumar; Kumbhakar, Manoj

    2017-02-17

    Despite numerous efforts, there are several fundamental ambiguities regarding the photoluminescence of carbon dots (CDs). Spectral shift measurements display characteristic of both π-π* and n-π* transitions for the main absorption or excitation band at ∼350 nm, contrary to common assignment of exclusive n-π* transition. Additionally, the generally perceived core-state transition at ∼250 nm, involving sp(2)-networked carbogenic domains shielded from external environments, needs to be reassessed because it fails to explain the observed fluorescence quenching and spectral shift. These results have been explained based on the molecular origin of PL in CDs invoking the similarity between CD and citrazinic acid. Fluorescent derivatives of the latter are recognized to be produced during citric-acid-based CD synthesis. Concentration-dependent spectral splitting of the main excitation band in combination with the temperature-dependent PL results has been envisioned assuming self-assembly of CDs into various H-aggregates.

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

    PubMed Central

    Jakobs, Maximilian; Franze, Kristian; Zemel, Assaf

    2015-01-01

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

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

    PubMed

    Jakobs, Maximilian; Franze, Kristian; Zemel, Assaf

    2015-01-01

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

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

    PubMed

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

    2013-01-01

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

  19. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

    PubMed

    Yang, Shengfeng; Chen, Youping

    2015-03-08

    In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

  20. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    PubMed

    Lemmin, Thomas; Soto, Cinque S; Clinthorne, Graham; DeGrado, William F; Dal Peraro, Matteo

    2013-01-01

    The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM) domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.

  1. An atomistic model of slip formation

    NASA Technical Reports Server (NTRS)

    Halicioglu, T.; Cooper, D. M.

    1984-01-01

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

  2. Quantum Corrections to the 'Atomistic' MOSFET Simulations

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

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

    PubMed

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

    2015-03-01

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

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

    PubMed

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

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

  5. A Hybrid DSMC/Free-Molecular Model of the Enceldus South Polar Plume

    NASA Astrophysics Data System (ADS)

    Keat Yeoh, Seng; Chapman, T. A.; Goldstein, D. B.; Varghese, P. L.; Trafton, L. M.

    2012-10-01

    Cassini first detected a gas-particle plume over the south pole of Enceladus in 2005. Since then, the plume has been a very active area of research because unlocking its mystery may help answer many lingering questions and open doors to new possibilities, such as the existence of extra-terrestrial life. Here, we present a hybrid model of the Enceladus gas-particle plume. Our model places eight sources on the surface of Enceladus based on the locations and jet orientations determined by Spitale and Porco (2007). We simulate the expansion of water vapor into vacuum, in the presence of dust particles from each source. The expansion is divided into two regions: the dense, collisional region near the source is simulated using the direct simulation Monte Carlo method, and the rarefied, collisionless region farther out is simulated using a free-molecular model. We also incorporate the effects of a sublimation atmosphere, a sputtered atmosphere and the background E-ring. Our model results are matched with the Cassini in-situ data, especially the Ion and Neutral Mass Spectrometer (INMS) water density data collected during the E2, E3, E5 and E7 flybys and the Ultraviolet Imaging Spectrograph (UVIS) stellar occultation observation made in 2005. Furthermore, we explore the time-variability of the plume by adjusting the individual source strengths to obtain a best curve-fit to the water density data in each flyby. We also analyze the effects of grains on the gas through a parametric study. We attempt to constrain the source conditions and gain insight on the nature of the source via our detailed models.

  6. Scoring multipole electrostatics in condensed-phase atomistic simulations.

    PubMed

    Bereau, Tristan; Kramer, Christian; Monnard, Fabien W; Nogueira, Elisa S; Ward, Thomas R; Meuwly, Markus

    2013-05-09

    Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  8. Crystallized Silicon Nanostructures - Experimental Characterization and Atomistic Simulations

    SciTech Connect

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

    2014-07-01

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

  9. Atomistic modeling at experimental strain rates and timescales

    NASA Astrophysics Data System (ADS)

    Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.

    2016-12-01

    Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.

  10. Atomistic simulations of CO vibrations in ices relevant to astrochemistry.

    PubMed

    Plattner, Nuria; Meuwly, Markus

    2008-06-23

    The experimental absorption band of carbon monoxide (CO) in mixed ices has been extensively studied in the past. The astrophysical interest in this band is related to its characteristic shape, which appears to depend on the surrounding ice structure. Herein, molecular dynamics simulations are carried out to analyze the relationship between the structure of the ice and the infrared (IR) spectrum of embedded CO molecules at different concentrations. Instead of conventional force fields, anharmonic potentials are used for the bonded interactions. The electrostatic interactions are more accurately described by means of fluctuating atomic multipole moments (up to quadrupole). The experimentally observed splitting of the CO absorption band (gas phase: 2143 cm(-1)) into a blue- (2152 cm(-1)) and a red-shifted (2138 cm(-1)) signal is also found in the simulations. Complementary atomistic simulations allow us to relate the spectra with the structural features. The distinction between interstitial and substitutional CO molecules as the origin of this splitting is found to be qualitatively correct. However, at increasing CO concentrations, additional effects-such as mutual interactions between CO molecules-become important, and the simplistic picture needs to be revised.

  11. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

    Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...

    2017-02-16

    A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin2β + B·cos2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

  12. Atomistic calculations of dislocation core energy in aluminium

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.

    2017-02-01

    A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.

  13. Molecular dynamics-based selectivity for Fast-Field-Cycling relaxometry by Overhauser and solid effect dynamic nuclear polarization

    NASA Astrophysics Data System (ADS)

    Neudert, Oliver; Mattea, Carlos; Stapf, Siegfried

    2017-03-01

    In the last decade nuclear spin hyperpolarization methods, especially Dynamic Nuclear Polarization (DNP), have provided unprecedented possibilities for various NMR techniques by increasing the sensitivity by several orders of magnitude. Recently, in-situ DNP-enhanced Fast Field Cycling (FFC) relaxometry was shown to provide appreciable NMR signal enhancements in liquids and viscous systems. In this work, a measurement protocol for DNP-enhanced NMR studies is introduced which enables the selective detection of nuclear spin hyperpolarized by either Overhauser effect or solid effect DNP. Based on field-cycled DNP and relaxation studies it is shown that these methods allow for the independent measurement of polymer and solvent nuclear spins in a concentrated solution of high molecular weight polybutadiene in benzene doped with α,γ-bisdiphenylene-β-phenylallyl radical. Appreciable NMR signal enhancements of about 10-fold were obtained for both constituents. Moreover, qualitative information about the dynamics of the radical and solvent was obtained. Selective DNP-enhanced FFC relaxometry is applied for the measurement of the 1H nuclear magnetic relaxation dispersion of both constituents with improved precision. The introduced method is expected to greatly facilitate NMR studies of complex systems with multiple overlapping signal contributions that cannot be distinguished by standard methods.

  14. Molecular dynamics-based selectivity for Fast-Field-Cycling relaxometry by Overhauser and solid effect dynamic nuclear polarization.

    PubMed

    Neudert, Oliver; Mattea, Carlos; Stapf, Siegfried

    2017-03-01

    In the last decade nuclear spin hyperpolarization methods, especially Dynamic Nuclear Polarization (DNP), have provided unprecedented possibilities for various NMR techniques by increasing the sensitivity by several orders of magnitude. Recently, in-situ DNP-enhanced Fast Field Cycling (FFC) relaxometry was shown to provide appreciable NMR signal enhancements in liquids and viscous systems. In this work, a measurement protocol for DNP-enhanced NMR studies is introduced which enables the selective detection of nuclear spin hyperpolarized by either Overhauser effect or solid effect DNP. Based on field-cycled DNP and relaxation studies it is shown that these methods allow for the independent measurement of polymer and solvent nuclear spins in a concentrated solution of high molecular weight polybutadiene in benzene doped with α,γ-bisdiphenylene-β-phenylallyl radical. Appreciable NMR signal enhancements of about 10-fold were obtained for both constituents. Moreover, qualitative information about the dynamics of the radical and solvent was obtained. Selective DNP-enhanced FFC relaxometry is applied for the measurement of the (1)H nuclear magnetic relaxation dispersion of both constituents with improved precision. The introduced method is expected to greatly facilitate NMR studies of complex systems with multiple overlapping signal contributions that cannot be distinguished by standard methods.

  15. Molecular frame photoemission by a comb of elliptical high-order harmonics: a sensitive probe of both photodynamics and harmonic complete polarization state.

    PubMed

    Veyrinas, K; Gruson, V; Weber, S J; Barreau, L; Ruchon, T; Hergott, J-F; Houver, J-C; Lucchese, R R; Salières, P; Dowek, D

    2016-12-16

    Due to the intimate anisotropic interaction between an XUV light field and a molecule resulting in photoionization (PI), molecular frame photoelectron angular distributions (MFPADs) are most sensitive probes of both electronic/nuclear dynamics and the polarization state of the ionizing light field. Consequently, they encode the complex dipole matrix elements describing the dynamics of the PI transition, as well as the three normalized Stokes parameters s1, s2, s3 characterizing the complete polarization state of the light, operating as molecular polarimetry. The remarkable development of advanced light sources delivering attosecond XUV pulses opens the perspective to visualize the primary steps of photochemical dynamics in time-resolved studies, at the natural attosecond to few femtosecond time-scales of electron dynamics and fast nuclear motion. It is thus timely to investigate the feasibility of measurement of MFPADs when PI is induced e.g., by an attosecond pulse train (APT) corresponding to a comb of discrete high-order harmonics. In the work presented here, we report MFPAD studies based on coincident electron-ion 3D momentum imaging in the context of ultrafast molecular dynamics investigated at the PLFA facility (CEA-SLIC), with two perspectives: (i) using APTs generated in atoms/molecules as a source for MFPAD-resolved PI studies, and (ii) taking advantage of molecular polarimetry to perform a complete polarization analysis of the harmonic emission of molecules, a major challenge of high harmonic spectroscopy. Recent results illustrating both aspects are reported for APTs generated in unaligned SF6 molecules by an elliptically polarized infrared driving field. The observed fingerprints of the elliptically polarized harmonics include the first direct determination of the complete s1, s2, s3 Stokes vector, equivalent to (ψ, ε, P), the orientation and the signed ellipticity of the polarization ellipse, and the degree of polarization P. They are compared to so

  16. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids.

    PubMed

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-08-06

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space-time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.

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

    PubMed

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

    2015-04-08

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  20. Gd(iii) and Mn(ii) complexes for dynamic nuclear polarization: small molecular chelate polarizing agents and applications with site-directed spin labeling of proteins.

    PubMed

    Kaushik, Monu; Bahrenberg, Thorsten; Can, Thach V; Caporini, Marc A; Silvers, Robert; Heiliger, Jörg; Smith, Albert A; Schwalbe, Harald; Griffin, Robert G; Corzilius, Björn

    2016-10-21

    We investigate complexes of two paramagnetic metal ions Gd(3+) and Mn(2+) to serve as polarizing agents for solid-state dynamic nuclear polarization (DNP) of (1)H, (13)C, and (15)N at magnetic fields of 5, 9.4, and 14.1 T. Both ions are half-integer high-spin systems with a zero-field splitting and therefore exhibit a broadening of the mS = -1/2 ↔ +1/2 central transition which scales inversely with the external field strength. We investigate experimentally the influence of the chelator molecule, strong hyperfine coupling to the metal nucleus, and deuteration of the bulk matrix on DNP properties. At small Gd-DOTA concentrations the narrow central transition allows us to polarize nuclei with small gyromagnetic ratio such as (13)C and even (15)N via the solid effect. We demonstrate that enhancements observed are limited by the available microwave power and that large enhancement factors of >100 (for (1)H) and on the order of 1000 (for (13)C) can be achieved in the saturation limit even at 80 K. At larger Gd(iii) concentrations (≥10 mM) where dipolar couplings between two neighboring Gd(3+) complexes become substantial a transition towards cross effect as dominating DNP mechanism is observed. Furthermore, the slow spin-diffusion between (13)C and (15)N, respectively, allows for temporally resolved observation of enhanced polarization spreading from nuclei close to the paramagnetic ion towards nuclei further removed. Subsequently, we present preliminary DNP experiments on ubiquitin by site-directed spin-labeling with Gd(3+) chelator tags. The results hold promise towards applications of such paramagnetically labeled proteins for DNP applications in biophysical chemistry and/or structural biology.

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

    SciTech Connect

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

    2015-09-01

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

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

    SciTech Connect

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

    2015-07-21

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

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

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

    PubMed

    Ueda, Junichi; Miyamoto, Kensuke

    2003-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  6. Spontaneous Athermal Cross-Slip Nucleation at Screw Dislocation Intersections in FCC Metals and L1(2) Intermetallics Investigated via Atomistic Simulations

    DTIC Science & Technology

    2013-01-01

    results. 2. Simulation technique The atomistic simulations described here employed the three-dimensional (3-D) parallel molecular dynamics (MD) code...dislocation takes to spontaneously cross-slip at the mildly-repulsive 120o intersection, molecular dynamics constant NVT simulations at a low temperature of...of the screw dislocation at the intersection. Similar molecular dynamics simulations were Figure 2. (colour online) A dislocation line representation

  7. Atomistic modeling of thermodynamic equilibrium of plutonium

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  8. Atomistic simulation on indented defects in silicon.

    PubMed

    Trandinh, Long; Cheon, Seong Sik; Kang, Woojong

    2013-12-01

    Silicon is known as one of the widely used materials in electronic fields for its excellent semiconductive characteristics. However, these characteristics are vulnerable to internal defects, which randomly exist in any materials. In the present study, defects in single crystalline silicon thin film were investigated by atomistic simulation of nano-indentation at zero temperature. The Tersoff potential and the spherical indenter were applied to the model of silicon. The symmetric axis parameter method is novelly proposed to identify defects in the diamond cubic structure. Under the nanoindentation condition, the ring slip appears close to the indentation region on the free surface and propagates along with [110]/(111). The dislocation is initiated closely to the ring slip and emitted on the (111) plane by the dissociation into two partial dislocations. It was found that the symmetric axis parameter method successfully separated the perfect dislocations, the partial dislocations and the stacking fault from perfect structure, i.e., diamond cubic structure, even though it was not able to distinguish between glide set and shuffle set dislocations.

  9. Strain Functionals for Characterizing Atomistic Geometries

    NASA Astrophysics Data System (ADS)

    Kober, Edward; Rudin, Sven

    The development of a set of strain tensor functionals that are capable of characterizing arbitrarily ordered atomistic structures is described. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the moments of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. Other methods used to characterize atomic structures, such as the Steinhardt parameters or the centrosymmetry metric, can be derived from this more general approach. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. They allow material phases, deformations, and a large number of defect structures to be readily identified and classified. Applications to the analysis of shock-loaded samples of Cu, Ta and Ti will be presented. This strain functional basis can also then be used for developing interatomic potential functions, and an initial application to Cu will be presented.

  10. Free energy of steps using atomistic simulations

    NASA Astrophysics Data System (ADS)

    Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

    The properties of solid-liquid interfaces are known to play critical roles in solidification processes. Particularly special importance is given to thermodynamic quantities that describe the equilibrium state of these surfaces. For example, on the solid-liquid-vapor heteroepitaxial growth of semiconductor nanowires the crystal nucleation process on the faceted solid-liquid interface is influenced by the solid-liquid and vapor-solid interfacial free energies, and also by the free energies of associated steps at these faceted interfaces. Crystal-growth theories and mesoscale simulation methods depend on quantitative information about these properties, which are often poorly characterized from experimental measurements. In this work we propose an extension of the capillary fluctuation method for calculation of the free energy of steps on faceted crystal surfaces. From equilibrium atomistic simulations of steps on (111) surfaces of Copper we computed accurately the step free energy for different step orientations. We show that the step free energy remains finite at all temperature up to the melting point and that the results obtained agree with the more well established method of thermodynamic integration if finite size effects are taken into account. The research of RF and MA at UC Berkeley were supported by the US National Science Foundation (Grant No. DMR-1105409). TF acknowledges support through a postdoctoral fellowship from the Miller Institute for Basic Research in Science.

  11. Stress in titania nanoparticles: An atomistic study

    SciTech Connect

    Darkins, Robert; Sushko, Maria L.; Liu, Jun; Duffy, Dorothy M.

    2014-04-24

    Stress engineering is becoming an increasingly important method for controlling electronic, optical, and magnetic properties of nanostructures, although the concept of stress is poorly defined at the nanoscale. We outline a methodology for computing bulk and surface stress in nanoparticles using atomistic simulation. The method is applicable to ionic and non- ionic materials alike and may be extended to other nanostructures. We apply it to spherical anatase nanoparticles ranging from 2 to 6 nm in diameter and obtain a surface stress of 0.89 N/m, in agreement with experimental measurements. Based on the extent that stress inhomogeneities at the surface are transmitted into the bulk, two characteristic length-scales are identified: below 3 nm bulk and surface regions cannot be defined and the available analytic theories for stress are not applicable, and above about 5 nm the stress becomes well-described by the theoretical Young-Laplace equation. The effect of a net surface charge on the bulk stress is also investigated. It is found that moderate surface charges can induce significant bulk stresses, on the order of 100 MPa, in nanoparticles within this size range.

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

    NASA Astrophysics Data System (ADS)

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

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

  13. Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

    PubMed

    Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

    2016-12-13

    Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

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

    NASA Astrophysics Data System (ADS)

    Norman, Paul Erik

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

  15. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

    2009-01-01

    Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

  16. An atomistic model for cross-linked HNBR elastomers used in seals

    NASA Astrophysics Data System (ADS)

    Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

    2015-03-01

    Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

  17. Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

    NASA Astrophysics Data System (ADS)

    Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

    2011-08-01

    Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

  18. Mapping Strain-rate Dependent Dislocation-Defect Interactions by Atomistic Simulations

    SciTech Connect

    Fan, Yue; Osetskiy, Yury N; Yip, Sidney; Yildiz-Botterud, Bilge

    2013-01-01

    Probing the mechanisms of defect-defect interactions at strain rates lower than 106 s-1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose a novel atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation-defect interactions at virtually any strain rate, exemplified within 10-7 to 107 s-1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIA) under shear deformation. Using an activation-relaxation algorithm (1), we uncover a unique strain-rate dependent trigger mechanism that allows the SIA cluster to be absorbed during the process leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain-rate and temperature. Our predictions of a crossover from a defect recovery at the low strain rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s-1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed.

  19. Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

    PubMed Central

    Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

    2013-01-01

    Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

  20. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    NASA Technical Reports Server (NTRS)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  1. Atomistic Simulation of Sea Spray Particles

    NASA Astrophysics Data System (ADS)

    Gokturk, H.

    2012-12-01

    Particles generated by ocean wave spray play an important role in many atmospheric processes such as cloud condensation, cycling of elements like chlorine, and scattering of sunlight reaching the ocean surface [1-2]. Indeed, artificially spraying droplets of seawater to the atmosphere by marine vessels roaming the ocean has been suggested as a geoengineering method to combat global warming [3]. One of the interesting aspects of ocean spray particles is that they include dissolved salt ions. Typically a liter of seawater contains about 3.5 g of salt which is mostly sodium chloride. Hydrated salt ions of the particle create a molecular structure which is different from that of pure water. An objective of this research is to investigate the influence of the dissolved ions on the properties of the particles by using first principle quantum mechanical calculations. Another objective is to probe the interaction of carbon dioxide (CO2) with such particles to understand whether the ions might enhance the absorption of atmospheric CO2 into the particles. Atomic models used in the calculations consist of a salt ion, for example sodium (Na+) ion surrounded by water molecules. Calculations are performed by using the DFT method with B3LYP hybrid functional and Pople type basis sets augmented with polarization and diffuse functions. Results of the calculations indicate that average binding energy of water molecules nearest to the ion is 0.7 eV per molecule for Na+ and 0.5 eV per molecule for Cl-. Water molecules are bound to the ion with significantly greater energy than that of the hydrogen bond (~0.2 eV) which is the binding mechanism of pure water. Higher binding energy of the particles explains why they serve well as condensation nuclei. As expected, binding energy decreases with increasing distance from the ion. It becomes comparable to that of the hydrogen bond at a distance of about 2 nm which corresponds to approximately 7 layers of water molecules surrounding the ion

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  4. Comparison of the applicability of mass spectrometer ion sources using a polarity- molecular weight scattergram with a 600 sample in-house chemical library.

    PubMed

    Sugimura, Natsuhiko; Furuya, Asami; Yatsu, Takahiro; Shibue, Toshimichi

    2015-01-01

    To provide a practical guideline for the selection of a mass spectrometer ion source, we compared the applicability of three types of ion source: direct analysis in real time (DART), electrospray ionization (ESI) and fast atom bombardment (FAB), using an in-house high-resolution mass spectrometry sample library consisting of approximately 600 compounds. The great majority of the compounds (92%), whose molecular weights (MWs) were broadly distributed between 150 and 1000, were detected using all the ion sources. Nevertheless, some compounds were not detected using specific ion sources. The use of FAB resulted in the highest sample detection rate (>98%), whereas the detection rates obtained using DART and ESI were slightly lower (>96%). A scattergram constructed using MW and topological polar surface area (tPSA) as a substitute for molecular polarity showed that the performance of ESI was weak in the low-MW (<400), low-polarity (tPSA<60) area, whereas the performance of DART was weak in the high-MW (>800) area. These results might provide guidelines for the selection of ion sources for inexperienced mass spectrometry users.

  5. A general library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models

    PubMed Central

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

    2009-01-01

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

  6. Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: a sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation.

    PubMed

    Ma, Haibo; Ma, Yingjin

    2012-12-07

    Polar and non-polar solutes (acetone and benzene) dissolved in ambient water and supercritical water are investigated theoretically using a sequential quantum mechanics (QM)/molecular mechanics (MM) method which combines classical molecular dynamics simulations and QM/MM calculations. From the detailed analysis of the dependence of the QM region size and point charge background region size as well as the different functionals, it is found that the inclusion of the solvent molecules within the first solvation shell into the QM region to account for the exchange-correlation between a solute and neighboring solvent molecules is important for the highly accurate spectral shift calculations, especially vital for the non-polar solutes whose interactions with the solvents are dominated by the quantum dispersions. At the same time, sufficiently large surrounding partial charge region (r(cutoff) ≥15 Å) as well as the functional corrections to describe the long-range dispersion-corrections are also essential for the study of the electronic excited states in condensed phase. Our calculated solvatochromic shift values and their density dependencies at ambient and high temperature conditions are found to be in good agreements with experimental observations. This indicates that sound theoretical studies of solvatochromic shift can be achieved provided that a reasonable computational scheme with sufficiently large N(water) (QM) and r(cutoff) values is implemented. We also find both of aqueous acetone and aqueous benzene under high temperatures present three distinctive regions: low-density gas-like region, supercritical region, and high-density liquid-like region. The plateau behavior of solvatochromic shift in the supercritical region can be ascribed to the solvent clustering around the solute, which is a fundamental phenomenon of supercritical fluids (SCFs). The density dependence of our calculated coordination number of the first solvation shell nicely reproduces the trend

  7. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids

    PubMed Central

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-01-01

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246

  8. Atomistic simulation of defects formation and structure transitions in U-Mo alloys at swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Kolotova, L. N.; Starikov, S. V.

    2017-01-01

    At irradiation of swift heavy ions, the track formation frequently takes place in nuclear materials. There is a large interest to understanding of the mechanisms of defects/track formation at this phenomenon. In this work, the atomistic simulation of defects formation and melting in U-Mo alloys at irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes at irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation at irradiation in the various conditions are calculated.

  9. Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.

    PubMed

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state (2)H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C-(2)H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of (13)C-(1)H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For (2)H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes.

  10. Cholesterol-Induced Suppression of Membrane Elastic Fluctuations at the Atomistic Level

    PubMed Central

    Molugu, Trivikram R.

    2017-01-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state 2H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C–2H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of 13C–1H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For 2H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes. PMID:27154600

  11. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

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

  12. Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids

    NASA Astrophysics Data System (ADS)

    Ranganathan, Raghavan

    Viscoelasticity, a ubiquitous material property, can be tuned to engineer a wide range of fascinating applications such as mechanical dampers, artificial tissues, functional foams and optoelectronics, among others. Traditionally, soft matter such as polymers and polymer composites have been used extensively for viscoelastic damping applications, owing to the inherent viscous nature of interactions between polymer chains. Although this leads to good damping characteristics, the stiffness in these materials is low, which in turn leads to limitations. In this context, hard inorganic materials and composites are promising candidates for enhanced damping, owing to their large stiffness and, in some cases large loss modulus. Viscoelasticity in these materials has been relatively unexplored and atomistic mechanisms responsible for damping are not apparent. Therefore, the overarching goal of this work is to understand mechanisms for viscoelastic damping in various classes of inorganic composites and alloys at an atomistic level from molecular dynamics simulations. We show that oscillatory shear deformation serves as a powerful probe to explain mechanisms for exceptional damping in hitherto unexplored systems. The first class of inorganic materials consists of crystalline phases of a stiff inclusion in a soft matrix. The two crystals within the composite, namely the soft and a stiff phase, individually show a highly elastic behavior and a very small loss modulus. On the other hand, a composite with the two phases is seen to exhibit damping that is about 20 times larger than predicted theoretical bounds. The primary reason for the damping is due to large anharmonicity in phonon-phonon coupling, resulting from the composite microstructure. A concomitant effect is the distribution of shear strain, which is observed to be highly inhomogeneous and mostly concentrated in the soft phase. Interestingly, the shear frequency at which the damping is greatest is observed to scale with

  13. Selective solid-phase extraction using molecularly imprinted polymer for the analysis of polar organophosphorus pesticides in water and soil samples.

    PubMed

    Zhu, Xiaolan; Yang, Jun; Su, Qingde; Cai, Jibao; Gao, Yun

    2005-10-28

    An analytical methodology for the analysis of four polar organophophorus pesticides (monocrotophos, mevinphos, phosphamidon, omethoate) in water and soil samples incorporating a molecularly imprinted solid-phase extraction (MISPE) process using a monocrotophos-imprinted polymer was developed. Binding study demonstrated that the polymer showed excellent affinity and high selectivity to monocrotophos. The MISPE procedure including the clean-up step to remove any interferences was optimized. The accuracy and selectivity of the MISPE process developed were verified using a non-imprinted (blank) polymer and a classical ENVI-18 cartridge as the SPE matrix during control experiments. The use of MISPE improved the accuracy and precision of the GC method and lowered the limit of detection. The recoveries of four polar organophosphorus pesticides (OPPs) extracted from 1 L of river water at a 100 ng/L spike level were in the range of 77.5-99.1%. The recoveries of organophosphorus pesticides extracted from a 5-g soil sample at the 100 microg/kg level were in the range of 79.3-93.5%. The limit of detection varied from 10 to 32 ng/L in water and from 12 to 34 microg/kg in soil samples. The molecularly imprinted polymer (MIP) enabled the selective extraction of four organophosphorus pesticides successfully from water and soil samples, demonstrating the potential of molecularly imprinted solid-phase extraction for rapid, selective, and cost-effective sample pretreatment.

  14. On the polarity of GaN micro- and nanowires epitaxially grown on sapphire (0001) and Si(111) substrates by metal organic vapor phase epitaxy and ammonia-molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Alloing, B.; Vézian, S.; Tottereau, O.; Vennéguès, P.; Beraudo, E.; Zuniga-Pérez, J.

    2011-01-01

    The polarity of GaN micro- and nanowires grown epitaxially by metal organic vapor phase epitaxy on sapphire substrates and by molecular-beam epitaxy, using ammonia as a nitrogen source, on sapphire and silicon substrates has been investigated. On Al2O3(0001), whatever the growth technique employed, the GaN wires show a mixture of Ga and N polarities. On Si(111), the wires grown by ammonia-molecular beam epitaxy are almost entirely Ga-polar (around 90%) and do not show inversion domains. These results can be understood in terms of the growth conditions employed during the nucleation stage.

  15. On the polarity of GaN micro- and nanowires epitaxially grown on sapphire (0001) and Si(111) substrates by metal organic vapor phase epitaxy and ammonia-molecular beam epitaxy

    SciTech Connect

    Alloing, B.; Vezian, S.; Tottereau, O.; Vennegues, P.; Beraudo, E.; Zuniga-Perez, J.

    2011-01-03

    The polarity of GaN micro- and nanowires grown epitaxially by metal organic vapor phase epitaxy on sapphire substrates and by molecular-beam epitaxy, using ammonia as a nitrogen source, on sapphire and silicon substrates has been investigated. On Al{sub 2}O{sub 3}(0001), whatever the growth technique employed, the GaN wires show a mixture of Ga and N polarities. On Si(111), the wires grown by ammonia-molecular beam epitaxy are almost entirely Ga-polar (around 90%) and do not show inversion domains. These results can be understood in terms of the growth conditions employed during the nucleation stage.

  16. Graviresponse and its regulation from the aspect of molecular levels in higher plants: growth and development, and auxin polar transport in etiolated pea seedlings under microgravity.

    PubMed

    Miyamoto, Kensuke; Hoshino, Tomoki; Hitotsubashi, Reiko; Tanimoto, Eiichi; Ueda, Junichi

    2003-10-01

    In STS-95 space experiments we have demonstrated that microgravity conditions resulted in automorphosis in etiolated pea (Pisum sativum L. cv. Alaska) seedlings (Ueda et al. 1999). Automorphosis-like growth and development in etiolated pea seedlings were also induced under simulated microgravity conditions on a 3-dimensional (3-D) clinostat, epicotyls being the most oriented toward the direction far from the cotyledons. Detail analysis of epicotyl bending revealed that within 36 h after watering, no significant difference in growth direction of epicotyls was observed in between seedlings grown on the 3-D clinostat and under 1 g conditions, differential growth near the cotyledonary node resulting in epicotyl bending of ca. 45 degrees toward the direction far from the cotyledons. Thereafter epicotyls continued to grow almost straightly keeping this orientation on the 3-D clinostat. On the other hand, the growth direction in etiolated seedlings changed to antigravity direction by negative gravitropic response under 1 g conditions. Automorphological epicotyl bending was also phenocopied by the application of auxin polar transport inhibitors such as 9-hydroxyfluorene-9-carboxylic acid, N-(1-naphtyl)phthalamic acid and 2,3,5-triiodobenzoic acid. These results together with the fact that auxin polar transport activity in etiolated pea epicotyls was substantially reduced in space suggested that reduced auxin polar transport is closely related to automorphosis. Strenuous efforts to learn how gravity contributes to the auxin polar transport in etiolated pea epicotyls in molecular bases resulted in successful identification of PsPIN2 and PsAUX1 encoding putative auxin-efflux and influx carrier proteins, respectively. Based on the results of these gene expression under simulated microgravity conditions, a possible role of PsPIN2 and PsAUX1 genes for auxin polar transport in etiolated pea seedlings will be discussed.

  17. Rate dependence of grain boundary sliding via time-scaling atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hammami, Farah; Kulkarni, Yashashree

    2017-02-01

    Approaching experimentally relevant strain rates has been a long-standing challenge for molecular dynamics method which captures phenomena typically on the scale of nanoseconds or at strain rates of 107 s-1 and higher. Here, we use grain boundary sliding in nanostructures as a paradigmatic problem to investigate rate dependence using atomistic simulations. We employ a combination of time-scaling computational approaches, including the autonomous basin climbing method, the nudged elastic band method, and kinetic Monte Carlo, to access strain rates ranging from 0.5 s-1 to 107 s-1. Combined with a standard linear solid model for viscoelastic behavior, our simulations reveal that grain boundary sliding exhibits noticeable rate dependence only below strain rates on the order of 10 s-1 but is rate independent and consistent with molecular dynamics at higher strain rates.

  18. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    DOE PAGES

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

    2017-01-26

    When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

  19. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    NASA Astrophysics Data System (ADS)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  20. Coupling LAMMPS and the vl3 Framework for Co-Visualization of Atomistic Simulations

    SciTech Connect

    Rizzi, Silvio; Hereld, Mark; Insley, Joseph; Malakar, Preeti; Papka, Michael E.; Uram, Thomas; Vishwanath, Venkatram

    2016-01-01

    In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future research avenues based on our results.

  1. Biophysical and biochemical aspects of antifreeze proteins: Using computational tools to extract atomistic information.

    PubMed

    Kar, Rajiv K; Bhunia, Anirban

    2015-11-01

    Antifreeze proteins (AFPs) are the key biomolecules that protect species from extreme climatic conditions. Studies of AFPs, which are based on recognition of ice plane and structural motifs, have provided vital information that point towards the mechanism responsible for executing antifreeze activity. Importantly, the use of experimental techniques has revealed key information for AFPs, but the exact microscopic details are still not well understood, which limits the application and design of novel antifreeze agents. The present review focuses on the importance of computational tools for investigating (i) molecular properties, (ii) structure-function relationships, and (iii) AFP-ice interactions at atomistic levels. In this context, important details pertaining to the methodological approaches used in molecular dynamics studies of AFPs are also discussed. It is hoped that the information presented herein is helpful for enriching our knowledge of antifreeze properties, which can potentially pave the way for the successful design of novel antifreeze biomolecular agents.

  2. Atomistic simulation of tensile deformation behavior of ∑5 tilt grain boundaries in copper bicrystal.

    PubMed

    Zhang, Liang; Lu, Cheng; Tieu, Kiet

    2014-08-01

    Experiments on polycrystalline metallic samples have indicated that Grain boundary (GB) structure can affect many material properties related to fracture and plasticity. In this study, atomistic simulations are employed to investigate the structures and mechanical behavior of both symmetric and asymmetric ∑5[0 0 1] tilt GBs of copper bicrystal. First, the equilibrium GB structures are generated by molecular statics simulation at 0K. The results show that the ∑5 asymmetric GBs with different inclination angles (φ) are composed of only two structural units corresponding to the two ∑5 symmetric GBs. Molecular dynamics simulations are then conducted to investigate the mechanical response and the underlying deformation mechanisms of bicrystal models with different ∑5 GBs under tension. Tensile deformation is applied under both 'free' and 'constrained' boundary conditions. Simulation results revealed different mechanical properties of the symmetric and asymmetric GBs and indicated that stress state can play an important role in the deformation mechanisms of nanocrystalline materials.

  3. Molecular Arrangement in Self-Assembled Azobenzene-Containing Thiol Monolayers at the Individual Domain Level Studied through Polarized Near-Field Raman Spectroscopy

    PubMed Central

    Chaigneau, Marc; Picardi, Gennaro; Ossikovski, Razvigor

    2011-01-01

    6-[4-(phenylazo)phenoxy]hexane-1-thiol self-assembled monolayers deposited on a gold surface form domain-like structures possessing a high degree of order with virtually all the molecules being identically oriented with respect to the surface plane. We show that, by using polarized near-field Raman spectroscopy, it is possible to derive the Raman scattering tensor of the ordered layer and consequently, the in-plane molecular orientation at the individual domain level. More generally, this study extends the application domain of the near-field Raman scattering selection rules from crystals to ordered organic structures. PMID:21541056

  4. Three Dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Wijesinghe, Sanith; Hornung, Richard; Garcia, Alejandro; Hadjiconstantinou, Nicolas

    2002-11-01

    An adaptive mesh and algorithmic refinement (AMAR) scheme to model multi-scale, compressible continuum-atomistic hydrodynamics is presented. The AMAR technique applies the atomistic description as the finest level of refinement in regions where the continuum description is expected to fail, such as in regions of high flow gradients and discontinous material interfaces. In the current implementation the atomistic description is provided by the direct simulation Monte Carlo (DSMC). The continuum flow is modeled using the compressible flow Euler equations and is solved using a second order Godunov scheme. Coupling is achieved by conservation of fluxes across the continuum-atomistic grid boundaries. The AMAR data structures are supported by a C++ object oriented framework (Structured Adaptive Mesh Refinement Application Infrastructure - SAMRAI) which allows for efficient parallel implementation. Current work is focused on extending AMAR to simulations of gas mixtures. This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract number W-7405-Eng-48.

  5. Bridging the macroscopic and atomistic descriptions of the electrocaloric effect.

    PubMed

    Ponomareva, I; Lisenkov, S

    2012-04-20

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba(0.5)Sr(0.5)TiO(3) alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency.

  6. Structure, function and molecular adaptations of haemoglobins of the polar cartilaginous fish Bathyraja eatonii and Raja hyperborea.

    PubMed

    Verde, Cinzia; De Rosa, M Cristina; Giordano, Daniela; Mosca, Donato; De Pascale, Donatella; Raiola, Luca; Cocca, Ennio; Carratore, Vitale; Giardina, Bruno; Di Prisco, Guido

    2005-07-15

    Cartilaginous fish are very ancient organisms. In the Antarctic sea, the modern chondrichthyan genera are poorly represented, with only three species of sharks and eight species of skates; the paucity of chondrichthyans is probably an ecological consequence of unusual trophic or habitat conditions in the Southern Ocean. In the Arctic, there are 26 species belonging to the class Chondrichthyes. Fish in the two polar regions have been subjected to different regional histories that have influenced the development of diversity: Antarctic marine organisms are highly stenothermal, in response to stable water temperatures, whereas the Arctic communities are exposed to seasonal temperature variations. The structure and function of the oxygen-transport haem protein from the Antarctic skate Bathyraja eatonii and from the Arctic skate Raja hyperborea (both of the subclass Elasmobranchii, order Rajiformes, family Rajidae) is reported in the present paper. These species have a single major haemoglobin (Hb 1; over 80% of the total). The Bohr-proton and the organophosphate-binding sites are absent. Thus the haemoglobins of northern and southern polar skates appear functionally similar, whereas differences were observed with several temperate elasmobranchs. Such evidence suggests that, in temperate and polar habitats, physiological adaptations have evolved along distinct pathways, whereas, in this case, the effect of the differences characterizing the two polar environments is negligible.

  7. Visualizing the Positive-Negative Interface of Molecular Electrostatic Potentials as an Educational Tool for Assigning Chemical Polarity

    ERIC Educational Resources Information Center

    Schonborn, Konrad; Host, Gunnar; Palmerius, Karljohan

    2010-01-01

    To help in interpreting the polarity of a molecule, charge separation can be visualized by mapping the electrostatic potential at the van der Waals surface using a color gradient or by indicating positive and negative regions of the electrostatic potential using different colored isosurfaces. Although these visualizations capture the molecular…

  8. Atomistic Mechanism of Plastic Deformation During Nano-indentation of Titanium Aluminide

    NASA Astrophysics Data System (ADS)

    Rino, Jose; Dasilva, Claudio

    2013-06-01

    The mechanisms governing defect nucleation in solids are of great interest in all material science branches. Atomistic computer simulations such as Molecular Dynamics (MD), has been providing more understanding of subsurface deformations, bringing out details of atomic structures and dynamics of defects within the material. In the present work we show the first simulation measurements within an atomistic resolution of the mechanical properties of titanium aluminide intermetallic compound (TiAl), which is a promising candidate for high temperature applications with remarkable properties, such as: attractive combination of low density, high melting temperature, high elastic modulus, and strength retention at elevated temperatures, besides its good creep properties. Through calculations of local pressure, local shear stress and spatial rearrangements of atoms beneath the indenter, it was possible to quantify the indentation damage on the structure. We have founded that prismatic dislocations mediate the emission and interaction of dislocations and the activated slip planes are associated with the Thompson tetrahedron. Furthermore, using the load-penetration depth response, we were able to estimate the elastic modulus and the hardness of the TiAl alloy. All our findings are in well agreement with experimental results.

  9. A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra.

    PubMed

    Alves, Cassio; Iacovelli, Federico; Falconi, Mattia; Cardamone, Francesca; Morozzo Della Rocca, Blasco; de Oliveira, Cristiano L P; Desideri, Alessandro

    2016-05-23

    A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.

  10. Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2013-10-01

    In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

  11. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    PubMed

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

  12. Molecular photoelectron angular distribution rotations in multi-photon resonant ionization of H{sub 2}{sup +} by circularly polarized ultraviolet laser pulses

    SciTech Connect

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

    2015-04-14

    We study effects of pulse durations on molecular photoelectron angular distributions (MPADs) in ultrafast circular polarization ultraviolet resonant ionization processes. Simulations performed on aligned H{sub 2}{sup +} by numerically solving time dependent Schrödinger equations show rotations of MPADs with respect to the molecular symmetry axes. It is found that in multi-photon resonant ionization processes, rotation angles are sensitive to pulse durations, which we attribute to the coherent resonant excitation between the ground state and the intermediate excited electronic state induced by Rabi oscillations. Multi-photon nonresonant and single photon ionization processes are simulated and compared which exhibit a constant rotation angle. An asymmetry parameter is introduced to describe the pulse duration sensitivity by perturbation theory models. Influence of pulse frequency detunings on MPADs is also investigated where oscillations of rotations are absent at long pulse durations due to nonresonance excitation.

  13. Free energy functionals for polarization fluctuations: Pekar factor revisited

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-02-01

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  14. Free energy functionals for polarization fluctuations: Pekar factor revisited.

    PubMed

    Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

    2017-02-14

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  15. Free energy functionals for polarization fluctuations: Pekar factor revisited

    DOE PAGES

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-02-13

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. This separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom, within dielectric continuum models. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. We study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. But, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

  16. NMR and DFT study on media effects on proton transfer in hydrogen bonding: concept of molecular probe with an application to ionic and super-polar liquids.

    PubMed

    Balevicius, Vytautas; Gdaniec, Zofia; Aidas, Kestutis

    2009-10-14

    Media effects of ionic and super-polar liquids on the state of H-bonding were studied by NMR and DFT methods. The proton sharing (positioning) in the H-bond was monitored following the chemical shifts of picolinic acid N-oxide (PANO) used as the molecular probe. The relationships between PANO 1H and 13C chemical shifts and proton position in the O-H...O bridge were calibrated using traditional organic solvents and other H-bond complexes of pyridine N-oxide with acids to increase the H-bond strength. A reliable parameter for H-bond monitoring was proposed. The state of the H-bond in ionic liquid media is largely governed by the dielectric properties of the bulk media. A drastic fall-out of PANO/[BuMePyr][TfO] from the general dielectric scheme built using solvents with increasing dielectric constant (from chloroform to water and culminating with formamide) was observed. On a molecular level this effect indicates that the ionic liquid [BuMePyr][TfO] can act on H-bonded systems as a stimulant of proton transfer. In 'super-polar' media (formamide) the intramolecular H-bond system converts into an intermolecular one forming a neutral H-bond complex of PANO with the formamide molecule.

  17. Atomistic model of the spider silk nanostructure

    NASA Astrophysics Data System (ADS)

    Keten, Sinan; Buehler, Markus J.

    2010-04-01

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

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

    PubMed

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

    2014-01-21

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

  19. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

    PubMed

    Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

    2016-12-01

    The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

  20. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)1

    PubMed Central

    Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang; Brookes, Emre H.; Chen, Jianhan; Irving, Thomas C.; Krueger, Susan; Barlow, David J.; Edler, Karen J.; Scott, David J.; Terrill, Nicholas J.; King, Stephen M.; Butler, Paul D.; Curtis, Joseph E.

    2016-01-01

    The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic ‘bottlebrush’ polymers. PMID:27980506

  1. Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems.

    PubMed

    Firaha, Dzmitry S; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara

    2016-11-28

    In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

  2. Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen:  The Effect of Explicitly Including Solvent Polarization.

    PubMed

    Geerke, Daan P; Thiel, Stephan; Thiel, Walter; van Gunsteren, Wilfred F

    2007-07-01

    In a previous combined QM/MM molecular dynamics (MD) study from our laboratory on the identity SN2 reaction between a chloride anion and an amino chloride in liquid dimethyl ether (DME), an increase in the free energy activation barrier was observed in the condensed phase when compared to the gas-phase activation energy. Here we reproduce these findings, but when comparing the condensed-phase potential of mean force (PMF) with the free energy profile in the gas phase (obtained from Monte Carlo simulations), we observe a smaller solvent effect on the activation barrier of the reaction. In a next step, we introduce an explicit description of electronic polarization in the MM (solvent) part of the system. A polarizable force field for liquid DME was developed based on the charge-on-spring (COS) model, which was calibrated to reproduce thermodynamic properties of the nonpolarizable model in classical MD simulations. The COS model was implemented into the MNDO/GROMOS interface in a special version of the QM/MM software ChemShell, which was used to investigate the effect of solvent polarization on the free energy profile of the reaction under study. A higher activation barrier was obtained using the polarizable solvent model than with the nonpolarizable force field, due to a better solvation of and a stronger polarization of solvent molecules around the separate reactants. The obtained PMFs were subjected to an energy-entropy decomposition of the relative solvation free energies of the reactant complex along the reaction coordinate, to investigate in a quantitative manner whether the solvent (polarization) effects are mainly due to favorable QM-MM (energetic) interactions.

  3. Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems

    NASA Astrophysics Data System (ADS)

    Firaha, Dzmitry S.; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara

    2016-11-01

    In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

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

    NASA Astrophysics Data System (ADS)

    Davantès, Athénaïs; Lefèvre, Grégory

    2016-11-01

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

  5. Molecular orientation behavior of chiral nematic liquid crystals based on the presence of blue phases using polarized microscopic FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Matsumura, Masanori; Katayama, Norihisa

    2016-07-01

    Study on molecular orientation behavior of highly twisted chiral nematic liquid crystals (N∗LCs) expressing blue phases (BPs) is important for developing new devices. This study examines the change of molecular orientation of N∗LCs due to the presence of BPs. Polarized microscopic FT-IR spectroscopy was used to study the in- and out-of-plane molecular orientations of N∗LCs that undergo a phase transition involving BPs. The band intensity ratio of CN to CH2 stretching modes (CN/CH2) in the IR spectra was used to determine the orientation of N∗LC molecules. The measured spectra indicated that the helical axis of N∗LC molecules was perpendicular to the substrate before heating and inclined on the substrate after cooling the sample which has phase transition from BP I to chiral nematic (N∗). The N∗LC molecule in the cell of rubbed orientation film exhibited the in-plane anisotropy after a heating-cooling ramp only in samples that passed through BP I. These results indicate that the changes of molecular orientation of N∗LC by phase transition are affected by BP I.

  6. Production of Molecular Iodine and Tri-iodide in the Frozen Solution of Iodide: Implication for Polar Atmosphere.

    PubMed

    Kim, Kitae; Yabushita, Akihiro; Okumura, Masanori; Saiz-Lopez, Alfonso; Cuevas, Carlos A; Blaszczak-Boxe, Christopher S; Min, Dae Wi; Yoon, Ho-Il; Choi, Wonyong

    2016-02-02

    The chemistry of reactive halogens in the polar atmosphere plays important roles in ozone and mercury depletion events, oxidizing capacity, and dimethylsulfide oxidation to form cloud-condensation nuclei. Among halogen species, the sources and emission mechanisms of inorganic iodine compounds in the polar boundary layer remain unknown. Here, we demonstrate that the production of tri-iodide (I3(-)) via iodide oxidation, which is negligible in aqueous solution, is significantly accelerated in frozen solution, both in the presence and the absence of solar irradiation. Field experiments carried out in the Antarctic region (King George Island, 62°13'S, 58°47'W) also showed that the generation of tri-iodide via solar photo-oxidation was enhanced when iodide was added to various ice media. The emission of gaseous I2 from the irradiated frozen solution of iodide to the gas phase was detected by using cavity ring-down spectroscopy, which was observed both in the frozen state at 253 K and after thawing the ice at 298 K. The accelerated (photo-)oxidation of iodide and the subsequent formation of tri-iodide and I2 in ice appear to be related with the freeze concentration of iodide and dissolved O2 trapped in the ice crystal grain boundaries. We propose that an accelerated abiotic transformation of iodide to gaseous I2 in ice media provides a previously unrecognized formation pathway of active iodine species in the polar atmosphere.

  7. Understanding atomistic phenomenon for hydrogen storage in complex metal hydrides

    NASA Astrophysics Data System (ADS)

    Chopra, Irinder Singh

    The storage of hydrogen into metals in the form of complex metal hydrides is one of the most promising methods. However, the incorporation and release of hydrogen requires very high temperatures. The discovery that the addition of Ti compounds lowers NaAlH4 decomposition barriers closer to ambient conditions, has re-ignited the field, and it is believed that surface processes are responsible for H2 dissociation and mass transport required to form the hydrogenated materials. Such surface reactions mechanisms are however difficult to study with typical spectroscopic and imaging surface science tools. Alanes lack contrast under electron microscopes and can modify the Scanning Tunneling Microscopy (STM) tips. Infrared spectroscopy would be a sensitive probe to investigate the adsorption of hydrogen providing, but has so far failed to detect chemisorbed hydrogen on Ti-doped Al surfaces due to the weak Al-H dynamic dipole moment. Thus despite extensive investigations, the fundamental mechanisms of the role of Ti and alane formation have remained elusive. In this study combining surface infrared (IR) spectroscopy and density functional theory (DFT), we provide atomistic details about the role of Ti as a catalyst for hydrogen uptake and alane formation and evolution on single crystal Al(111) and Al(100) surfaces. We are able to detect H indirectly by using CO as a probe molecule of the weak Al-H species. We demonstrate that aluminum doped with very small amounts of titanium (in a specific configuration) can activate molecular hydrogen at temperatures as low as 90K. Once dissociated, hydrogen spills over from these catalytic sites on to the Al surface and protects the surface from further reactions. We also show that, on Ti-doped Al surfaces, the diffusion dynamics are severely altered by Ti doping (Atomic hydrogen and AlH3 are trapped at the Ti sites) as indicated by a marked decrease of higher alane concentrations, which is deleterious for hydrogen storage for which mass

  8. Molten salt eutectics from atomistic simulations.

    PubMed

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

    2011-09-01

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

  9. Atomistic Simulations of Ternary Polymer Electrolytes Containing Ionic Liquids: Ion Transport and Viscoelastic Behavior

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    Influence of the BMIMPF6 ionic liquid on ion transport and viscoelastic properties of ternary polymer electrolytes containing polyethylene oxide solvated with LiPF6 salt and the underlying mechanisms are investigated. By employing atomistic molecular dynamics and trajectory extended kinetic Monte Carlo simulation techniques, we observe enhanced ionic mobilities and conductivities of the PEOLiPF6-BMIMPF ternary electrolytes upon the addition ionic liquid into the PEOLiPF6 binary electrolyte. The dispersion of the BMIMPF6 ionic liquid into the PEOLiPF6 electrolyte is found to (a) promote dissociation of existing LiPF6 ion-pairs and (b) slightly accelerate the polymer segmental dynamics. Together, these effects are observed to collectively give rise to an increase in ionic mobilities and conductivities of the ternary polymer electrolyte. On the other hand, Rouse analysis reveals that the storage and loss modulus of the ternary polymer electrolytes are coupled to their ion conducting properties.

  10. Atomistic multiscale simulation of the structure and properties of an amorphous OXD-7 layer

    NASA Astrophysics Data System (ADS)

    Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander

    2013-12-01

    The structure and properties of an amorphous 1,3-bis(2-(4-tert-butylphenyl)-1,3,4-oxadiazol-5-yl)benzene (OXD-7) layer are investigated by atomistic multiscale simulation combining quantum chemical (DFT, TDDFT) and molecular dynamics (MD, AMBER force field) calculations. Three stable OXD-7 conformers are found on its ground-state DFT potential energy surface. The force-field parameters of torsion angles lacking in the AMBER force field are determined by fitting to the results of MP2 calculations for a model oxadiazole derivative. The OXD-7 absorption band shape and HOMO and LUMO energy distributions in an amorphous film are found by TDDFT/DFT calculations for sample points obtained by MD calculations.

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

    PubMed Central

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

    2010-01-01

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

  12. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    NASA Astrophysics Data System (ADS)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

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

    SciTech Connect

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R.

    2014-04-15

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

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

    NASA Astrophysics Data System (ADS)

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R.

    2014-04-01

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

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

    PubMed

    Lin, Wenzhi; Foley, Andrew; Alam, Khan; Wang, Kangkang; Liu, Yinghao; Chen, Tianjiao; Pak, Jeongihm; Smith, Arthur R

    2014-04-01

    Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without

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

    PubMed

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

    2013-01-16

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

  17. Asymptotic analysis of microscopic impenetrability constraints for atomistic systems

    NASA Astrophysics Data System (ADS)

    Braides, A.; Gelli, M. S.

    2016-11-01

    We analyze systems of atomistic interactions on a triangular lattice allowing for fracture under a geometric condition on the triangles corresponding to a microscopic impenetrability constraint. Such systems can be thought as a computational simulation of materials undergoing brittle fracture. We show that in the small-deformation regime such approximation can be validated analytically in the framework of variational models of fracture. Conversely, in a finite-deformation regime various pathologies show that the continuum approximation of such a system differs from the usual variational representations of fracture and either needs new types of formulations on the continuum, or a proper interpretation of the atomistic constraints limiting their range and adapting them to a dynamical framework.

  18. Atomistic Simulation of Displacement Cascades in Zircon

    SciTech Connect

    Devanathan, Ram; Weber, William J.; Corrales, Louis R.; BP McGrail and GA Cragnolino

    2002-05-06

    Low energy displacement cascades in zircon (ZrSiO4) initiated by a Zr primary knock-on atom have been investigated by molecular dynamics simulations using a Coulombic model for long-range interactions, Buckingham potential for short-range interactions and Ziegler-Biersack potentials for close pair interactions. Displacements were found to occur mainly in the O sublattice, and O replacements by a ring mechanism were predominant. Clusters containing Si interstitials bridged by O interstitials, vacancy clusters and anti-site defects were found to occur. This Si-O-Si bridging is considerable in quenched liquid ZrSiO4.

  19. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    DTIC Science & Technology

    2006-02-01

    Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued

  20. The atomistic representation of first strain-gradient elastic tensors

    NASA Astrophysics Data System (ADS)

    Admal, Nikhil Chandra; Marian, Jaime; Po, Giacomo

    2017-02-01

    We derive the atomistic representations of the elastic tensors appearing in the linearized theory of first strain-gradient elasticity for an arbitrary multi-lattice. In addition to the classical second-Piola) stress and elastic moduli tensors, these include the rank-three double-stress tensor, the rank-five tensor of mixed elastic moduli, and the rank-six tensor of strain-gradient elastic moduli. The atomistic representations are closed-form analytical expressions in terms of the first and second derivatives of the interatomic potential with respect to interatomic distances, and dyadic products of relative atomic positions. Moreover, all expressions are local, in the sense that they depend only on the atomic neighborhood of a lattice site. Our results emanate from the condition of energetic equivalence between continuum and atomistic representations of a crystal, when the kinematics of the latter is governed by the Cauchy-Born rule. Using the derived expressions, we prove that the odd-order tensors vanish if the lattice basis admits central-symmetry. The analytical expressions are implemented as a KIM compliant algorithm to compute the strain gradient elastic tensors for various materials. Numerical results are presented to compare representative interatomic potentials used in the literature for cubic crystals, including simple lattices (fcc Al and Cu and bcc Fe and W) and multi-lattices (diamond-cubic Si). We observe that central potentials exhibit generalized Cauchy relations for the rank-six tensor of strain-gradient elastic moduli. In addition, this tensor is found to be indefinite for many potentials. We discuss the relationship between indefiniteness and material stability. Finally, the atomistic representations are specialized to central potentials in simple lattices. These expressions are used with analytical potentials to study the sensitivity of the elastic tensors to the choice of the cutoff radius.

  1. Atomistic Modeling of Co Growth on Cu(111

    NASA Technical Reports Server (NTRS)

    Khalil, Joseph; Bozzolo, Guillermo; Farias, Daniel; deParga, Vazquez; deMiguel, J. J.; Miranda, R.

    2002-01-01

    The BFS method for alloys is applied to the study of Co growth on Cu(111). The parameterization of the Co-Cu system is obtained from first-principles calculations, and tested against known experimental features for low coverage Co deposition on Cu(100) and Cu(111). Atomistic simulations are performed to investigate the behavior of Co on Cu(111) as a function of coverage.

  2. Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions.

    PubMed

    Takahashi, Hideaki; Omi, Atsushi; Morita, Akihiro; Matubayasi, Nobuyuki

    2012-06-07

    We present a simple and exact numerical approach to compute the free energy contribution δμ in solvation due to the electron density polarization and fluctuation of a quantum-mechanical solute in the quantum-mechanical/molecular-mechanical (QM/MM) simulation combined with the theory of the energy representation (QM/MM-ER). Since the electron density fluctuation is responsible for the many-body QM-MM interactions, the standard version of the energy representation method cannot be applied directly. Instead of decomposing the QM-MM polarization energy into the pairwise additive and non-additive contributions, we take sum of the polarization energies in the QM-MM interaction and adopt it as a new energy coordinate for the method of energy representation. Then, it is demonstrated that the free energy δμ can be exactly formulated in terms of the energy distribution functions for the solution and reference systems with respect to this energy coordinate. The benchmark tests were performed to examine the numerical efficiency of the method with respect to the changes in the individual properties of the solvent and the solute. Explicitly, we computed the solvation free energy of a QM water molecule in ambient and supercritical water, and also the free-energy change associated with the isomerization reaction of glycine from neutral to zwitterionic structure in aqueous solution. In all the systems examined, it was demonstrated that the computed free energy δμ agrees with the experimental value, irrespective of the choice of the reference electron density of the QM solute. The present method was also applied to a prototype reaction of adenosine 5'-triphosphate hydrolysis where the effect of the electron density fluctuation is substantial due to the excess charge. It was demonstrated that the experimental free energy of the reaction has been accurately reproduced with the present approach.

  3. Formation of molecular complexes of salicylic acid, acetylsalicylic acid, and methyl salicylate in a mixture of supercritical carbon dioxide with a polar cosolvent

    NASA Astrophysics Data System (ADS)

    Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.

    2015-08-01

    The solvate structures formed by salicylic acid, acetylsalicylic acid, and methyl salicylate in supercritical (SC) carbon dioxide with a polar cosolvent (methanol, 0.03 mole fractions) at a density of 0.7 g/cm3 and a temperature of 318 K were studied by the molecular dynamics method. Salicylic and acetylsalicylic acids were found to form highly stable hydrogen-bonded complexes with methanol via the hydrogen atom of the carboxyl group. For methyl salicylate in which the carboxyl hydrogen is substituted by a methyl radical, the formation of stable hydrogen bonds with methanol was not revealed. The contribution of other functional groups of the solute to the interactions with the cosolvent was much smaller. An analysis of correlations between the obtained data and the literature data on the cosolvent effect on the solubility of the compounds in SC CO2 showed that the dissolving ability of SC CO2 with respect to a polar organic substance in the presence of a cosolvent increased only when stable hydrogen-bonded complexes are formed between this substance and the cosolvent.

  4. Electronic structure, morphology and emission polarization of enhanced symmetry InAs quantum-dot-like structures grown on InP substrates by molecular beam epitaxy

    SciTech Connect

    Maryński, A.; Sĕk, G.; Musiał, A.; Andrzejewski, J.; Misiewicz, J.; Gilfert, C.; Reithmaier, J. P.; Capua, A.; Karni, O.; Gready, D.; Eisenstein, G.; Atiya, G.; Kaplan, W. D.; Kölling, S.

    2013-09-07

    The optical and structural properties of a new kind of InAs/InGaAlAs/InP quantum dot (QD)-like objects grown by molecular beam epitaxy have been investigated. These nanostructures were found to have significantly more symmetrical shapes compared to the commonly obtained dash-like geometries typical of this material system. The enhanced symmetry has been achieved due to the use of an As{sub 2} source and the consequent shorter migration length of the indium atoms. Structural studies based on a combination of scanning transmission electron microscopy (STEM) and atom probe tomography (APT) provided detailed information on both the structure and composition distribution within an individual nanostructure. However, it was not possible to determine the lateral aspect ratio from STEM or APT. To verify the in-plane geometry, electronic structure calculations, including the energy levels and transition oscillator strength for the QDs have been performed using an eight-band k·p model and realistic system parameters. The results of calculations were compared to measured polarization-resolved photoluminescence data. On the basis of measured degree of linear polarization of the surface emission, the in-plane shape of the QDs has been assessed proving a substantial increase in lateral symmetry. This results in quantum-dot rather than quantum-dash like properties, consistent with expectations based on the growth conditions and the structural data.

  5. Molecular dynamics of glycine ions in alanine doped TGS single crystal as probed by polarized laser raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Bajpai, P. K.; Verma, A. L.

    2012-10-01

    Polarized Raman spectra of pure and alanine doped tri-glycine sulfate (TGS) single crystals at 12 K in different scattering geometries are analyzed. Sub species modes due to three crystallographically distinguishable glycine ions G (I), G (II) and G (III) are assigned. It is observed that alanine doping does not change the crystalline field and acts as local perturbation only. The major changes due to doping are observed in the relative intensities of different modes; most of the modes associated with G (I) and SO42- ions show reversal behavior in relative intensity at high doping concentration. The observed spectral changes are analyzed in terms of reorientation of G (I) ions with sub species modes of G (II)/ G (III) following the reorientation due to complex hydrogen bonding network.

  6. Molecular dynamics of glycine ions in alanine doped TGS single crystal as probed by polarized laser Raman spectroscopy.

    PubMed

    Bajpai, P K; Verma, A L

    2012-10-01

    Polarized Raman spectra of pure and alanine doped tri-glycine sulfate (TGS) single crystals at 12 K in different scattering geometries are analyzed. Sub species modes due to three crystallographically distinguishable glycine ions G (I), G (II) and G (III) are assigned. It is observed that alanine doping does not change the crystalline field and acts as local perturbation only. The major changes due to doping are observed in the relative intensities of different modes; most of the modes associated with G (I) and SO(4)(2-) ions show reversal behavior in relative intensity at high doping concentration. The observed spectral changes are analyzed in terms of reorientation of G (I) ions with sub species modes of G (II)/ G (III) following the reorientation due to complex hydrogen bonding network.

  7. Levels of Arabidopsis thaliana Leaf Phosphatidic Acids, Phosphatidylserines, and Most Trienoate-Containing Polar Lipid Molecular Species Increase during the Dark Period of the Diurnal Cycle.

    PubMed

    Maatta, Sara; Scheu, Brad; Roth, Mary R; Tamura, Pamela; Li, Maoyin; Williams, Todd D; Wang, Xuemin; Welti, Ruth

    2012-01-01

    Previous work has demonstrated that plant leaf polar lipid fatty acid composition varies during the diurnal (dark-light) cycle. Fatty acid synthesis occurs primarily during the light, but fatty acid desaturation continues in the absence of light, resulting in polyunsaturated fatty acids reaching their highest levels toward the end of the dark period. In this work, Arabidopsis thaliana were grown at constant (21°C) temperature with 12-h light and 12-h dark periods. Collision induced dissociation time-of-flight mass spectrometry (MS) demonstrated that 16:3 and 18:3 fatty acid content in membrane lipids of leaves are higher at the end of the dark than at the end of the light period, while 16:1, 16:2, 18:0, and 18:1 content are higher at the end of the light period. Lipid profiling of membrane galactolipids, phospholipids, and lysophospholipids by electrospray ionization triple quadrupole MS indicated that the monogalactosyldiacylglycerol, phosphatidylglycerol, and phosphatidylcholine classes include molecular species whose levels are highest at end of the light period and others that are highest at the end of the dark period. The levels of phosphatidic acid (PA) and phosphatidylserine classes were higher at the end of the dark period, and molecular species within these classes either followed the class pattern or were not significantly changed in the diurnal cycle. Phospholipase D (PLD) is a family of enzymes that hydrolyzes phospholipids to produce PA. Analysis of several PLD mutant lines suggests that PLDζ2 and possibly PLDα1 may contribute to diurnal cycling of PA. The polar lipid compositional changes are considered in relation to recent data that demonstrate phosphatidylcholine acyl editing.

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

    PubMed

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

    2016-09-23

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

  9. Atomistic Simulation of Collision Cascades in Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2006-09-01

    Defect production in energetic collision cascades in zircon has been studied by molecular dynamics simulation using a partial charge model combined with the Ziegler-Biersack-Littmark potential. Energy dissipation, defect accumulation, Si-O-Si polymerization, and Zr coordination number were examined for 10 keV and 30 keV U recoils simulated in the constant NVE ensemble. For both energies an amorphous core was produced with features similar to that of melt quenched zircon. Disordered Si ions in this core were polymerized with an average degree of polymerization of 1.5, while disordered Zr ions showed a coordination number of about 6 in agreement with EXAFS results. These results suggest that nano-scale phase separation into silica- and zirconia-rich regions occurs in the amorphous core.

  10. Atomistic approach for simulating plasmons in nanostructures

    NASA Astrophysics Data System (ADS)

    Sakko, Arto; Rossi, Tuomas P.; Enkovaara, Jussi; Nieminen, Risto M.

    2014-05-01

    Recent experimental and theoretical works have demonstrated that quantum mechanical effects play an important role in materials design of some novel nano-plasmonic materials. In this work, electronic structure calculations are used to study these effects for the optical properties of metal nanostructures and small flakes of graphene. Their optical response is shown to depend on their exact atomic composition, and their similarities (size-dependent resonance frequency) and differences (metallic vs. semiconducting material) are discussed. The open-source computer code GPAW is used for the simulations, which can be done for systems of thousands of valence electrons. The calculations automatically include quantum effects such as tunneling, nonlocal response, and molecular orbital hybridization.

  11. Polarized cells, polar actions.

    PubMed

    Maddock, J R; Alley, M R; Shapiro, L

    1993-11-01

    The recognition of polar bacterial organization is just emerging. The examples of polar localization given here are from a variety of bacterial species and concern a disparate array of cellular functions. A number of well-characterized instances of polar localization of bacterial proteins, including the chemoreceptor complex in both C. crescentus and E. coli, the maltose-binding protein in E. coli, the B. japonicum surface attachment proteins, and the actin tail of L. monocytogenes within a mammalian cell, involve proteins or protein complexes that facilitate bacterial interaction with the environment, either the extracellular milieux or that within a plant or mammalian host. The significance of this observation remains unclear. Polarity in bacteria poses many problems, including the necessity for a mechanism for asymmetrically distributing proteins as well as a mechanism by which polar localization is maintained. Large structures, such as a flagellum, are anchored at the pole by means of the basal body that traverses the peptidoglycan wall. But for proteins and small complexes, whether in the periplasm or the membrane, one must invoke a mechanism that prevents the diffusion of these proteins away from the cell pole. Perhaps the periplasmic proteins are retained at the pole by the presence of the periseptal annulus (35). The constraining features for membrane components are not known. For large aggregates, such as the clusters of MCP, CheA, and CheW complexes, perhaps the size of the aggregate alone prevents displacement. In most cases of cellular asymmetry, bacteria are able to discriminate between the new pole and the old pole and to utilize this information for localization specificity. The maturation of new pole to old pole appears to be a common theme as well. Given numerous examples reported thus far, we propose that bacterial polarity displays specific rules and is a more general phenomenon than has been previously recognized.

  12. Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme.

    PubMed

    Asada, Toshio; Ando, Kanta; Sakurai, Koji; Koseki, Shiro; Nagaoka, Masataka

    2015-10-28

    An efficient approach to evaluate free energy gradients (FEGs) within the quantum mechanical/molecular mechanical (QM/MM) framework has been proposed to clarify reaction processes on the free energy surface (FES) in molecular assemblies. The method is based on response kernel approximations denoted as the charge and the atom dipole response kernel (CDRK) model that include explicitly induced atom dipoles. The CDRK model was able to reproduce polarization effects for both electrostatic interactions between QM and MM regions and internal energies in the QM region obtained by conventional QM/MM methods. In contrast to charge response kernel (CRK) models, CDRK models could be applied to various kinds of molecules, even linear or planer molecules, without using imaginary interaction sites. Use of the CDRK model enabled us to obtain FEGs on QM atoms in significantly reduced computational time. It was also clearly demonstrated that the time development of QM forces of the solvated propylene carbonate radical cation (PC˙(+)) provided reliable results for 1 ns molecular dynamics (MD) simulation, which were quantitatively in good agreement with expensive QM/MM results. Using FEG and nudged elastic band (NEB) methods, we found two optimized reaction paths on the FES for decomposition reactions to generate CO2 molecules from PC˙(+), whose reaction is known as one of the degradation mechanisms in the lithium-ion battery. Two of these reactions proceed through an identical intermediate structure whose molecular dipole moment is larger than that of the reactant to be stabilized in the solvent, which has a high relative dielectric constant. Thus, in order to prevent decomposition reactions, PC˙(+) should be modified to have a smaller dipole moment along two reaction paths.

  13. Molecular orientation and lattice ordering of C60 molecules on the polar FeO/Pt(111) surface.

    PubMed

    Qin, Zhihui; Liu, Cunding; Chen, Jian; Guo, Qinmin; Yu, Yinghui; Cao, Gengyu

    2012-01-14

    C(60) molecules assemble into close packing layer under the domination of the intermolecular interaction when deposited onto Pt(111)-supported FeO layer kept at 400 K. From corresponding high resolution scanning tunneling microscopy (STM) image, a kind of C(60) molecular orientational ordering stabilized by the intermolecular interaction is revealed as C(60)/FeO(111)-(√133 × √133) R17.5° structure and determined from the commensurability between the C(60) nearest-neighbor distance and the lattice of the underlying oxygen layer. Moreover, due to the inhomogeneously distributed work function of the underlying FeO layer, the C(60) molecular electronic state is periodically modulated resulting in a bright-dim STM contrast. In addition, one coincidence lattice ordering is determined as 8 × 8 superstructure with respect to the C(60) primitive cell, which overlays a 3 × 3 moiré cell of the underlying FeO layer.

  14. Molecular orientation and lattice ordering of C60 molecules on the polar FeO/Pt(111) surface

    NASA Astrophysics Data System (ADS)

    Qin, Zhihui; Liu, Cunding; Chen, Jian; Guo, Qinmin; Yu, Yinghui; Cao, Gengyu

    2012-01-01

    C60 molecules assemble into close packing layer under the domination of the intermolecular interaction when deposited onto Pt(111)-supported FeO layer kept at 400 K. From corresponding high resolution scanning tunneling microscopy (STM) image, a kind of C60 molecular orientational ordering stabilized by the intermolecular interaction is revealed as C60/FeO(111)-(√133 × √133) R17.5° structure and determined from the commensurability between the C60 nearest-neighbor distance and the lattice of the underlying oxygen layer. Moreover, due to the inhomogeneously distributed work function of the underlying FeO layer, the C60 molecular electronic state is periodically modulated resulting in a bright-dim STM contrast. In addition, one coincidence lattice ordering is determined as 8 × 8 superstructure with respect to the C60 primitive cell, which overlays a 3 × 3 moiré cell of the underlying FeO layer.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  16. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    NASA Astrophysics Data System (ADS)

    Vedula, Ravi Pramod Kumar

    profiles, inherent in strain-engineered Ge nanofins, on their transport properties. Fully atomistic simulations, involving a combination molecular dynamics simulations with first-principles based force-fields and semi-empirical tight binding calculations, coupled with linearized Boltzmann model are used to calculate the hole transport properties of realistic Ge nanofins (heights 5-15nm and widths 5nm-40nm). Our simulations predict the technological limit of phonon limited hole mobility improvement in Ge channel PMOS devices (H<15nm) and present geometric guidelines for patterning nanofins to engineer high performance uniaxial devices conducive to the existing top-down fabrication approaches. From these calculations, we demonstrate that realistic modeling of the devices requires a reduction in the empiricism of fitting parameters and incorporation of new multi-scale, multi-resolution approach spanning across various spatial and temporal scales. Such physics based predictive multiscale models facilitate an integrated approach for rapid development and pave the way for designing new advanced materials and devices.

  17. TUTORIAL: Electrical resistance: an atomistic view

    NASA Astrophysics Data System (ADS)

    Datta, Supriyo

    2004-07-01

    This tutorial article presents a 'bottom-up' view of electrical resistance starting from something really small, like a molecule, and then discussing the issues that arise as we move to bigger conductors. Remarkably, no serious quantum mechanics is needed to understand electrical conduction through something really small, except for unusual things like the Kondo effect that are seen only for a special range of parameters. This article starts with energy level diagrams (section 2), shows that the broadening that accompanies coupling limits the conductance to a maximum of q2/h per level (sections 3, 4), describes how a change in the shape of the self-consistent potential profile can turn a symmetric current-voltage characteristic into a rectifying one (sections 5, 6), shows that many interesting effects in molecular electronics can be understood in terms of a simple model (section 7), introduces the non-equilibrium Green function (NEGF) formalism as a sophisticated version of this simple model with ordinary numbers replaced by appropriate matrices (section 8) and ends with a personal view of unsolved problems in the field of nanoscale electron transport (section 9). Appendix A discusses the Coulomb blockade regime of transport, while appendix B presents a formal derivation of the NEGF equations. MATLAB codes for numerical examples are listed in appendix C. (The appendices are available in the online version only.)

  18. An atomistic methodology of energy release rate for graphene at nanoscale

    SciTech Connect

    Zhang, Zhen; Lee, James D.; Wang, Xianqiao

    2014-03-21

    Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough.

  19. Long-time atomistic simulations with the Parallel Replica Dynamics method

    NASA Astrophysics Data System (ADS)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  20. Polarization measurement through combination polarizers

    NASA Astrophysics Data System (ADS)

    Bai, Yunfeng; Li, Linjun; He, Zhelong; Liu, Yanwei; Ma, Cheng; Shi, Guang; Liu, Lu

    2014-02-01

    Polarization measurement approaches only using polarizer and grating is present. The combination polarizers consists of two polarizers: one is γ degree with the X axis; the other is along the Y axis. Binary grating is covered by the combination polarizers, and based on Fraunhofer diffraction, the diffraction intensity formula is deduced. The polarization state of incident light can be gotten by fitting the diffraction pattern with the deduced formula. Compared with the traditional polarization measurement method, this measurement only uses polarizer and grating, therefore, it can be applied to measure a wide wavelength range without replacing device in theory.

  1. Exploring Conceptual Frameworks of Models of Atomic Structures and Periodic Variations, Chemical Bonding, and Molecular Shape and Polarity: A Comparison of Undergraduate General Chemistry Students with High and Low Levels of Content Knowledge

    ERIC Educational Resources Information Center

    Wang, Chia-Yu; Barrow, Lloyd H.

    2013-01-01

    The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…

  2. A coupling atomistic-continuum approach for modeling mechanical behavior of nano-crystalline structures

    NASA Astrophysics Data System (ADS)

    Khoei, A. R.; Aramoon, A.; Jahanbakhshi, F.; DorMohammadi, H.

    2014-08-01

    In this article, a novel approach is presented for the concurrent coupling of continuum-atomistic model in the nano-mechanical behavior of atomic structures. The study is focused on the static concurrent multi-scale simulation, which is able to effectively capture the surface effects intrinsic in the molecular mechanics modeling. The Hamiltonian approach is applied to combine the continuum and molecular models with the same weight in the overlapping domain. A Lagrange-multiplier method is employed over the overlapping domain for coupling the continuum nodal displacement with the atomic lattice deformation. A multiple-step algorithm is developed to decouple the solution process in the atomic and continuum domains. The mass and stiffness matrices of continuum domain are computed based on the linear bridging map of the atomic lattice displacement, laid underneath the continuum grid to the element displacements. Numerical simulation results present that the stress and displacement contours of the presented coupling method are in good agreement with those obtained from the molecular mechanics simulation.

  3. Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B

    SciTech Connect

    Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert; Loos, Katja; Fels, Gregor

    2011-04-01

    Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using docking tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.

  4. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGES

    Stukowski, Alexander

    2012-05-28

    Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

  5. Predicting dislocation climb and creep from explicit atomistic details.

    PubMed

    Kabir, Mukul; Lau, Timothy T; Rodney, David; Yip, Sidney; Van Vliet, Krystyn J

    2010-08-27

    Here we report kinetic Monte Carlo simulations of dislocation climb in heavily deformed, body-centered cubic iron comprising a supersaturation of vacancies. This approach explicitly incorporates the effect of nonlinear vacancy-dislocation interaction on vacancy migration barriers as determined from atomistic calculations, and enables observations of diffusivity and climb over time scales and temperatures relevant to power-law creep. By capturing the underlying microscopic physics, the calculated stress exponents for steady-state creep rates agree quantitatively with the experimentally measured range, and qualitatively with the stress dependence of creep activation energies.

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

    SciTech Connect

    Maxwell, R; Baumann, T; Taylor, B

    2002-01-29

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

  7. Cell polarity: mechanochemical patterning.

    PubMed

    Goehring, Nathan W; Grill, Stephan W

    2013-02-01

    Nearly every cell type exhibits some form of polarity, yet the molecular mechanisms vary widely. Here we examine what we term 'chemical systems' where cell polarization arises through biochemical interactions in signaling pathways, 'mechanical systems' where cells polarize due to forces, stresses and transport, and 'mechanochemical systems' where polarization results from interplay between mechanics and chemical signaling. To reveal potentially unifying principles, we discuss mathematical conceptualizations of several prototypical examples. We suggest that the concept of local activation and global inhibition - originally developed to explain spatial patterning in reaction-diffusion systems - provides a framework for understanding many cases of cell polarity. Importantly, we find that the core ingredients in this framework - symmetry breaking, self-amplifying feedback, and long-range inhibition - involve processes that can be chemical, mechanical, or even mechanochemical in nature.

  8. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

    PubMed Central

    2016-01-01

    We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration (“peek”), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production

  9. Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

    NASA Astrophysics Data System (ADS)

    Rezaei Mianroodi, Jaber; Svendsen, Bob

    2015-04-01

    The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  11. Atomistic methodologies for material properties of 2D materials at the nanoscale

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen

    Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our

  12. Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

    DOE PAGES

    Taylor, Christopher D.

    2012-01-01

    Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies ofmore » the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.« less

  13. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    SciTech Connect

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

    1993-08-01

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

  14. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    1993-08-01

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

  15. 3d visualization of atomistic simulations on every desktop

    NASA Astrophysics Data System (ADS)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

  16. Atomistically-informed Dislocation Dynamics in fcc Crystals

    SciTech Connect

    Martinez, E; Marian, J; Arsenlis, T; Victoria, M; Perlado, J M

    2006-09-06

    We develop a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our findings to the plastic behavior of monocrystalline fcc metals.

  17. Quantum transport in RTD and atomistic modeling of nanostructures

    NASA Astrophysics Data System (ADS)

    Jiang, Zhengping

    As devices are scaled down to nanometer scale, new materials and device structures are introduced to extend Moore's law beyond Si devices. In this length scale, carrier transport moves from classical transport to quantum transport; material granularity has more and more impacts on performance. Computer Aided Design (CAD) becomes essential for both industrial and educational purposes. First part focuses on physical models and numerical issues in nano-scale devices modeling. Resonance Tunneling Diode (RTD) is simulated and used to illustrate phenomena in carrier transport. Non-Equilibrium Green's Function (NEGF) formulism is employed in quantum transport simulation. Inhomogeneous energy grid is used in energy integration, which is critical to capture essential physics in RTD simulation. All simulation results could be reproduced by developed simulators RTDNEGF and NEMO5. In nanostructures, device length becomes comparable to material granularity; it is not proper to consider materials as continuous in many situations. Second part of this work resolves this problem by introducing atomistic modeling method. Valley degeneracy in Si (110) QW is investigated. Inconsistency of experimental observations is resolved by introducing miscut in surface. Impacts of strain and electric field on electronic bandstructure are studied. Research of SiGe barrier disorder effects on valley splitting in Si (100) QW is then conducted. Behaviors of valley splitting in different well widths under electric field are predicted by atomistic simulation. Nearest neighbor empirical tight-binding method is used in electronic calculation and VFF Keating model is used in strain relaxation.

  18. Atomistic Simulation of High-Density Uranium Fuels

    DOE PAGES

    Garcés, Jorge Eduardo; Bozzolo, Guillermo

    2011-01-01

    We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

  19. Atomistic simulation of ion beam patterning with crater functions

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  20. A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

    NASA Technical Reports Server (NTRS)

    Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

    1997-01-01

    The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.

  1. Atomistic migration mechanisms of atomically flat, stepped, and kinked grain boundaries

    NASA Astrophysics Data System (ADS)

    Hadian, R.; Grabowski, B.; Race, C. P.; Neugebauer, J.

    2016-10-01

    We studied the migration behavior of mixed tilt and twist grain boundaries in the vicinity of a symmetric tilt <111 > Σ 7 grain boundary in aluminum. We show that these grain boundaries fall into two main categories of stepped and kinked grain boundaries around the atomically flat symmetric tilt boundary. Using these structures together with size converged molecular dynamics simulations and investigating snapshots of the boundaries during migration, we obtain an intuitive and quantitative description of the kinetic and atomistic mechanisms of the migration of general mixed grain boundaries. This description is closely related to well-known concepts in surface growth such as step and kink-flow mechanisms and allows us to derive analytical kinetic models that explain the dependence of the migration barrier on the driving force. Using this insight we are able to extract energy barrier data for the experimentally relevant case of vanishing driving forces that are not accessible from direct molecular dynamics simulations and to classify arbitrary boundaries based on their mesoscopic structures.

  2. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations.

    PubMed

    Alessandri, Riccardo; Uusitalo, Jaakko J; de Vries, Alex H; Havenith, Remco W A; Marrink, Siewert J

    2017-03-07

    Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor-acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)-phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device.

  3. Atomistic Modeling of Mechanical Loss in Pure and Doped Amorphous Oxides

    NASA Astrophysics Data System (ADS)

    Trinastic, Jonathan; Hamdan, Rashid; Cheng, Hai-Ping

    2014-03-01

    The mechanical dissipation in the oxide coatings of many precision measurement systems is a major source of thermal noise that limits the performance of such devices. A good candidate for a coating material to reduce the mechanical loss is tantala (Ta2O5) doped with titania (TiO2). Here, we numerically calculate the mechanical loss (internal friction) in these and other promising oxides based on the double well model. Using classical, atomistic molecular dynamics simulations, we estimate the density of double wells in the energy landscape of the amorphous oxides and the distribution of barrier heights, in addition to the deformation potentials, the elastic constants and vibrational frequencies at both the bottom of the potential wells and at the saddle points, all of which are relevant to the internal friction calculation. We use two versions of the bisection method to find the double well densities and distributions. All methods used in these calculations are implemented in DL-POLY molecular dynamics simulation software. These calculations will provide experimentalists with a better guide into which material combinations might be better choice for reducing the mechanical loss.

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    2011-11-07

    We present results of atomistic modelling of surface growth and sputtering using a multi-time scale molecular dynamics-on-the-fly kinetic Monte Carlo scheme which allows simulations to be carried out over realistic experimental times. The method uses molecular dynamics to model the fast processes and then calculates the diffusion barriers for the slow processes on-the-fly, without any preconceptions about what transitions might occur. The method is applied to the growth of metal and oxide materials at impact energies typical for both vapour deposition and magnetron sputtering. The method can be used to explain growth processes, such as the filling of vacancies and the formation of stacking faults. By tuning the variable experimental parameters on the computer, a parameter set for optimum crystalline growth can be determined. The method can also be used to model sputtering where the particle interactions with the surface occur at a higher energy. It is shown how a steady state can arise in which interstitial clusters are continuously being formed below the surface during an atom impact event which also recombine or diffuse to the surface between impact events. For fcc metals the near surface region remains basically crystalline during the erosion process with a pitted topography which soon attains a steady state roughness.

  6. Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water.

    PubMed

    Manzoni, Vinícius; Lyra, Marcelo L; Coutinho, Kaline; Canuto, Sylvio

    2011-10-14

    A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π(∗) excitation energy and the (15)N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π(∗) excitation energies of pyridazine and pyrazine are 32,070 ± 80 cm(-1) and 32,675 ± 60 cm(-1), respectively, in good agreement with the corresponding I-MM/QM results of 32,540 ± 80 cm(-1) and 32,710 ± 60 cm(-1) and the experimental results of 33,450-33,580 cm(-1) and 32,700-33,300 cm(-1). For the (15)N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4 ± 1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42-54 ppm and 17-22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM

  7. Grafting heteroelement-rich groups on graphene oxide: Tuning polarity and molecular interaction with bio-ionic liquid for enhanced lubrication.

    PubMed

    Mu, Liwen; Shi, Yijun; Guo, Xiaojing; Zhuang, Wei; Chen, Long; Ji, Tuo; Hua, Jing; Wang, Huaiyuan; Zhu, Jiahua

    2017-07-15

    Two different heteroelement-rich molecules have been successfully grafted on graphene oxide (GO) sheets which were then used as lubricant additives in bio-ionic liquid. The grafting was processed with reactions between GO sheets and synthesized heteroelement-rich molecules (Imidazol-1-yl phosphonic dichloride and 1H-1,2,4-triazol-1-yl phosphonic dichloride, respectively). The modified GO (m-GO) was added into [Choline][Proline] ([CH][P]) bio-ionic liquid, and has been demonstrated effective additive in promoting lubrication. Different characterization techniques have been utilized to study the reaction between GO and the two modifiers. The effect of molecular structure of the modifiers on the rheological and tribological properties of m-GO/[CH][P] lubricants was systematically investigated. Both theoretical calculation and experimental results demonstrated that the introduced heteroelement-rich groups are beneficial to increase the robustness of lubrication film by intensified hydrogen bonding and enhance the lubricant/friction surface adhesion by increased polarity of the m-GO. As a result, the interfacial lubrication could be significantly improved by these newly developed m-GO/[CH][P] lubricants.

  8. Determination of anisotropic optical constants and surface coverage of molecular films using polarized visible ATR spectroscopy. Application to adsorbed cytochrome c films.

    PubMed

    Runge, Anne F; Rasmussen, Nicole C; Saavedra, S Scott; Mendes, Sergio B

    2005-01-13

    This article describes a method to determine the anisotropic optical constants and surface coverage of molecular films using polarized attenuated total reflectance (ATR) absorbance measurements. We have extended the transfer-matrix formalism to describe birefringent and dichroic films in ATR geometries and have combined it with an iterative numerical procedure to determine the anisotropic values of both the real (n) and imaginary (k) parts of the complex refractive index of the film under investigation. Anisotropic values of the imaginary part of the refractive index (k) allow for the determination of the surface coverage and one order parameter of the film. To illustrate this approach, we have used cytochrome c (cyt c) protein films adsorbed to glass and indium tin oxide (ITO) surfaces. Experimental results show that cyt c films on these surfaces, which were formed under identical conditions, have significant differences in their surface coverages (11.2 +/- 0.4 pmol/cm(2) on glass and 21.7 +/- 0.9 pmol/cm(2) on ITO); however, their order parameters are similar (0.30 +/- 0.02 on glass and 0.36 +/- 0.04 on ITO).

  9. Morphological and microstructural stability of N-polar InAlN thin films grown on free-standing GaN substrates by molecular beam epitaxy

    SciTech Connect

    Hardy, Matthew T. Storm, David F.; Downey, Brian P.; Katzer, D. Scott; Meyer, David J.; McConkie, Thomas O.; Smith, David J.; Nepal, Neeraj

    2016-03-15

    The sensitivity of the surface morphology and microstructure of N-polar-oriented InAlN to variations in composition, temperature, and layer thickness for thin films grown by plasma-assisted molecular beam epitaxy (PAMBE) has been investigated. Lateral compositional inhomogeneity is present in N-rich InAlN films grown at low temperature, and phase segregation is exacerbated with increasing InN fraction. A smooth, step-flow surface morphology and elimination of compositional inhomogeneity can be achieved at a growth temperature 50 °C above the onset of In evaporation (650 °C). A GaN/AlN/GaN/200-nm InAlN heterostructure had a sheet charge density of 1.7 × 10{sup 13 }cm{sup −2} and no degradation in mobility (1760 cm{sup 2}/V s) relative to 15-nm-thick InAlN layers. Demonstration of thick-barrier high-electron-mobility transistors with good direct-current characteristics shows that device quality, thick InAlN layers can be successfully grown by PAMBE.

  10. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.

    PubMed

    Giese, Timothy J; York, Darrin M

    2007-11-21

    This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridization or specific covalent bonding environment). This strategy for determination of QMMM nonbonding interactions becomes tedious to parametrize and lacks robust transferability. Problems occur in the study of chemical reactions where the "atom type" is a complex function of the reaction coordinate. This is particularly problematic for reactions, where atoms or localized functional groups undergo changes in charge state and hybridization. In the present work we propose a new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems. The model is based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. The model is chemically significant since it properly correlates atomic size, softness, polarizability, and dispersion terms with minimal one-body parameters that are functions of the atomic charge. Tests of the model are examined for rare-gas interactions with neutral and charged atoms in order to demonstrate improved transferability. The present work provides a new framework for modeling QMMM interactions with improved accuracy and transferability.

  11. Quantifying chain reptation in entangled polymer melts: topological and dynamical mapping of atomistic simulation results onto the tube model.

    PubMed

    Stephanou, Pavlos S; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G; Kröger, Martin

    2010-03-28

    The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability psi(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed psi(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic

  12. Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: atomistic and coarse-grained simulations.

    PubMed

    Cheng, Yuan; Li, Dechang; Ji, Baohua; Shi, Xinghua; Gao, Huajian

    2010-09-01

    Nanoparticles such as fullerenes and carbon nanotubes have been extensively studied for biomedical applications. In this paper, we report the design of carbon nanotubes as HIV-1 protease inhibitors. Docking and molecular dynamics calculations are performed using an atomistic model to explore the optimal interaction structure and free energy between the nanotube and HIV-1 protease. A coarse-grained model is then developed based on the atomistic model, allowing us to investigate the dynamic behaviors of the protease in the bound and unbound states. The dynamic process reveals that the carbon nanotube is able to bind to the active site of the protease and prevent the active flaps from opening up, thus blocking the function of the protease. This process is strongly influenced by the size of the nanotube. The binding of carbon nanotubes to an alternative binding site other than the active site is also explored. Therefore, carbon nanotube-based inhibitors have great potential for application as HIV-1 protease inhibitors.

  13. Atomistic Conversion Reaction Mechanism of WO 3 in Secondary Ion Batteries of Li, Na, and Ca

    SciTech Connect

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

    2016-04-13

    Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes during lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.

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

    PubMed Central

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

    2015-01-01

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

  15. SUPRAMOLECULAR SYSTEMS BEHAVIOR AT THE AIR-WATER INTERFACE. MOLECULAR DYNAMIC SIMULATION STUDY

    SciTech Connect

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

    2008-08-28

    Atomistic molecular dynamics simulation (MDS) was development to investigate the structural and dynamic properties of a monolayer of supramolecular systems. The simulations were performed at room temperature, on inclusion complexes (ICs) of {alpha}-cyclodextrin (CD) with poly(ethylene-oxide)(PEO), poly({epsilon}-caprolactone)(PEC) and poly(tetrahydrofuran)(PTHF). The simulations were carried out for a surface area of 30A ring . The trajectories of the MDS show that the system more stable was IC-PEC, being the less stable IC-PEO. The disordered monolayer for the systems was proved by the orientation correlation function and the radial distribution function between the polar groups of ICs and the water molecules. We found that the system IC-PEC was more stable that the systems IC-PTHF and IC-PEO.

  16. Multiresolution molecular mechanics: Implementation and efficiency

    NASA Astrophysics Data System (ADS)

    Biyikli, Emre; To, Albert C.

    2017-01-01

    Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

  17. Shock Hugoniot behavior of single crystal titanium using atomistic simulations

    NASA Astrophysics Data System (ADS)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

    Atomistic shock simulations are performed for single crystal titanium using four different interatomic potentials at impact velocities ranging from 0.5 km/s to 2.0 km/s. These potentials comprise of three parameterizations in the formulation of the embedded atom method and one formulation of the modified embedded atom method. The capability of the potentials to model the shock deformation and failure behavior is investigated by computing the shock hugoniot response of titanium and comparing to existing experimental data. In addition, the capability to reproduce the shock induced alpha (α) to omega (ω) phase transformation seen in Ti is investigated. The shock wave structure is discussed and the velocities for the elastic, plastic and the α-ω phase transformation waves are calculated for all the interatomic potentials considered.

  18. Redox reactions with empirical potentials: atomistic battery discharge simulations.

    PubMed

    Dapp, Wolf B; Müser, Martin H

    2013-08-14

    Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

  19. Pathfinder: A parallel search algorithm for concerted atomistic events

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    2007-02-01

    An algorithm has been designed to search for the escape paths with the lowest activation barriers when starting from a local minimum-energy configuration of a many-atom system. The pathfinder algorithm combines: (1) a steered eigenvector-following method that guides a constrained escape from the convex region and subsequently climbs to a transition state tangentially to the eigenvector corresponding to the lowest negative Hessian eigenvalue; (2) discrete abstraction of the atomic configuration to systematically enumerate concerted events as linear combinations of atomistic events; (3) evolutionary control of the population dynamics of low activation-barrier events; and (4) hybrid task + spatial decompositions to implement massive search for complex events on parallel computers. The program exhibits good scalability on parallel computers and has been used to study concerted bond-breaking events in the fracture of alumina.

  20. Atomistic design of semiconductor nanostructures with optimal thermoelectric properties

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    2008-03-01

    The search for novel materials with optimal thermoelectric properties (for either thermoelectric power generation or heat dissipation) is an active field of research. We present atomistic and ab-initio simulations of selected nanomaterials, aimed at predicting thermal conductivities and electronic transport properties, and ultimately at designing materials with optimal thermoelectric figure of merit. In particular we focus on carbon nanotubes [1], silicon wires [2] and nanoporous silicon [3] and we discuss both strategies and algorithms to optimize thermoelectric properties at the nanoscale. [1] D. Donadio and G.Galli, Phys. Rev. Lett. 2007 (in press). [2] T.Vo, A.Williamson, V.Lordi and G.Galli (submitted) and J.Reed, A.Williamson, E.Schwegler and G.Galli (submitted). [3] J.-H. Lee, J.C.Grossman, J.Reed and G.Galli, Appl. Phys. Lett. 2007 (in press).

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

    DOE PAGES

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

    2015-11-16

    Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

  2. Experimentally driven atomistic model of 1,2 polybutadiene

    SciTech Connect

    Gkourmpis, Thomas; Mitchell, Geoffrey R.

    2014-02-07

    We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

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

    NASA Astrophysics Data System (ADS)

    Aghaei Anvigh, Samira

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

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

    PubMed

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

    2015-01-01

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

  5. Large degree of polarization of photoluminescence caused by anisotropic strain in nonpolar a-plane MgxZn1-xO layers grown by plasma-assisted molecular beam epitaxy.

    PubMed

    Chen, X Y; Pan, X H; Chen, W; Chen, S S; Huang, J Y; Ye, Z Z

    2016-10-15

    A large degree of polarization (ρ) of photoluminescence (PL) approximate to 1 is obtained in each nonpolar a-plane MgxZn1-xO layer grown by plasma-assisted molecular beam epitaxy (MBE) with x=0.01, 0.03, and 0.10, respectively. Anisotropic in-plane strains are selectively introduced by using foreign substrates and doping with different Mg contents, which strongly modify the valence band structures, leading to anisotropic optical properties. A polarized Raman measurement shows that anisotropic in-plane strains along the y and z axes increase with the increasing Mg contents. Polarized PL spectra show that ρ gradually increases to 0.97 with decreasing in-plane strains, resulting from an increasing difference in transition energy (ΔE) between E⊥c and E‖c caused by a lift of the degeneracy of valence band structures. The obtained highly polarized emission is close to linear polarized light, which is desirable in the backlighting of liquid crystal displays.

  6. DL-FIND: an open-source geometry optimizer for atomistic simulations.

    PubMed

    Kästner, Johannes; Carr, Joanne M; Keal, Thomas W; Thiel, Walter; Wander, Adrian; Sherwood, Paul

    2009-10-29

    Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.

  7. Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

    NASA Astrophysics Data System (ADS)

    Konuk Onat, Mine; Durukanoglu, Sondan

    2012-02-01

    We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the <100> axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

  8. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    DOE PAGES

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized tomore » compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.« less

  9. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  10. Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

    NASA Astrophysics Data System (ADS)

    Bondi, Robert J.; Fox, Brian P.; Marinella, Matthew J.

    2016-03-01

    First-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influence on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.

  11. Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

    DOE PAGES

    Bondi, Robert James; Fox, Brian Philip; Marinella, Matthew J.

    2016-03-22

    In this study, first-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influencemore » on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.« less

  12. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized Systems

    NASA Astrophysics Data System (ADS)

    Ho, Phay; Knight, Christopher; Young, Linda; Tegze, Miklos; Faigel, Gyula

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Contract No. DE-AC02-06CH11357.

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

    NASA Astrophysics Data System (ADS)

    Rouhi, S.; Ansari, R.

    2012-01-01

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

  14. Atomistic finite element model for axial buckling of single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Rouhi, S.

    2010-11-01

    An atomistic finite element model is developed to study the buckling behavior of single-walled carbon nanotubes with different boundary conditions. By treating nanotubes as space-frame structures, in which the discrete nature of nanotubes is preserved, they are modeled using three-dimensional elastic beam elements for the bonds and point mass elements for the atoms. The elastic moduli of the beam elements are determined via a linkage between molecular mechanics and structural mechanics. Based on this model, the critical compressive forces of single-walled carbon nanotubes with different boundary conditions, geometries as well as chiralities are obtained and then compared. It is indicated that at low aspect ratios, the critical buckling load of nanotubes decreases considerably with increasing aspect ratios, whereas at higher aspect ratios, buckling load slightly decreases as the aspect ratio increases. It is also indicated that increasing aspect ratio at a given radius results in the convergence of buckling envelops associated with armchair and zigzag nanotubes.

  15. Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

    NASA Astrophysics Data System (ADS)

    Guin, Laurent; Raphanel, Jean L.; Kysar, Jeffrey W.

    2016-06-01

    Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.

  16. Development and assessment of atomistic models for predicting static friction coefficients

    NASA Astrophysics Data System (ADS)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  17. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

    PubMed Central

    Yang, Shengfeng; Chen, Youping

    2015-01-01

    In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

  18. Atomistic Analysis of Room Temperature Quantum Coherence in Two-Dimensional CdSe Nanostructures.

    PubMed

    Pal, Sougata; Nijjar, Parmeet; Frauenheim, Thomas; Prezhdo, Oleg V

    2017-03-02

    Recent experiments on CdSe nanoplatelets synthesized with precisely controlled thickness that eliminates ensemble disorder have allowed accurate measurement of quantum coherence at room temperature. Matching exactly the CdSe cores of the experimentally studied particles and considering several defects, we establish the atomistic origins of the loss of coherence between heavy and light hole excitations in two-dimensional CdSe and CdSe/CdZnS core/shell structures. The coherence times obtained using molecular dynamics based on tight-binding density functional theory are in excellent agreement with the measured values. We show that a long coherence time is a consequence of both small fluctuations in the energy gap between the excited state pair, which is much less than thermal energy, and a slow decay of correlation between the energies of the two states. Anionic defects at the core/shell interface have little effect on the coherence lifetime, while cationic defects strongly perturb the electronic structure, destroying the experimentally observed coherence. By coupling to the same phonon modes, the heavy and light holes synchronize their energy fluctuations, facilitating long-lived coherence. We further demonstrate that the electronic excitations are localized close to the surface of these narrow nanoscale systems, and therefore, they couple most strongly to surface acoustic phonons. The established features of electron-phonon coupling and the influence of defects, surfaces, and core/shell interfaces provide important insights into quantum coherence in nanoscale materials in general.

  19. Atomistic details of protein dynamics and the role of hydration water

    SciTech Connect

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

    The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread over a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.

  20. Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting

    PubMed Central

    2011-01-01

    Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear. PMID:22078069

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

    PubMed Central

    Asthagiri, D; Bashford, D

    2002-01-01

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

  2. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    SciTech Connect

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized to compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.

  3. Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Xu, Shaofeng; Liu, Jiabin; Li, Xiaoyan; Wei, Yujie; Wang, Hongtao; Gao, Huajian; Yang, Wei

    2017-01-01

    The interest in promoting deformation twinning for plasticity is mounting for advanced materials. In contrast to disordered grain boundaries, highly organized twin boundaries are beneficial to promoting strength-ductility combination. Twinning deformation typically involves the kinetics of stacking faults, its interplay with dislocations, as well as the interactions between dislocations and twin boundaries. While the latter has been intensively studied, the dynamics of stacking faults has been rarely touched upon. In this work, we report new physical insights on the stacking fault dynamics in twin induced plasticity (TWIP) steels. The atomistic simulation is made possible by a newly introduced approach: meta-atom molecular dynamics simulation. The simulation suggests that the stacking fault interactions are dominated by dislocation reactions that take place spontaneously, different from the existing mechanisms. Whether to generate a single stacking fault, or a twinning partial and a trailing partial dislocation, depends upon a unique parameter, namely the stacking fault energy. The latter in turn determines the deformation twinning characteristics. The complex twin-slip and twin-dislocation interactions demonstrate the dual role of deformation twins as both the dislocation barrier and dislocation storage. This duality contributes to the high strength and high ductility of TWIP steels.

  4. Atomistic simulation of CO2 solubility in poly(ethylene oxide) oligomers

    NASA Astrophysics Data System (ADS)

    Hong, Bingbing; Panagiotopoulos, Athanassios Z.

    2014-06-01

    We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henry's constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henry's constant. Dependence of the calculated Henry's constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length.

  5. Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.

    2016-11-01

    We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.

  6. Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

    NASA Astrophysics Data System (ADS)

    Pan, Xiaoliang; Schwartz, Steven

    2015-03-01

    It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

  7. Void Growth and Coalescence in Dynamic Fracture from the Atomistic Level

    SciTech Connect

    Rudd, R E

    2010-09-30

    An important example of multiscale material response is the fracture of ductile solids. In the process of ductile fracture, voids nucleate, grow and coalesce, and it is this linking process that creates the fracture. Ductile fracture has typically been modeled at the continuum level, in a variety of models that may or may not model voids explicitly. Previously we have studied the plasticity associated with void growth in fcc metals, focusing on copper. In the work discussed here we examine void growth in single crystal and polycrystalline body-centered cubic (bcc) metals (V, Nb, Ta, Mo and W) subjected to tension at a high rate and high triaxiality. Large-scale atomistic models provide detailed information on void nucleation and growth and the plasticity generated as voids coalesce, based solely on the constitutive properties inherent in the interatomic forces. The details of the plasticity may be used to inform dislocation dynamics and continuum plasticity models in order to develop models that scale beyond the nanoscale. We also discuss concurrent multiscale modeling of void growth using Coarse-Grained Molecular Dynamics.

  8. Porosity evolution at high strain rates: atomistic simulations, dislocation analysis, and constitutive modeling

    NASA Astrophysics Data System (ADS)

    Bringa, Eduardo; Ruestes, Carlos; Rodriguez Nieva, Joaquin; Tramontina, Diego; Tang, Yizhe; Meyers, Marc

    2015-06-01

    Mimicking shock compression experiments, our molecular dynamics simulations explore the mechanical response and plasticity effects under uniaxial high strain rate compression (10**7/s to 10**9/s) for Au and Ta single crystals with a collection of spherical nanovoids, with a radius of 3-4 nm, resulting in an initial porosity of %-10%. Dislocation analysis was used to evaluate and quantify the evolution of plasticity. The evolution of dislocations configuration and densities were predicted and successfully compared to an analysis based on Ashby's concept of geometrically-necessary dislocations. The temperature excursion during plastic deformation was used to estimate the mobile dislocation density. The results obtained are compared with a variety of dislocation-based constitutive models. Plastic activity leads to a decrease in porosity until voids disappear completely. Based on the atomistic simulations, a densification regime was observed in all nanoporous samples studied. With these results, a new strain- based porosity model for metals is proposed for simulations at the continuum scale. EB, CR and DT thank support from PICT-0092 and a SeCTyP-UNCuyo grant.

  9. Atomistic Studies of Cation Transport in Tetragonal ZrO2 During Zirconium Corrosion

    SciTech Connect

    Xian-Ming Bai; Yongfeng Zhang; Michael R. Tonks

    2013-10-01

    Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is one of the major degradation mechanisms of these alloys. During corrosion the transport of oxidizing species in zirconium dioxide (ZrO2) determines the corrosion kinetics. Previously it has been argued that the outward diffusion of cation ions is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO2. The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration barriers of some defect clusters can be much lower than those of point defects. The migration of Zr interstitials at some special grain boundaries is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  11. Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

    NASA Astrophysics Data System (ADS)

    Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

    2017-03-01

    Ti-7Al is a good model material for mimicking the α phase response of near-α and α+β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

  12. Atomistic details of protein dynamics and the role of hydration water

    DOE PAGES

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

    The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

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

    PubMed

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

    2014-02-05

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

  14. Atomistic simulation of the structure and elastic properties of gold nanowires

    NASA Astrophysics Data System (ADS)

    Diao, Jiankuai; Gall, Ken; Dunn, Martin L.

    2004-09-01

    We performed atomistic simulations to study the effect of free surfaces on the structure and elastic properties of gold nanowires aligned in the <1 0 0> and <1 1 1> crystallographic directions. Computationally, we formed a nanowire by assembling gold atoms into a long wire with free sides by putting them in their bulk fcc lattice positions. We then performed a static relaxation on the assemblage. The tensile surface stresses on the sides of the wire cause the wire to contract along the length with respect to the original fcc lattice, and we characterize this deformation in terms of an equilibrium strain versus the cross-sectional area. While the surface stress causes wires of both orientations and all sizes to increasingly contract with decreasing cross-sectional area, when the cross-sectional area of a <1 0 0> nanowire is less than 1.83 nm×1.83 nm, the wire undergoes a phase transformation from fcc to bct, and the equilibrium strain increases by an order of magnitude. We then applied a uniform uniaxial strain incrementally to 1.2% to the relaxed nanowires in a molecular statics framework. From the simulation results we computed the effective axial Young's modulus and Poisson's ratios of the nanowire as a function of cross-sectional area. We used two approaches to compute the effective elastic moduli, one based on a definition in terms of the strain derivative of the total energy and another in terms of the virial stress often used in atomistic simulations. Both give quantitatively similar results, showing an increase in Young's modulus with a decrease of cross-sectional area in the nanowires that do not undergo a phase transformation. Those that undergo a phase transformation experience an increase of about a factor of three of Young's modulus. The Poisson's ratio of the <1 0 0> wires that do not undergo a phase transformation show little change with the cross-sectional area. Those wires that undergo a phase transformation experience an increase of about 10% in

  15. Atomistic modeling of phonon bandstructure and transport for optimal thermal management in nanoscale devices

    NASA Astrophysics Data System (ADS)

    Sundaresan, Sasi Sekaran

    Monte Carlo based statistical approach to solve Boltzmann Transport Equation (BTE) has become a norm to investigate heat transport in semiconductors at sub-micron regime, owing mainly to its ability to characterize realistically sized device geometries qualitatively. One of the primary issues with this technique is that the approach predominantly uses empirically fitted phonon dispersion relations as input to determine the properties of phonons so as to predict the thermal conductivity of specified material geometry. The empirically fitted dispersion relations assume harmonic approximation thereby failing to account for thermal expansion, interaction of lattice waves, effect of strain on spring stiffness, and accurate phonon-phonon interaction. To circumvent this problem, in this work, a coupled molecular mechanics-Monte Carlo (MM-MC) platform has been developed and used to solve the phonon Boltzmann Transport Equation (BTE) for the calculation of thermal conductivity of several novel and emerging nanostructures. The use of the quasi-anharmonic MM approach (as implemented in the open source NEMO 3-D software toolkit) not only allows one to capture the true atomicity of the underlying lattice but also enables the simulation of realistically-sized structures containing millions of atoms. As compared to the approach using an empirically fitted phonon dispersion relation, here, a 17% increase in the thermal conductivity for a silicon nanowire due to the incorporation of atomistic corrections in the LA (longitudinal acoustic) branch alone has been reported. The atomistically derived thermal conductivity as calculated from the MM-MC framework is then used in the modular design and analysis of (i) a silicon nanowire based thermoelectric cooler (TEC) unit, and (ii) a GaN/InN based nanostructured light emitting device (LED). It is demonstrated that the use of empirically fitted phonon bandstructure parameters overestimates the temperature difference between the hot and the

  16. Polarization Aberrations

    NASA Technical Reports Server (NTRS)

    Mcguire, James P., Jr.; Chipman, Russell A.

    1990-01-01

    The analysis of the polarization characteristics displayed by optical systems can be divided into two categories: geometrical and physical. Geometrical analysis calculates the change in polarization of a wavefront between pupils in an optical instrument. Physical analysis propagates the polarized fields wherever the geometrical analysis is not valid, i.e., near the edges of stops, near images, in anisotropic media, etc. Polarization aberration theory provides a starting point for geometrical design and facilitates subsequent optimization. The polarization aberrations described arise from differences in the transmitted (or reflected) amplitudes and phases at interfaces. The polarization aberration matrix (PAM) is calculated for isotropic rotationally symmetric systems through fourth order and includes the interface phase, amplitude, linear diattenuation, and linear retardance aberrations. The exponential form of Jones matrices used are discussed. The PAM in Jones matrix is introduced. The exact calculation of polarization aberrations through polarization ray tracing is described. The report is divided into three sections: I. Rotationally Symmetric Optical Systems; II. Tilted and Decentered Optical Systems; and Polarization Analysis of LIDARs.

  17. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    NASA Technical Reports Server (NTRS)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; Biegel, Bryan (Technical Monitor)

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  19. Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences.

    PubMed

    Cronin, Matthew A; Rincon, Gonzalo; Meredith, Robert W; MacNeil, Michael D; Islas-Trejo, Alma; Cánovas, Angela; Medrano, Juan F

    2014-01-01

    We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

  20. Circularly Polarized MHOHG with Bichromatic Circularly Polarized Laser Pulses

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  1. Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

    PubMed Central

    Komarov, Pavel V; Khokhlov, Alexei R

    2013-01-01

    Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

  2. Size effects of 109° domain walls in rhombohedral barium titanate single crystals—A molecular statics analysis

    NASA Astrophysics Data System (ADS)

    Endres, Florian; Steinmann, Paul

    2016-01-01

    Ferroelectric functional materials are of great interest in science and technology due to their electromechanically coupled material properties. Therefore, ferroelectrics, such as barium titanate, are modeled and simulated at the continuum scale as well as at the atomistic scale. Due to recent advancements in related manufacturing technologies the modeling and simulation of smart materials at the nanometer length scale is getting more important not only to predict but also fundamentally understand the complex material behavior of such materials. In this study, we analyze the size effects of 109° nanodomain walls in ferroelectric barium titanate single crystals in the rhombohedral phase using a recently proposed extended molecular statics algorithm. We study the impact of domain thicknesses on the spontaneous polarization, the coercive field, and the lattice constants. Moreover, we discuss how the electromechanical coupling of an applied electric field and the introduced strain in the converse piezoelectric effect is affected by the thickness of nanodomains.

  3. Size effects of 109° domain walls in rhombohedral barium titanate single crystals—A molecular statics analysis

    SciTech Connect

    Endres, Florian Steinmann, Paul

    2016-01-14

    Ferroelectric functional materials are of great interest in science and technology due to their electromechanically coupled material properties. Therefore, ferroelectrics, such as barium titanate, are modeled and simulated at the continuum scale as well as at the atomistic scale. Due to recent advancements in related manufacturing technologies the modeling and simulation of smart materials at the nanometer length scale is getting more important not only to predict but also fundamentally understand the complex material behavior of such materials. In this study, we analyze the size effects of 109° nanodomain walls in ferroelectric barium titanate single crystals in the rhombohedral phase using a recently proposed extended molecular statics algorithm. We study the impact of domain thicknesses on the spontaneous polarization, the coercive field, and the lattice constants. Moreover, we discuss how the electromechanical coupling of an applied electric field and the introduced strain in the converse piezoelectric effect is affected by the thickness of nanodomains.

  4. Polar Bear

    USGS Publications Warehouse

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

    1988-01-01

    Polar bears are long-lived, late-maturing carnivores that have relatively low rates of reproduction and natural mortality. Their populations are susceptible to disturbance from human activities, such as the exploration and development of mineral resources or hunting. Polar bear populations have been an important renewable resource available to coastal communities throughout the Arctic for thousands of years.

  5. Atomistic modeling of electronic structure and transport in disordered nanostructures

    NASA Astrophysics Data System (ADS)

    Kharche, Neerav

    As the Si-CMOS technology approaches the end of the International Technology Roadmap for Semiconductors (ITRS), the semiconductor industry faces a formidable challenge to continue the transistor scaling according to Moore's law. To continue the scaling of classical devices, alternative channel materials such as SiGe, carbon nanotubes, nanowires, and III-V based materials are being investigated along with novel 3D device geometries. Researchers are also investigating radically new quantum computing devices, which are expected to perform calculations faster than the existing classical Si-CMOS based structures. Atomic scale disorders such as interface roughness, alloy randomness, non-uniform strain, and dopant fluctuations are routinely present in the experimental realization of such devices. These disorders now play an increasingly important role in determining the electronic structure and transport properties as device sizes enter the nanometer regime. This work employs the atomistic tight-binding technique, which is ideally suited for modeling systems with local disorders on an atomic scale. High-precision multi-million atom electronic structure calculations of (111) Si surface quantum wells and (100) SiGe/Si/SiGe heterostructure quantum wells are performed to investigate the modulation of valley splitting induced by atomic scale disorders. The calculations presented here resolve the existing discrepancies between theoretically predicted and experimentally measured valley splitting, which is an important design parameter in quantum computing devices. Supercell calculations and the zone-unfolding method are used to compute the bandstructures of inhomogeneous nanowires made of AlGaAs and SiGe and their connection with the transmission coefficients computed using non-equilibrium Green's function method is established. A unified picture of alloy nanowires emerges, in which the nanodevice (transmission) and nanomaterials (bandstructure) viewpoints complement each other

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

    PubMed

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

    2015-04-14

    Unusual electronic states arise at ferroelectric domain walls due to the local symmetry reduction, strain gradients and electrostatics. This particularly applies to improper ferroelectrics, where the polarization is induced by a structural or magnetic order parameter. Because of the subordinate nature of the polarization, the rigid mechanical and electrostatic boundary conditions that constrain domain walls in proper ferroics are lifted. Here we show that spin-driven ferroelectricity promotes the emergence of charged domain walls. This provides new degrees of flexibility for c