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

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2009-04-01

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

  4. 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.

  5. 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.

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

    PubMed Central

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

    2015-01-01

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

  7. 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.

  8. Molecular cooperativity and compatibility via full atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kwan Yang, Kenny

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

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

    SciTech Connect

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

    2014-04-07

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

  10. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    SciTech Connect

    Jay A Brandes

    2009-09-23

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  13. Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics

    NASA Astrophysics Data System (ADS)

    Tolladay, Mat; Ivanov, Dmitry; Allan, Neil L.; Scarpa, Fabrizio

    2017-09-01

    We calculate the tensile and shear moduli of a series of boron nitride nanotubes and their piezoelectric response to applied loads. We compare in detail results from a simple molecular mechanics (MM) potential, the universal force field, with those from the atomistic finite element method (AFEM) using both Euler-Bernoulli and Timoshenko beam formulations. The MM energy minimisations are much more successful than those using the AFEM, and we analyse the failure of the latter approach both qualitatively and quantitatively.

  14. Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

    DTIC Science & Technology

    2014-10-01

    Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge...differences in .mol2 file formatting between various molecule building programs (e.g., field width, number format), Antechamber may fail to read

  15. Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics.

    PubMed

    Tolladay, Mat; Ivanov, Dmitry; Allan, Neil L; Scarpa, Fabrizio

    2017-09-01

    We calculate the tensile and shear moduli of a series of boron nitride nanotubes and their piezoelectric response to applied loads. We compare in detail results from a simple molecular mechanics (MM) potential, the universal force field, with those from the atomistic finite element method (AFEM) using both Euler-Bernoulli and Timoshenko beam formulations. The MM energy minimisations are much more successful than those using the AFEM, and we analyse the failure of the latter approach both qualitatively and quantitatively.

  16. 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.

  17. 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.

  18. Molecular Recognition Effects in Atomistic Models of Imprinted Polymers

    PubMed Central

    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. PMID:21954325

  19. 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.

  20. 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

  1. 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.

  2. Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics.

    PubMed

    Vila Verde, Ana; Beltramo, Peter J; Maranas, Janna K

    2011-05-17

    We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.

  3. Unraveling Mg(2+)-RNA binding with atomistic molecular dynamics.

    PubMed

    Cunha, Richard A; Bussi, Giovanni

    2017-05-01

    Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg(2+) on an 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 nontrivial interplay between RNA conformational entropy and divalent cation binding. © 2017 Cunha and Bussi; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. 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.

  5. PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.

    PubMed

    Graham, James A; Essex, Jonathan W; Khalid, Syma

    2017-04-24

    Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of internal coordinates directly from atomistic molecular dynamics simulation trajectories. The derivation of bespoke parameters from atomistic simulations improves the quality of the CG model compared to the use of generic parameters derived from other molecules, while automation greatly reduces the time required. The ease of configuration of PyCGTOOL enables the rapid investigation of multiple atom-to-bead mappings and topologies. Although we present PyCGTOOL used in combination with the GROMACS molecular dynamics engine its use of standard trajectory input libraries means that it is in principle compatible with other software. The software is available from the URL https://github.com/jag1g13/pycgtool as the following doi: 10.5281/zenodo.259330 .

  6. 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

  7. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

  8. 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.

  9. Comparisons Between Integral Equation Theory and Molecular Dynamics Simulations for Atomistic Models of Polyethylene Liquids

    SciTech Connect

    Curro, John G.; Webb III, Edmund B.; Grest, Gary S.; Weinhold, Jeffrey D.; Putz, Mathias; McCoy, John D.

    1999-07-21

    Molecular dynamics (MD) simulations were performed on dense liquids of polyethylene chains of 24 and 66 united atom CH{sub 2} units. A series of models was studied ranging in atomistic detail from coarse-grained, freely-jointed, tangent site chains to realistic, overlapping site models subjected to bond angle restrictions and torsional potentials. These same models were also treated with the self-consistent, polymer reference interaction site model (PRISM) theory. The intramolecular and total structure factors, as well as, the intermolecular radial distribution functions g(r) and direct correlation functions C(r) were obtained from theory and simulation. Angular correlation functions were also simulation obtained from the MD simulations. Comparisons between theory and reveal that PRISM theory works well for computing the intermolecular structure of coarse-grained chain models, but systematically underpredicts the extent of intermolecular packing as more atomistic details are introduced into the model. A consequence of g(r) having insufficient structure is that the theory yields an isothermal compressibility that progressively becomes larger, relative to the simulations, as overlapping the PRISM sites and angular restrictions are introduced into the model. We found that theory could be considerably improved by adding a tail function to C(r) beyond the effective hard core diameter. The range of this tail function was determined by requiring the theory to yield the correct compressibility.

  10. 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.

  11. First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

    SciTech Connect

    von Lilienfeld, O. Anatole

    2013-02-26

    A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we give an introduction to an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via “alchemical” interpolations involving fractional nuclear charges in the electronic Hamiltonian. We address Taylor expansions in CCS, property nonlinearity, improved predictions using reference compound pairs, and the ounce-of-gold prize challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. Here, these relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schrödinger equation.

  12. First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

    DOE PAGES

    von Lilienfeld, O. Anatole

    2013-02-26

    A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we give an introduction to an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via “alchemical” interpolations involving fractional nuclear charges in the electronic Hamiltonian. We address Taylor expansions in CCS, property nonlinearity, improved predictions using reference compound pairs, and the ounce-of-gold prizemore » challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. Here, these relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schrödinger equation.« less

  13. 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.

  14. 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

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

    PubMed

    Oakes, V; Furini, S; Domene, C

    2016-01-01

    The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. On the atomistic mechanisms of alkane (methane-pentane) separation by distillation: a molecular dynamics study.

    PubMed

    Zahn, Dirk

    2007-11-01

    Insights into the liquid-vapor transformation of methane-pentane mixtures were obtained from transition path sampling molecular dynamics simulations. This case study of the boiling of non-azeotropic mixtures demonstrates an unprejudiced identification of the atomistic mechanisms of phase separation in the course of vaporization which form the basis of distillation processes. From our simulations we observe spontaneous segregation events in the liquid mixture to trigger vapor nucleation. The formation of vapor domains stabilizes and further promotes the separation process by preferential evaporation of methane molecules. While this discrimination holds for all mixtures of different composition studied, a full account of the boiling process requires a more complex picture. At low methane concentration the nucleation of the vapor domains includes both methane and pentane molecules. The pentane molecules, however, tend to form small aggregates and undergo rapid re-condensation within picoseconds to nanoseconds scales. Accordingly, two aspects of selectivity accounting for methane-pentane separation in the course of liquid-vapor transformations were made accessible to molecular dynamics simulations: spontaneous segregation in the liquid phase leading to selective vapor nucleation and growth favoring methane vaporization and selective re-condensation of pentane molecules.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.

    PubMed

    Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J

    2017-08-14

    Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Evidence from infrared dichroism, x-ray diffraction, and atomistic computer simulation for a ``zigzag'' molecular shape in tilted smectic liquid crystal phases

    NASA Astrophysics Data System (ADS)

    Jang, W. G.; Glaser, M. A.; Park, C. S.; Kim, K. H.; Lansac, Y.; Clark, N. A.

    2001-11-01

    Infrared dichroism (IR) and atomistic computer simulation are employed to probe molecular shape in smectic liquid crystal phases where the optic axis is tilted relative to the layer normal. Polar plots of absorption profiles due to core (phenyl, C-C) and tail (alkyl or methylene, CH2) vibrations in the tilted synclinic (smectic-C) phase of a variety of materials show the phenyl (core) IR absorbance symmetry axes to be consistently tilted at larger angle from the layer normal than the alkyl or methylene (tail). This suggests that, on average, the tails are less tilted than the cores. Furthermore, we find that optic axis tilt angle is close to the core tilt angle measured by IR dichroism, as expected, since liquid crystal birefringence arises primarily from the cores. These results are in accord with the ``zigzag'' model of Bartolino, Doucet, and Durand. However, we find that only a small fraction of the tail, the part nearest the core, is tilted, and only this part contributes significantly to layer contraction upon molecular tilt.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

    PubMed

    van der Vaart, Arjan

    2015-05-01

    Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  19. 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.

  20. 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

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

    PubMed

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

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

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

    PubMed

    Frolov, Andrey I; Kiselev, Michael G

    2014-10-09

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

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

    PubMed

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

    2015-12-28

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

  5. Understanding the Interaction of Pluronics L61 and L64 with a DOPC Lipid Bilayer: An Atomistic Molecular Dynamics Study

    DOE PAGES

    Ileri Ercan, Nazar; Stroeve, Pieter; Tringe, Joseph W.; ...

    2016-09-13

    In this paper, we investigate the interactions of Pluronics L61 and L64 with a dioleylphosphatidylcholine (DOPC) lipid bilayer by atomistic molecular dynamics simulations using the all-atom OPLS force field. Our results show that the initial configuration of the polymer with respect to the bilayer determines its final conformation within the bilayer. When the polymer is initially placed at the lipid/water interface, we observe partial insertion of the polymer in a U-shaped conformation. On the other hand, when the polymer is centered at the bilayer, it stabilizes to a transmembrane state, which facilitates water transport across the bilayer. We show thatmore » membrane thickness decreases while its fluidity increases in the presence of Pluronics. When the polymer concentration inside the bilayer is high, pore formation is initiated with L64. Finally, our results show good agreement with existing experimental data and reveal that the hydrophilic/lipophilic balance of the polymer plays a critical role in the interaction mechanisms as well as in the dynamics of Pluronics with and within the bilayer.« less

  6. Understanding the Interaction of Pluronics L61 and L64 with a DOPC Lipid Bilayer: An Atomistic Molecular Dynamics Study

    SciTech Connect

    Ileri Ercan, Nazar; Stroeve, Pieter; Tringe, Joseph W.; Faller, Roland

    2016-09-13

    In this paper, we investigate the interactions of Pluronics L61 and L64 with a dioleylphosphatidylcholine (DOPC) lipid bilayer by atomistic molecular dynamics simulations using the all-atom OPLS force field. Our results show that the initial configuration of the polymer with respect to the bilayer determines its final conformation within the bilayer. When the polymer is initially placed at the lipid/water interface, we observe partial insertion of the polymer in a U-shaped conformation. On the other hand, when the polymer is centered at the bilayer, it stabilizes to a transmembrane state, which facilitates water transport across the bilayer. We show that membrane thickness decreases while its fluidity increases in the presence of Pluronics. When the polymer concentration inside the bilayer is high, pore formation is initiated with L64. Finally, our results show good agreement with existing experimental data and reveal that the hydrophilic/lipophilic balance of the polymer plays a critical role in the interaction mechanisms as well as in the dynamics of Pluronics with and within the bilayer.

  7. Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations.

    PubMed

    Van Lehn, Reid C; Alexander-Katz, Alfredo

    2015-04-28

    Gold nanoparticles (NPs) have been increasingly used in biological applications that involve potential contact with cellular membranes. As a result, it is essential to gain a physical understanding of NP-membrane interactions to guide the design of next-generation bioactive nanoparticles. In previous work, we showed that charged, amphiphilic NPs can fuse with lipid bilayers after contact between protruding solvent-exposed lipid tails and the NP monolayer. Fusion was only observed at the high-curvature edges of large bilayer defects, but not in low-curvature regions where protrusions are rarely observed. Here, we use atomistic molecular dynamics simulations to show that the same NPs can also fuse with low-curvature bilayers in the absence of defects if NP-protrusion contact occurs, generalizing the results of our previous work. Insertion proceeds without applying biasing forces to the NP, driven by the hydrophobic effect, and involves the transient generation of bilayer curvature. We further find that NPs with long hydrophobic ligands can insert a single ligand into the bilayer core in a manner similar to the binding of peripheral proteins. Such anchoring may precede insertion, revealing potential methods for engineering NP monolayers to enhance NP-bilayer fusion in systems with a low likelihood of lipid tail protrusions. These results reveal new pathways for NP-bilayer fusion and provide fundamental insight into behavior at the nano-bio interface.

  8. 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}.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

  12. 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

  13. 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.

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

    PubMed

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

    2014-08-06

    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.

  15. Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.

    PubMed

    Kubiak-Ossowska, Karina; Mulheran, Paul A; Nowak, Wieslaw

    2014-08-21

    The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.

  16. Atomistic simulations of melting and solidification using temperature accelerated molecular dynamics

    NASA Astrophysics Data System (ADS)

    Yu, Tang-Qing; Samanta, Amit; E, Weinan; Tuckerman, Mark; vanden-Eijnden, Eric

    2013-03-01

    A detailed understanding of melting/solidification mechanisms in metals remains obscure, though over the years many simulations and experiments have been performed for clarifying it. We have applied the enhanced-sampling method, Temperature-Accelerated Molecular Dynamics, to study the melting/solidification of FCC metals like copper, nickel under the constant temperature and pressure conditions. Free energy surfaces along Steinhardt order parameters and local density are obtained and minimum free energy path (MFEP) between the metastable states are calculated. An analysis of the atomic structure along the MFEP, reveals that an interplay between orientation ordering and positional ordering governs this phase transition.

  17. 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

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

    PubMed

    Eike, David M; Maginn, Edward J

    2006-04-28

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

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

    NASA Astrophysics Data System (ADS)

    Prisner, Thomas; Denysenkov, Vasyl; Sezer, Deniz

    2016-03-01

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

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. 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.

  3. 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.

  4. 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

  5. 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).

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

    PubMed

    Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

    2014-10-14

    Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

  11. Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

    PubMed Central

    Lettieri, S.; Zuckerman, D.M.

    2011-01-01

    Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

  12. 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

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

    PubMed

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

    2012-07-01

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

  14. Molecular Mechanism of Overhauser Dynamic Nuclear Polarization in Insulating Solids.

    PubMed

    Pylaeva, Svetlana; Ivanov, Konstantin L; Baldus, Marc; Sebastiani, Daniel; Elgabarty, Hossam

    2017-05-18

    Dynamic nuclear polarization (DNP), a technique that significantly enhances NMR signals, is experiencing a renaissance owing to enormous methodological developments. In the heart of DNP is a polarization transfer mechanism that endows nuclei with much larger electronic spin polarization. Polarization transfer via the Overhauser effect (OE) is traditionally known to be operative only in liquids and conducting solids. Very recently, surprisingly strong OE-DNP in insulating solids has been reported, with a DNP efficiency that increases with the magnetic field strength. Here we offer an explanation for these perplexing observations using a combination of molecular dynamics and spin dynamics simulations. Our approach elucidates the underlying molecular stochastic motion, provides cross-relaxation rates, explains the observed sign of the NMR enhancement, and estimates the role of nuclear spin diffusion. The presented theoretical description opens the door for rational design of novel polarizing agents for OE-DNP in insulating solids.

  15. 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.

  16. 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

  17. Atomistic Insights into Nucleation and Formation of Hexagonal Boron Nitride on Nickel from First-Principles-Based Reactive Molecular Dynamics Simulations.

    PubMed

    Liu, Song; van Duin, Adri C T; van Duin, Diana M; Liu, Bin; Edgar, James H

    2017-04-25

    Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni-B and Ni-N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.

  18. 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.

  19. 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.

  20. 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

  1. Molecular link between auxin and ROS-mediated polar growth.

    PubMed

    Mangano, Silvina; Denita-Juarez, Silvina Paola; Choi, Hee-Seung; Marzol, Eliana; Hwang, Youra; Ranocha, Philippe; Velasquez, Silvia Melina; Borassi, Cecilia; Barberini, María Laura; Aptekmann, Ariel Alejandro; Muschietti, Jorge Prometeo; Nadra, Alejandro Daniel; Dunand, Christophe; Cho, Hyung-Taeg; Estevez, José Manuel

    2017-05-16

    Root hair polar growth is endogenously controlled by auxin and sustained by oscillating levels of reactive oxygen species (ROS). These cells extend several hundred-fold their original size toward signals important for plant survival. Although their final cell size is of fundamental importance, the molecular mechanisms that control it remain largely unknown. Here we show that ROS production is controlled by the transcription factor RSL4, which in turn is transcriptionally regulated by auxin through several auxin response factors (ARFs). In this manner, auxin controls ROS-mediated polar growth by activating RSL4, which then up-regulates the expression of genes encoding NADPH oxidases (also known as RESPIRATORY BURST OXIDASE HOMOLOG proteins) and class III peroxidases, which catalyze ROS production. Chemical or genetic interference with ROS balance or peroxidase activity affects root hair final cell size. Overall, our findings establish a molecular link between auxin and ROS-mediated polar root hair growth.

  2. 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.

  3. 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.

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

    SciTech Connect

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

    2006-09-25

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

  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. 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.

  7. 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.

  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. 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.

  12. 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.

  13. Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations.

    PubMed

    Bucher, Denis; Hsu, Yuan-Hao; Mouchlis, Varnavas D; Dennis, Edward A; McCammon, J Andrew

    2013-01-01

    Group VI Ca²⁺-independent phospholipase A₂ (iPLA₂) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA₂ or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA₂ in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA₂ at the membrane surface. The models show that an anchoring region (residues 710-724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA₂ models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA₂ and related enzymes.

  14. 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

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

    PubMed

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

    2016-01-14

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

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

    NASA Astrophysics Data System (ADS)

    Kawakami, Tomonori; Shigemoto, Isamu; Matubayasi, Nobuyuki

    2012-12-01

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

  17. Atomistic simulation of graphene-based polymer nanocomposites

    SciTech Connect

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

    2016-05-18

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

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

    PubMed

    Kubbinga, Henk

    2012-01-01

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

  19. From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Hassan, Sergio A.; Mehler, Ernest L.

    Biological macromolecules and other polymers belong to the class of mesoscopic systems, with characteristic length scale of the order of a nanometer. Although microscopic models would be the preferred choice in theoretical calculations, their use in computer simulations becomes prohibitive for large systems or long simulation times. On the other hand, the use of purely macroscopic models in the mesoscopic domain may introduce artifacts, with effects that are difficult to assess and that may compromise the reliability of the calculations. Here is proposed an approach with the aim of minimizing the empirical nature of continuum approximations of solvent effects within the scope of molecular mechanics (MM) approximations in mesoscopic systems. Using quantum chemical methods, the potential generated by the molecular electron density is first decomposed in a multicenter-multipole expansion around predetermined centers. The monopole and dipole terms of the expansion at each site create electric fields that polarize the surrounding aqueous medium whose dielectric properties can be described by the classical theory of polar liquids. Debye's theory allows a derivation of the dielectric profiles created around isolated point charges and dipoles that can incorporate Onsager reaction field corrections. A superposition of screened Coulomb potentials obtained from this theory makes possible a simple derivation of a formal expression for the total electrostatic energy and the polar component of the solvation energy of the system. A discussion is presented on the physical meaning of the model parameters, their transferability, and their convergence to calculable quantities in the limit of simple systems. The performance of this continuum approximation in computer calculations of amino acids in the context of an atomistic force field is discussed. Applications of a continuum model based on screened Coulomb potentials in multinanosecond simulations of peptides and proteins are

  20. 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

  1. 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.

  2. Molecular architecture of the sheathed polar flagellum in Vibrio alginolyticus.

    PubMed

    Zhu, Shiwei; Nishikino, Tatsuro; Hu, Bo; Kojima, Seiji; Homma, Michio; Liu, Jun

    2017-09-25

    Vibrio species are Gram-negative rod-shaped bacteria that are ubiquitous and often highly motile in aqueous environments. Vibrio swimming motility is driven by a polar flagellum covered with a membranous sheath, but this sheathed flagellum is not well understood at the molecular level because of limited structural information. Here, we use Vibrio alginolyticus as a model system to study the sheathed flagellum in intact cells by combining cryoelectron tomography (cryo-ET) and subtomogram analysis with a genetic approach. We reveal striking differences between sheathed and unsheathed flagella in V. alginolyticus cells, including a novel ring-like structure at the bottom of the hook that is associated with major remodeling of the outer membrane and sheath formation. Using mutants defective in flagellar motor components, we defined a Vibrio-specific feature (also known as the T ring) as a distinctive periplasmic structure with 13-fold symmetry. The unique architecture of the T ring provides a static platform to recruit the PomA/B complexes, which are required to generate higher torques for rotation of the sheathed flagellum and fast motility of Vibrio cells. Furthermore, the Vibrio flagellar motor exhibits an intrinsic length variation between the inner and the outer membrane bound complexes, suggesting the outer membrane bound complex can shift slightly along the axial rod during flagellar rotation. Together, our detailed analyses of the polar flagella in intact cells provide insights into unique aspects of the sheathed flagellum and the distinct motility of Vibrio species.

  3. 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.

  4. Collective alignment of polar filaments by molecular motors.

    SciTech Connect

    Ziebert, F.; Aranson, I. S.; Vershinin, M.; Gross, S. P.; Materials Science Division; Univ. of California at Irvine

    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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. Primary radiation damage of Zr-0.5%Nb binary alloy: atomistic simulation by molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Tikhonchev, M.; Svetukhin, V.; Kapustin, P.

    2017-09-01

    Ab initio calculations predict high positive binding energy (˜1 eV) between niobium atoms and self-interstitial configurations in hcp zirconium. It allows the expectation of increased niobium fraction in self-interstitials formed under neutron irradiation in atomic displacement cascades. In this paper, we report the results of molecular dynamics simulation of atomic displacement cascades in Zr-0.5%Nb binary alloy and pure Zr at the temperature of 300 K. Two sets of n-body interatomic potentials have been used for the Zr-Nb system. We consider a cascade energy range of 2-20 keV. Calculations show close estimations of the average number of produced Frenkel pairs in the alloy and pure Zr. A high fraction of Nb is observed in the self-interstitial configurations. Nb is mainly detected in single self-interstitial configurations, where its fraction reaches tens of percent, i.e. more than its tenfold concentration in the matrix. The basic mechanism of this phenomenon is the trapping of mobile self-interstitial configurations by niobium. The diffusion of pure zirconium and mixed zirconium-niobium self-interstitial configurations in the zirconium matrix at 300 K has been simulated. We observe a strong dependence of the estimated diffusion coefficients and fractions of Nb in self-interstitials produced in displacement cascades on the potential.

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

    PubMed

    Côté, Sébastien; Wei, Guanghong; Mousseau, Normand

    2014-07-01

    The huntingtin protein is characterized by a segment of consecutive glutamines (Q(N)) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (htt(NT)) positioned just before the Q(N) region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt(NT)Q(N) fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps-approach, reorganization, anchoring, and insertion-that are very diverse at the atomic level. On the membrane, the htt(NT) peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains-mainly Leu-4, Leu-7, Phe-11 and Leu-14-positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the htt(NT) peptide. These observations do not significantly change upon adding the Q(N) region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt(NT) region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q(N) region could also play a key role for the oligomerization of htt(NT)Q(N) on phospholipid membranes. © 2014 Wiley Periodicals, Inc.

  12. Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions

    NASA Astrophysics Data System (ADS)

    Renevey, Annick; Riniker, Sereina

    2017-03-01

    Reducing the number of degrees of freedom in molecular models—so-called coarse-graining—is a popular approach to increase the accessible time scales and system sizes in molecular dynamics simulations. It involves, however, per se a loss of information. In order to retain a high accuracy in the region of interest, hybrid methods that combine two levels of resolution in a single system are an attractive trade-off. Hybrid atomistic (AT)/coarse-grained (CG) simulations have previously been shown to preserve the secondary structure elements of AT proteins in CG water but to cause an artificial increase in intramolecular hydrogen bonds, resulting in a reduced flexibility of the proteins. Recently, it was found that the AT-CG interactions employed in these simulations were too favourable for apolar solutes and not favourable enough for polar solutes. Here, the AT-CG interactions are reparametrised to reproduce the solvation free energy of a series of AT alkanes and side-chain analogues in CG water, while retaining the good mixing behaviour of AT water with CG water. The new AT-CG parameters are tested in hybrid simulations of four proteins in CG water. Structural and dynamic properties are compared to those obtained in fully AT simulations and, if applicable, to experimental data. The results show that the artificial increase of intramolecular hydrogen bonds is drastically reduced, leading to a better reproduction of the structural properties and flexibility of the proteins in atomistic water, without the need for an atomistic solvent layer.

  13. 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.

  14. 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

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

    PubMed

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

    2016-05-11

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

  16. Secondary Water Pore Formation for Proton Transport in a ClC Exchanger Revealed by an Atomistic Molecular-Dynamics Simulation

    PubMed Central

    Ko, Youn Jo; Jo, Won Ho

    2010-01-01

    Abstract Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger, and how the protein brings about the coupled movement of both ions are still unknown. In this work, we use an atomistic molecular dynamics (MD) simulation to demonstrate that a previously unknown secondary water pore is formed inside an Escherichia coli ClC exchanger. The secondary water pore is bifurcated from the chloride ion pathway at E148. From the systematic simulations, we determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore, and that the highly conserved tyrosine residue Y445 functions as a barrier that separates the proton from the chloride ion pathways. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore, and we propose a new mechanism for the coupled transport of chloride ions and protons. It has been reported that several members of ClC proteins are not just channels that simply transport chloride ions across lipid bilayers; rather, they are exchangers that transport both the chloride ion and proton in opposite directions. However, the ion transit pathways and the mechanism of the coupled movement of these two ions have not yet been unveiled. In this article, we report a new finding (to our knowledge) of a water pore inside a prokaryotic ClC protein as revealed by computer simulation. This water pore is bifurcated from the putative chloride ion, and water molecules inside the new pore connect two glutamate residues that are known to be key residues for proton transport. On the basis of our simulation results, we conclude that the water wire that is formed inside the newly found pore acts as a proton pathway, which

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

    NASA Astrophysics Data System (ADS)

    Natarajan, Upendra

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

  18. 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.

  19. Spin-polarized transport properties of 1,3-dimethylpropynylidene-based molecular devices

    NASA Astrophysics Data System (ADS)

    Min, Y.; Zhong, C. G.; Yao, K. L.

    2017-10-01

    Based on non-equilibrium Green's function and density functional theory, a first-principles study of the spin-polarized transport properties and magnetism of 1,3-dimethylpropynylidene molecule sandwiched in two Ag electrodes is performed. Strong spin-polarized negative differential resistance and spin filtration effect are present. We also find that the net spin moments of molecular magnet abnormally decrease driven by electric field because the molecular orbitals around Fermi level have opposite spin direction and that non-spin-polarized electrical read out of spin states for single molecular magnets is possible.

  20. The origin of dust polarization in molecular outflows

    NASA Astrophysics Data System (ADS)

    Reissl, S.; Seifried, D.; Wolf, S.; Banerjee, R.; Klessen, R. S.

    2017-07-01

    Aims: Polarization measurements of dust grains aligned with the magnetic field direction are an established technique for tracing large-scale field structures. In this paper we present a case study to investigate the conditions that need to be met to detect a characteristic magnetic field substructure that is embedded in such a large-scale field. A helical magnetic field with a surrounding hourglass-shaped field is expected from theoretical predictions and self-consistent magnetohydrodynamical (MHD) simulations to be present in the specific case of protostellar outflows. Hence, such an outflow environment is the perfect environment for our study. Methods: We present synthetic polarization maps in the infrared and millimeter regime of simulations of protostellar outflows. The simulations were performed with the newly developed radiative transfer and polarization code POLARIS. The code is the first to include a self-consistent description of various alignment mechanisms such as the imperfect Davis-Greenstein (IDG) and the radiative torque (RAT) alignment. We investigated the effects of the grain size distribution, inclination, and applied alignment mechanism. Results: We find that the IDG mechanism cannot produce any measurable polarization degree (≥1%), whereas the RAT alignment produced polarization degrees of a few percent. Furthermore, we developed a method for identifying the origin of the polarization. We show that the helical magnetic field in the outflow can only be observed close to the outflow axis and at its tip, whereas in the surrounding regions the hourglass field in the foreground dominates the polarization. Furthermore, the polarization degree in the outflow lobe is lower than in the surroundings, in agreement with observations. We also find that the orientation of the polarization vector flips around at about a few hundred micrometers because of the transition from dichroic extinction to thermal re-emission. In order to avoid ambiguities when

  1. 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.

  2. 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.

  3. 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.

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

    SciTech Connect

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

    2016-08-15

    By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO{sub 3} thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO{sub 3} and iso-polarity LaAlO{sub 3} 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 LaAlO{sub 3} (111) substrate was more suitable than Nb-doped SrTiO{sub 3}. 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 LaNiO{sub 3} based superlattices.

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  7. Visualizing molecular polar order in tissues via electromechanical coupling

    PubMed Central

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

    2015-01-01

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

  8. 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.

  9. 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].

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

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

    PubMed Central

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

    2014-01-01

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

  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.

    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.

  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

    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.

  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. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Infrared Polarization of the Molecular Cloud Associated to IRAS 18236-1205

    NASA Astrophysics Data System (ADS)

    Luna, A.; Retes, R.; Devaraj, R.; Maya, Y. D.; Carrasco, L.

    2017-07-01

    We present the near-infrared polarization observations towards the star forming molecular cloud associated with the IRAS source 18236-1205, obtained with the near-infrared (NIR) imaging polarimeter POLICAN at the Guillermo Haro Astrophysical Observatory in Cananea, Sonora, México.

  13. 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

  14. 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

  15. 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.

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

    PubMed

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

    2011-04-12

    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.

  17. 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

  18. 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

  19. Magnetic field morphology in nearby molecular clouds as revealed by starlight and submillimetre polarization

    NASA Astrophysics Data System (ADS)

    Soler, J. D.; Alves, F.; Boulanger, F.; Bracco, A.; Falgarone, E.; Franco, G. A. P.; Guillet, V.; Hennebelle, P.; Levrier, F.; Martin, P. G.; Miville-Deschênes, M.-A.

    2016-12-01

    Within four nearby (d < 160 pc) molecular clouds, we statistically evaluated the structure of the interstellar magnetic field, projected on the plane of the sky and integrated along the line of sight, as inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz and from the optical and near-infrared polarization of background starlight. We compared the dispersion of the field orientation directly in vicinities with an area equivalent to that subtended by the Planck effective beam at 353 GHz (10') and using the second-order structure functions of the field orientation angles. We found that the average dispersion of the starlight-inferred field orientations within 10'-diameter vicinities is less than 20°, and that at these scales the mean field orientation is on average within 5° of that inferred from the submillimetre polarization observations in the considered regions. We also found that the dispersion of starlight polarization orientations and the polarization fractions within these vicinities are well reproduced by a Gaussian model of the turbulent structure of the magnetic field, in agreement with the findings reported by the Planck Collaboration at scales ℓ > 10' and for comparable column densities. At scales ℓ > 10', we found differences of up to 14.̊7 between the second-order structure functions obtained from starlight and submillimetre polarization observations in the same positions in the plane of the sky, but comparison with a Gaussian model of the turbulent structure of the magnetic field indicates that these differences are small and are consistent with the difference in angular resolution between both techniques. The differences between the second-order structure functions calculated with each technique suggests that the increase in the angular resolution obtained with the starlight polarization observations does not introduce significant corrections to the dispersion of polarization orientations used in the

  20. 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.

  1. 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.

  2. Atomistic study on dithiolated oligo-phenylenevinylene gated device

    SciTech Connect

    Mahmoud, Ahmed Lugli, Paolo

    2014-11-28

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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

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

    PubMed Central

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

    2013-01-01

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

  9. 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.

  10. 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.

  11. Macroscopic Polarization Enhancement Promoting Photo- and Piezoelectric-Induced Charge Separation and Molecular Oxygen Activation.

    PubMed

    Huang, Hongwei; Tu, Shuchen; Zeng, Chao; Zhang, Tierui; Reshak, Ali H; Zhang, Yihe

    2017-09-18

    Efficient photo- and piezoelectric-induced molecular oxygen activation are both achieved by macroscopic polarization enhancement on a noncentrosymmetric piezoelectric semiconductor BiOIO3 . The replacement of V(5+) ions for I(5+) in IO3 polyhedra gives rise to strengthened macroscopic polarization of BiOIO3 , which facilitates the charge separation in the photocatalytic and piezoelectric catalytic process, and renders largely promoted photo- and piezoelectric induced reactive oxygen species (ROS) evolution, such as superoxide radicals ((.) O2(-) ) and hydroxyl radicals ((.) OH). This work advances piezoelectricity as a new route to efficient ROS generation, and also discloses macroscopic polarization engineering on improvement of multi-responsive catalysis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. 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.

  13. 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.

  14. Nonadiabatic molecular high-order harmonic generation from polar molecules: Spectral redshift

    SciTech Connect

    Bian Xuebin; Bandrauk, Andre D.

    2011-04-15

    Molecular high-order harmonic generation (MHOHG) from the polar diatomic molecule HeH{sup 2+} in short intense laser fields is studied numerically. Due to the nonadiabatic response of the molecular dipole to the rapid change of laser intensity, a spectral redshift is predicted in high-intensity and ultrashort laser pulses, contrary to the blueshift observed in the harmonics generated from atoms in long laser pulses. The MHOHG temporal structures are investigated by a wavelet time-frequency analysis, which shows that the enhanced excitation of localized long lifetime excited states shifts the harmonic generation spectrum in the falling part of short laser pulses, due to the presence of a permanent dipole moment, and thus is unique to polar molecules.

  15. Evaluation of electronic polarization energy in oligoacene molecular crystals using the solvated supermolecular approach.

    PubMed

    Xu, Tao; Wang, Wenliang; Yin, Shiwei; Wang, Yun

    2017-06-07

    The solvated supermolecular approach, i.e., block-localized wave function coupled with polarizable continuum model (BLW/PCM), was proposed to calculate molecular ionization potential (IP), electron affinity (EA) in the solid phase, and related electronic polarization. Via the calculations of a solvated supermolecule (5M), including four closest molecules, BLW/PCM overcomes the limitation in the calculation for the monomer PCM, that is, nearly same electronic polarization for cation (P+) and anion (P-). The solvated supermolecular approach successfully described asymmetric behaviors of P+ and P- for oligoacene crystals. In addition, we also compared two charge-localized methods, i.e., BLW and constrained density functional theory (CDFT), to calculate the molecular IP and EA in supermolecules with/without PCM. Our results demonstrate that both the BLW and CDFT correctly estimate the EA and IP values in the gas phase cluster, whereas CDFT/PCM fails to evaluate the P- value of the bulk system.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2016-01-20

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

  3. Long-Timescale Molecular-Dynamics Simulations of the Major Urinary Protein Provide Atomistic Interpretations of the Unusual Thermodynamics of Ligand Binding

    PubMed Central

    Roy, Julie; Laughton, Charles A.

    2010-01-01

    Abstract The mouse major urinary protein (MUP) has proved to be an intriguing test bed for detailed studies on protein-ligand recognition. NMR, calorimetric, and modeling investigations have revealed that the thermodynamics of ligand binding involve a complex interplay between competing enthalpic and entropic terms. We performed six independent, 1.2 μs molecular-dynamics simulations on MUP—three replicates on the apo-protein, and three on the complex with the pheromone isobutylmethoxypyrazine. Our findings provide the most comprehensive picture to date of the structure and dynamics of MUP, and how they are modulated by ligand binding. The mechanical pathways by which amino acid side chains can transmit information regarding ligand binding to surface loops and either increase or decrease their flexibility (entropy-entropy compensation) are identified. Dewetting of the highly hydrophobic binding cavity is confirmed, and the results reveal an aspect of ligand binding that was not observed in earlier, shorter simulations: bound ligand retains extensive rotational freedom. Both of these features have significant implications for interpretations of the entropic component of binding. More generally, these simulations test the ability of current molecular simulation methods to produce a reliable and reproducible picture of protein dynamics on the microsecond timescale. PMID:20655850

  4. 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

  5. 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.

  6. 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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  9. 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.

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

    NASA Technical Reports Server (NTRS)

    Illing, R. M. E.

    1981-01-01

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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

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

    PubMed Central

    2017-01-01

    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. PMID:28167767

  19. 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.

  20. 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.

  1. 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.

  2. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

    NASA Astrophysics Data System (ADS)

    Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida

    2009-06-01

    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.

  3. 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

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

    PubMed

    Feng, Shiliang; Zhu, Weiping

    2014-12-21

    Chemotacting eukaryotic cells can sense shallow gradients of chemoattractants and respond by assuming an asymmetric shape with well-defined front and back regions. Such a striking polarization phenomenon is produced largely through the interconversions and interactions between several cellular components, including Rac GTPase (Rac), phosphoinositide 3-kinase (PI3K), tensin homology protein (PTEN), phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2). Here, we developed a mathematical model of cell polarization by exploring bidirectional molecular transport that arose from phosphoinositides (PIs) and Rac-mediated feedback loops. We assumed a static gradient of activated Rac derived from an external signal field as the internal trigger signal. The evolution of PI(3,4,5)P3 and PI(4,5)P2 along with PI3K and PTEN that act as activator and inhibitor, respectively, were described by a pair of coupled transient reaction-diffusion equations. The entire system was solved using a Lattice-Boltzmann method with an embedded Monte-Carlo method to track the stochastic translocation behaviors of discrete PI3K/PTEN molecules. We first showed that, upon a graded external stimulus, the Rac to PI(3,4,5)P3 cascade exhibited a short range positive-feedback loop, while the PTEN to PI(4,5)P2 cascade contributed another long range negative-feedback loop, which dominated the "forward" and "backward" molecular transport, respectively. Second, polarization was governed by the ratio of [PI3K] to [PTEN], and manifested a switch-like behavior. Third, with a uniform stimulus, spontaneous polarization could occur in PTEN-deficient cells. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Constrained Molecular Dynamics Modeling of Dielectric Response in Polar Polyethylene Analogs and Poly(vinylidene flouride)

    NASA Astrophysics Data System (ADS)

    Calame, Jeffrey

    2013-03-01

    A simplified molecular dynamics formalism for polymers, having united atoms with constrained bond lengths and bond angles along the backbone but allowing torsional motion, has been developed to model the dielectric response and ferroelectricity in polymers with permanent dipoles. Analytic relations existing on the backbone geometry and associated dihedral motion allow elimination of many dot and cross product evaluations. Also, constraint error correcting forces, symplectic integration with velocity prediction, random force excitation with damping and a momentum-conserving thermostat, and rapid neighbor list and long range force computation allow efficient computation and time steps as large as 20 fs to enable the study of relatively long time scale dielectric phenomena. Studies are performed on non-polar polyethylene for benchmarking, followed by a model system (polar polyethylene) which retains the molecular structure, dihedral potentials, and non-bonded interactions of polyethylene, except artificial partial charges are placed on the united atoms. The modeling is extended to poly(vinylidene fluoride) by changes to the molecular structure, potentials, and charges. Heterogeneous systems containing crystalline and amorphous arrangements of polymer chains are studied. Work supported by the U.S. Office of Naval Research.

  6. Determination of three-dimensional molecular orientation of type-I collagen by circularly-polarized second harmonic generation imaging

    NASA Astrophysics Data System (ADS)

    Zhuo, Guan-Yu; Hung, Wei-Han; Kao, Fu-Jen

    2017-04-01

    The content of collagen is up to 30% existing in mammals. It supports the main component of connective tissues such as skin, ligament, and cartilage. Among various types of collagen, type-I collagen is of the most abundance and has been broadly studied due to the importance in bioscience. Second harmonic generation (SHG) microscopy is an effective tool used to study the collagen organization without labeling. In this study, we used circular polarization instead of linear polarization to retrieve three-dimensional (3D) molecular orientation of type-I collagen with only two cross polarized SHG images without acquiring an image stack of varying polarization.

  7. 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.

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

    SciTech Connect

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

    2004-04-15

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

  9. Using polarized Raman spectroscopy and the pseudospectral method to characterize molecular structure and function

    NASA Astrophysics Data System (ADS)

    Weisman, Andrew L.

    Electronic structure calculation is an essential approach for determining the structure and function of molecules and is therefore of critical interest to physics, chemistry, and materials science. Of the various algorithms for calculating electronic structure, the pseudospectral method is among the fastest. However, the trade-off for its speed is more up-front programming and testing, and as a result, applications using the pseudospectral method currently lag behind those using other methods. In Part I of this dissertation, we first advance the pseudospectral method by optimizing it for an important application, polarized Raman spectroscopy, which is a well-established tool used to characterize molecular properties. This is an application of particular importance because often the easiest and most economical way to obtain the polarized Raman spectrum of a material is to simulate it; thus, utilization of the pseudospectral method for this purpose will accelerate progress in the determination of molecular properties. We demonstrate that our implementation of Raman spectroscopy using the pseudospectral method results in spectra that are just as accurate as those calculated using the traditional analytic method, and in the process, we derive the most comprehensive formulation to date of polarized Raman intensity formulas, applicable to both crystalline and isotropic systems. Next, we apply our implementation to determine the orientations of crystalline oligothiophenes -- a class of materials important in the field of organic electronics -- achieving excellent agreement with experiment and demonstrating the general utility of polarized Raman spectroscopy for the determination of crystal orientation. In addition, we derive from first-principles a method for using polarized Raman spectra to establish unambiguously whether a uniform region of a material is crystalline or isotropic. Finally, we introduce free, open-source software that allows a user to determine any of a

  10. 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.

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

    SciTech Connect

    Habasaki, Junko; Ngai, K. L.

    2015-04-28

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

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

    PubMed

    Habasaki, Junko; Ngai, K L

    2015-04-28

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

  13. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces.

    PubMed Central

    Nordgren, C E; Tobias, D J; Klein, M L; Blasie, J K

    2002-01-01

    We present a collection of molecular dynamics computer simulation studies on a model protein-membrane system, namely a cytochrome c monolayer attached to an organic self-assembled monolayer (SAM). Modifications of the system are explored, including the polarity of the SAM endgroups, the amount of water present for hydration, and the coordination number of the heme iron atom. Various structural parameters are measured, e.g., the protein radius of gyration and eccentricity, the deviation of the protein backbone from the x-ray crystal structure, the orientation of the protein relative to the SAM surface, and the profile structures of the SAM, protein, and water. The polar SAM appears to interact more strongly with the protein than does the nonpolar SAM. Increased hydration of the system tends to reduce the effects of other parameters. The choice of iron coordination model has a significant effect on the protein structure and the heme orientation. The overall protein structure is largely conserved, except at each end of the sequence and in one loop region. The SAM structure is only perturbed in the region of its direct contact with the protein. Our calculations are in reasonably good agreement with experimental measurements (polarized optical absorption/emission spectroscopy, x-ray interferometry, and neutron interferometry). PMID:12496067

  14. 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.

  15. 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.

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

    NASA Technical Reports Server (NTRS)

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

    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.

  17. 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.

  18. Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids.

    PubMed

    Thomas, Jason C; Rowley, Richard L

    2011-01-14

    A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.

  19. 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.

  20. 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.

  1. 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.

  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. Control of polarity of ZnO films grown by plasma-assisted molecular-beam epitaxy: Zn- and O-polar ZnO films on Ga-polar GaN templates

    NASA Astrophysics Data System (ADS)

    Hong, Soon-Ku; Hanada, Takashi; Ko, Hang-Ju; Chen, Yefan; Yao, Takafumi; Imai, Daisuke; Araki, Kiyoaki; Shinohara, Makoto

    2000-11-01

    We report on the growth of polarity-controlled ZnO films by plasma-assisted molecular-beam epitaxy. Different polar (Zn- and O-polar) ZnO films on unipolar (Ga-polar) GaN epilayers are selectively grown. Polarity of ZnO films is evaluated by coaxial impact collision ion scattering spectroscopy. Zn preexposure prior to ZnO growth results in Zn-polar ZnO films (Zn face), while O-plasma preexposure leads to the growth of O-polar ZnO films (O face). High-resolution transmission electron microscopy reveals the formation of an interface layer between ZnO and GaN epilayers in O-plasma preexposed samples, while no interface layer is observed in Zn preexposed samples. The interface layer is identified as single crystalline, monoclinic Ga2O3. We propose models for interface configurations at ZnO/GaN heterointerfaces, which can successfully explain the different polarities of the ZnO films.

  6. 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

  7. 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.

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

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

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

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

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

  10. 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

  11. 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.

  12. Directional melting of alumina via polarized microwave heating

    NASA Astrophysics Data System (ADS)

    Hu, Yuan; Nakano, Aiichiro; Wang, Joseph

    2017-01-01

    Dynamical instabilities and melting of crystals upon heating are fundamental problems in physics and materials science. Using molecular dynamics simulations, we found that drastically different melting temperatures and behaviors can be achieved in α-alumina using microwave heating, where the electric field is aligned with different crystallographic orientations. Namely, alumina melts much earlier at lower temperatures when the electric field is parallel to the c-axis. The atomistic mechanism was identified as selective liberation of the Al sublattice due to the shear instability along the c-axis. This directional melting concept may be used for triggering distinct dynamical instabilities and melting of dielectric crystals using polarized microwave fields.

  13. Single-crystal N-polar GaN p-n diodes by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Cho, YongJin; Hu, Zongyang; Nomoto, Kazuki; Xing, Huili Grace; Jena, Debdeep

    2017-06-01

    N-polar GaN p-n diodes are realized on single-crystal N-polar GaN bulk wafers by plasma-assisted molecular beam epitaxy growth. The current-voltage characteristics show high-quality rectification and electroluminescence characteristics with a high on currents ˜10 kA/cm2, low off currents <10-5 A/cm2, on/off current ratio of >109, and interband photon emission. The measured electroluminescence spectrum is dominated by a strong near-band edge emission, while deep level luminescence is greatly suppressed. A very low dislocation density leads to a high reverse breakdown electric field of ˜2.2 MV/cm without fields plates—the highest reported for N-polar epitaxial structures. The low leakage current N-polar diodes open up several potential applications in polarization-engineered photonic and electronic devices.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Anisotropic solid-liquid interface kinetics in silicon: an atomistically informed phase-field model

    NASA Astrophysics Data System (ADS)

    Bergmann, S.; Albe, K.; Flegel, E.; Barragan-Yani, D. A.; Wagner, B.

    2017-09-01

    We present an atomistically informed parametrization of a phase-field model for describing the anisotropic mobility of liquid-solid interfaces in silicon. The model is derived from a consistent set of atomistic data and thus allows to directly link molecular dynamics and phase field simulations. Expressions for the free energy density, the interfacial energy and the temperature and orientation dependent interface mobility are systematically fitted to data from molecular dynamics simulations based on the Stillinger-Weber interatomic potential. The temperature-dependent interface velocity follows a Vogel-Fulcher type behavior and allows to properly account for the dynamics in the undercooled melt.

  19. Atomistic simulations of high strain rate loading of nanocrystals

    NASA Astrophysics Data System (ADS)

    Bringa, E. M.; Tramontina, D.; Ruestes, C. J.; Tang, Y.; Meyers, M. A.; Gunkelmann, N.; Urbassek, H. M.

    2013-03-01

    Materials loaded at high strain rates can reach extreme temperature and pressure conditions. Most experiments on loading of simple materials use poly crystals, while most atomistic simulations of shock wave loading deal with single crystals, due to the higher computational cost of running polycrystal samples. Of course, atomistic simulations of polycrystals with micron-sized grains are beyond the capabilities of current supercomputers. On the other hand, nanocrystals (nc) with grain sizes below 50 nm can be obtained experimentally and modeled reasonably well at high strain rates, opening the possibility of nearly direct comparison between atomistic molecular dynamics (MD) simulations and experiments using high power lasers. We will discuss MD simulations and links to experiments for nc Cu and Ni, as model f.c.c. solids, and nc Ta and Fe, as model b.c.c. solids. In all cases, the microstructure resulting from loading depends strongly on grain size, strain rate and peak applied pressure. We will also discuss effects related to target porosity in nc's. E.M.B. thanks funding from PICT2008-1325.

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

    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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. One-loop vacuum polarization at m α7 and higher orders for three-body molecular systems

    NASA Astrophysics Data System (ADS)

    Karr, J.-Ph.; Hilico, L.; Korobov, Vladimir I.

    2017-04-01

    We present calculations of the one-loop vacuum polarization correction (Uehling potential) for the three-body problem in the NRQED formalism. The case of one-electron molecular systems is considered. Numerical results of the vacuum polarization contribution at m α7 and higher orders for the fundamental transitions (v =0 , L =0 )→( v'=1 , L'=0 ) in the H2+ and HD+ molecular ions are presented and compared with calculations performed in the adiabatic approximation. The residual uncertainty from this contribution in the transition frequencies is shown to be a few tens of Hz.

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

    PubMed

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

    2015-09-01

    Due to specific structural organization at the molecular level, several biomolecules (e.g., collagen, myosin etc.) which are strong generators of second harmonic generation (SHG) signals, exhibit unique responses depending on the polarization of the excitation light. By using the polarization second harmonic generation (p-SHG) technique, the values of the second order susceptibility components can be used to differentiate the types of molecule, which cannot be done by the use of a standard SHG intensity image. In this report we discuss how to implement p-SHG on a commercial multiphoton microscope and overcome potential artifacts in susceptibility (χ) image. Furthermore we explore the potential of p-SHG microscopy by applying the technique to different types of tissue in order to determine corresponding reference values of the ratio of second-order χ tensor elements. These values may be used as a bio-marker to detect any structural alterations in pathological tissue for diagnostic purposes. The SHG intensity image (red) in (a) shows the distribution of collagen fibers in ovary tissue but cannot determine the type of collagen fiber. However, the histogram distribution (b) for the values of the χ tensor element ratio can be used to quantitatively identify the types of collagen fibers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective.

    PubMed

    Stachowicz, Anna; Rogalski, Marek; Korchowiec, Jacek

    2013-10-01

    Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of β-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born-Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Atomistic study of boron-doped silicon

    SciTech Connect

    Fearn, M.; Pettifor, D.G.; Jefferson, J.H.

    1996-12-31

    Atomistic simulations using both tight-binding and density-functional approaches have been performed to investigate boron-related defects in silicon. In agreement with experiment, the boron interstitial is shown to be a negative-U center in the sense that its neutral charge state, with an associated Jahn-Teller distortion off the ideal tetrahedral site, is never the ground state for any value of the chemical potential in the gap. The possible consequences for an electron-assisted migration of the interstitial are discussed. The authors also find the boron substitutional defect to be a next-nearest neighbor of a silicon vacancy in agreement with EPR spectra. A semi-empirical tight-binding model of the boron-silicon system is validated by direct comparison with the accurate density-functional results and is then used to perform molecular dynamics simulations of boron diffusion at high temperatures. The mobility of the interstitial is found to be strongly charge-state dependent. Termination of the boron interstitial migration path by recombination with a silicon vacancy is shown to be a very likely process with a number of configurations having no barrier to capture when the boron is a near-neighbor of the vacancy.

  13. 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.

  14. 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

  15. Connecting Atomistic and Continuous Models of Elastodynamics

    NASA Astrophysics Data System (ADS)

    Braun, Julian

    2017-06-01

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. Atomistic Simulations of Bicelle Mixtures

    PubMed Central

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Abstract Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C10 tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of ∼3 nm−1. The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets. PMID:20550902

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

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

  11. Lattice-gas model for active vesicle transport by molecular motors with opposite polarities

    NASA Astrophysics Data System (ADS)

    Muhuri, Sudipto; Pagonabarraga, Ignacio

    2010-08-01

    We introduce a multispecies lattice-gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargos being carried by oppositely directed molecular motors, moving on a single biofilament. Building on a totally asymmetric exclusion process to characterize the motion of the interacting cargos, we allow for mass exchange with the environment, input, and output at filament boundaries and focus on the role of interconversion rates and how they affect the directionality of the net cargo transport. We quantify the effect of the various different competing processes in terms of nonequilibrium phase diagrams. The interplay of interconversion rates, which allow for flux reversal and evaporation-deposition processes, introduces qualitatively unique features in the phase diagrams. We observe regimes of three-phase coexistence, the possibility of phase re-entrance, and a significant flexibility in how the different phase boundaries shift in response to changes in control parameters. The moving steady-state solutions of this model allows for different possibilities for the spatial distribution of cargo vesicles, ranging from homogeneous distribution of vesicles to polarized distributions, characterized by inhomogeneities or shocks. Current reversals due to internal regulation emerge naturally within the framework of this model. We believe that this minimal model will clarify the understanding of many features of collective vesicle transport, apart from serving as the basis for building more exact quantitative models for vesicle transport relevant to various in vivo situations.

  12. Molecular Memory of Morphologies by Septins during Neuron Generation Allows Early Polarity Inheritance.

    PubMed

    Boubakar, Leila; Falk, Julien; Ducuing, Hugo; Thoinet, Karine; Reynaud, Florie; Derrington, Edmund; Castellani, Valérie

    2017-08-16

    Transmission of polarity established early during cell lineage history is emerging as a key process guiding cell differentiation. Highly polarized neurons provide a fascinating model to study inheritance of polarity over cell generations and across morphological transitions. Neural crest cells (NCCs) migrate to the dorsal root ganglia to generate neurons directly or after cell divisions in situ. Using live imaging of vertebrate embryo slices, we found that bipolar NCC progenitors lose their polarity, retracting their processes to round for division, but generate neurons with bipolar morphology by emitting processes from the same locations as the progenitor. Monitoring the dynamics of Septins, which play key roles in yeast polarity, indicates that Septin 7 tags process sites for re-initiation of process growth following mitosis. Interfering with Septins blocks this mechanism. Thus, Septins store polarity features during mitotic rounding so that daughters can reconstitute the initial progenitor polarity. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. 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.

  14. Atomistic simulations of bicelle mixtures.

    PubMed

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets. (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Atomistic modeling of dropwise condensation

    SciTech Connect

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

    2016-05-23

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

  16. Atomistic modeling of dropwise condensation

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  17. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Zavadlav, Julija; Praprotnik, Matej

    2017-09-01

    Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

  18. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics.

    PubMed

    Zavadlav, Julija; Praprotnik, Matej

    2017-09-21

    Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

  19. Heterogeneous Atomistic-Continuum Methods for Dense Fluid Systems

    NASA Astrophysics Data System (ADS)

    Hadjiconstantinou, Nicolas; Patera, Anthony

    1997-08-01

    We present new results obtained using the formulation and numerical solution procedure for heterogeneous atomistic--continuum representations of fluid flows presented in [1]. The ingredients are, from the atomistic side, non-equilibrium molecular dynamics, and from the continuum side, finite element solution; the matching is provided by a classical procedure, the Schwarz alternating method with overlapping subdomains. The technique is applied to the flow of two immiscible fluids in a microscale channel. The problem "presents" a particular modelling challenge because of the stress singularity at the moving contact line which is usually relieved through ad hoc methods, the most popular of which is the assumption of slip close to the contact line. The Heterogeneous method properly addresses the problem by treating the region near the contact line with molecular dynamics. References 1. Hadjiconstantinou N., Patera, A.T., Proceedings of the Sixth International Conference on Discrete Models for Fluid Mechanics, To appear as a special edition of the International Journal of Modern Physics C.

  20. Coarse graining atomistic simulations of plastically deforming amorphous solids

    NASA Astrophysics Data System (ADS)

    Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

    2017-05-01

    The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  2. 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.

  3. Growth, Structural, and Electrical Characterizations of N-Polar InAlN by Plasma-Assisted Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Dasgupta, Sansaptak; Nidhi; Choi, Soojeong; Wu, Feng; Speck, James S.; Mishra, Umesh K.

    2011-04-01

    N-polar InxAl1-xN (0.02 < x < 0.65) films were grown and characterized by plasma-assisted molecular beam epitaxy (PAMBE). Indium incorporation in the films was characterized both as a function of the impinging In and Al flux and the growth temperature. In incorporation in the film was found to decrease with increasing growth temperature (Tgr) for Tgr > 560 °C. A smooth surface morphology was obtained for In0.18Al0.82N lattice-matched to GaN. Subsequently, N-polar In0.18Al0.82N was used as a charge-inducing barrier in a N-polar GaN HEMT structure and electrical characterizations including current-voltage (I-V) measurements were performed.

  4. Growth and Characterization of N-Polar GaN Films on Si(111) by Plasma Assisted Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Dasgupta, Sansaptak; Nidhi; Wu, Feng; Speck, James S.; Mishra, Umesh K.

    2012-11-01

    Smooth N-polar GaN films were epitaxially grown by plasma assisted molecular beam epitaxy (PAMBE) on on-axis p-Si(111). The structural quality of the as-grown GaN films was further improved by insertion of AlGaN/GaN superlattice structures, resulting in reduced threading dislocation density and also efficient stress management in the GaN film to mitigate crack formation. The structural quality of these films was comparable to N-polar GaN grown on C-SiC by MBE. Convergent beam electron diffraction (CBED) imaging and KOH etch studies were performed to confirm the N-polarity of the sample. Room temperature photoluminescence measurements revealed strong GaN band-edge emission.

  5. 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.

  6. 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

  7. 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

  8. 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.

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

    PubMed

    Li, Xianfeng; Latour, Robert A

    2009-07-31

    A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 10(2), thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications.

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

    SciTech Connect

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

    2014-10-21

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

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

    PubMed

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

    2014-10-21

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

  12. 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

  13. Ultrafast molecular photoionization by two-color orthogonally polarized ultraviolet laser pulses: Effects of relative pulse phases

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

    We present molecular photoionization by two-color 2ω1 =ω2 orthogonally polarized ultraviolet laser pulses. Simulations are performed on aligned H+ by numerically solving time-dependent Schrödinger equations. Two ionization processes with one ω2 photon interfering with two ω1 photon absorption are studied at different molecular alignments. Molecular frame photoelectron momentum and angular distributions exhibit asymmetries which are functions of the relative pulse phase. For resonant excitation processes by the ω1 pulse, symmetric distributions are obtained. An attosecond ionization model is adopted to describe the ultrafast ionization dynamics. The dependence of the ionization asymmetry on the molecular alignment allows to further monitor interference effects on orbital symmetry.

  14. 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

  15. A 3D model for carbon monoxide molecular line emission as a potential cosmic microwave background polarization contaminant

    NASA Astrophysics Data System (ADS)

    Puglisi, G.; Fabbian, G.; Baccigalupi, C.

    2017-08-01

    We present a model for simulating carbon monoxide (CO) rotational line emission in molecular clouds, taking account of their 3D spatial distribution in galaxies with different geometrical properties. The model implemented is based on recent results in the literature and has been designed for performing Monte Carlo (MC) simulations of this emission. We compare the simulations produced with this model and calibrate them, both on the map and the power spectrum levels, using the second release of data from the Planck satellite for the Galactic plane, where the signal-to-noise ratio is highest. We use the calibrated model to extrapolate the CO power spectrum at low Galactic latitudes where no high sensitivity observations are available yet. We then forecast the level of unresolved polarized emission from CO molecular clouds which could contaminate the power spectrum of cosmic microwave background polarization B modes away from the Galactic plane. Assuming realistic levels of the polarization fraction, we show that the level of contamination is equivalent to a cosmological signal with r ≲ 0.02. The MC MOlecular Line Emission (mcmole3d) python package, which implements this model, is being made publicly available.

  16. 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.

  17. Three-dimensional Ising model of polarity formation in molecular crystals

    NASA Astrophysics Data System (ADS)

    Cannavacciuolo, Luigi; Hulliger, Jürg

    2017-10-01

    Polarity formation in a three-dimensional array of molecules is described as a symmetry breaking effect of a generalized Ising Hamiltonian. Geometrical constraints in conjunction with asymmetric multipole interactions are able to break the spin flip symmetry generating a non-vanishing average local polarization.

  18. Literature review report on atomistic modeling tools for FeCrAl alloys

    SciTech Connect

    Yongfeng Zhang; Daniel Schwen; Enrique Martinez

    2015-12-01

    This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing for better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    SciTech Connect

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

    2007-01-12

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

  4. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    SciTech Connect

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

    2005-12-31

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

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

    NASA Astrophysics Data System (ADS)

    Sen, Fatih Gurcag

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

  6. 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

  7. Molecular diffusion of stable water isotopes in polar firn as a proxy for past temperatures

    NASA Astrophysics Data System (ADS)

    Holme, Christian; Gkinis, Vasileios; Vinther, Bo

    2017-04-01

    Polar precipitation archived in ice caps contains information on past temperature conditions. Such information can be retrieved by measuring the water isotopic signals of δ{}18O and δD in ice cores. These signals have been attenuated during densification due to molecular diffusion in the firn column, where the magnitude of the diffusion is isotopologoue specific and temperature dependent. By utilizing the differential diffusion signal, dual isotope measurements of δ{}18O and δD enable multiple temperature reconstruction techniques. This study assesses how well six different methods can be used to reconstruct past surface temperatures from the diffusion-based temperature proxies. Two of the methods are based on the single diffusion lengths of δ{}18O and δD, three of the methods employ the differential diffusion signal, while the last uses the ratio between the single diffusion lengths. All techniques are tested on synthetic data in order to evaluate their accuracy and precision. In addition, a benchmark test is applied to thirteen high resolution data sets from Greenland and Antarctica, which represent a broad range of mean annual surface temperatures and accumulation rates. The presented methods are found to accurately reconstruct the temperatures of the synthetic data, and the estimated temperatures are shown to be unbiased. Both the benchmark test and the synthetic data test demonstrate that the most precise reconstructions are obtained when using the single isotope diffusion lengths, with precisions around 0.5 ^oC. In the benchmark test, the single isotope diffusion lengths are also found to reconstruct consistent temperatures with a root-mean-square-deviation of 0.7 ^oC. The techniques employing the differential diffusion signals are more uncertain, where the most precise method has a precision of 1.5 ^oC. The diffusion length ratio method is the least precise with a precision of 11.8 ^oC. The absolute temperature estimates from this method are also shown

  8. Photoionization of triatomic molecular ions {{\\rm{H}}}_{3}^{2+} by intense bichromatic circularly polarized attosecond UV laser pulses

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

    Photoionization of triatomic molecular ions has been studied for triangular and linear geometries by bichromatic circularly polarized attosecond UV laser pulses at frequencies {ω }2=2{ω }1. Simulations are performed on the single electron molecule {{{H}}}32+ by numerically solving time-dependent Schrödinger equations. We measure molecular frame photoelectron momentum distributions (MFPMDs), which show spiral electron vortex patterns as functions of the helicity of the pulse and the molecular geometry. The ionization interference effects arise from multi-pathway ionization, which give rise to the modulation of multi-center photoelectron spectra. We describe these phenomena in MFPMDs based on an ultrafast delta-function ionization model and attosecond perturbation ionization theory. Interference patterns in MFPMDs reflect the helicity and symmetry of the electric fields in the attosecond ionizing pulses.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  11. 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.

  12. 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.

  13. 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

  14. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  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. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Polarization transfer kinetics in a binary system of molecular luminescense centers in nanopores with a liquid crystal filler

    NASA Astrophysics Data System (ADS)

    Kucherenko, M. G.; Palem, A. A.

    2008-04-01

    We have studied the anisotropic activated luminescence of molecular centers introduced into spherical nanopores filled with a nematic liquid crystal possessing a homeotropic texture. The kinetics of the anisotropy of emission from these centers is traced during selective pulsed activation of the donor subsystem by a linearly polarized light in the case where the long-range nonradiative transfer of the electron excitation energy to the acceptor molecules takes place in a radially aligned two-component luminescent system. A theoretical model is proposed that takes into account the migration of excitations over the system of donor centers. Dependences of the kinetics of the anisotropy of acceptor luminescence on the nanopore radius, the Förster transfer rate, and some other parameters have been determined. A change in the sign of polarization of the activated luminescence signal has been observed.

  19. Hydrophobic tendencies of polar groups as a major force in molecular recognition.

    PubMed

    Chalikian, Tigran V

    2003-12-01

    Proteins and nucleic acids are able to adopt their native conformation and perform their biological role only in the presence of water with which they actively interact in a mutually modifying way. Traditionally, hydrophobic effect has been considered to be the major factor stabilizing biopolymeric structures. However, solvent reorganization around polar groups is an event thermodynamically more unfavorable than solvent reorganization around nonpolar groups. Consequently, burial of polar groups with formation of complementary solute-solute hydrogen bonds out of contact with water is an energetically favorable process that also provides a major force driving macromolecular association and folding. In contrast to nonpolar groups, polar groups may form their complementary intra- or intersolute hydrogen bonds out of contact with water only provided that an appropriate solute structure has been formed with properly positioned hydrogen bond donors and acceptors. Formation of such structures is disfavored entropically and may not be possible due to steric reasons. However, the interior of a folded protein, alpha-helices and beta-sheets, double helical nucleic acid structures, and protein-ligand interfaces all provide rigid matrices where polar groups may form their complementary hydrogen bonds. For these structures, the inward drive of polar groups represents a considerable stabilizing factor. Copyright 2003 Wiley Periodicals, Inc. Biopolymers 70: 492-496, 2003

  20. 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

  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. Identification of polar transformation products and high molecular weight polycyclic aromatic hydrocarbons (PAHs) in contaminated soil following bioremediation.

    PubMed

    Chibwe, Leah; Davie-Martin, Cleo L; Aitken, Michael D; Hoh, Eunha; Massey Simonich, Staci L

    2017-12-01

    Bioremediation is a technique commonly used to reduce the toxicity associated with polycyclic aromatic hydrocarbons (PAHs) in contaminated soils. However, the efficacy of bioremedial applications is evaluated based on the removal of a subset of parent (or unsubstituted) PAHs and does not incorporate toxic polar transformation products or the more mutagenic high molecular weight PAHs (MW≥302amu or MW302-PAHs). Previously, an effects-directed analysis approach was used to assess the effect of bioremediation on the toxicity of a coal tar-contaminated soil. Increased genotoxicity and developmental toxicity was measured postbioremedation in the more polar soil extract fractions, as compared to the less polar fractions where the targeted PAHs eluted, and could not be attributed to the 88 target PAHs analyzed for (including selected oxygen-containing PAHs). In this study, comprehensive two-dimensional gas chromatography time-of-flight and liquid chromatography quadrupole time-of-flight mass spectrometry were used to characterize transformation products in the soil extract fractions identified as toxic, previously. Additionally, the degradation of 12MW302-PAHs, picene (MW=278) and coronene (MW=300) were evaluated following bioremediation. Non-targeted analysis resulted in the tentative identification of 10 peaks with increased intensity postbioremediation (based on mass spectral library matching and fragmentation patterns from >5000 candidate peaks in the soil extracts). Several of these compounds contained oxygen, suggesting they would be relatively polar. MW302-PAHs were not significantly degraded during bioremediation, suggesting that the carcinogenic potential associated with these PAHs might remain unchanged. The results of this study suggest that polar transformation products, and MW302-PAHs, should be considered for realistic risk assessment of bioremediated soils. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2016-03-03

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

  7. 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.

  8. 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.

  9. Atomistic simulations of grain boundary migration in copper

    NASA Astrophysics Data System (ADS)

    Schönfelder, B.; Gottstein, G.; Shvindlerman, L. S.

    2006-06-01

    While the motion of twist boundaries can be readily studied by atomistic simulations with molecular dynamics (MD) under the action of an elastic driving force, the approach fails for tilt boundaries. This is due to the interaction of the elastic stress with the grain boundary (GB) structure, which causes plastic strain by GB sliding. A novel concept, the orientation correlated driving force, is introduced to circumvent this problem. It is shown that this concept can be successfully applied to the study of the migration of tilt boundaries. The migration behavior of several twist and tilt GBs was investigated. The transition from low-to high-angle boundaries can be captured, and a structural transition of tilt boundaries was found at high temperatures, which also affected the migration behavior. The results compare well with experimental results of the motion high-angle boundaries, but for low-angle boundaries, the agreement is poor.

  10. Atomistic Simulation of Dislocation-Defect Interactions in Cu

    SciTech Connect

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

    2001-01-01

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

  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. 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.

  13. 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.

  14. Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

    PubMed

    Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

    2017-05-04

    Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C1mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast

  15. Analysis of Molecular Orientation in Organic Semiconducting Thin Films Using Static Dynamic Nuclear Polarization Enhanced Solid-State NMR.

    PubMed

    Suzuki, Katsuaki; Kubo, Shosei; Aussenac, Fabien; Engelke, Frank; Fukushima, Tatsuya; Kaji, Hironori

    2017-10-09

    Molecular orientation in amorphous organic semiconducting thin film devices is an important issue affecting device performances. However, to date it has not been possible to analyze the "distribution" of the orientations. Although solid-state NMR (ssNMR) can provide information on the distribution of molecular orientations, the technique is limited because of the small amounts of sample in the devices and the low sensitivity of ssNMR. Here, we report the first application of dynamic nuclear polarization enhanced ssNMR (DNP-ssNMR) to orientational analysis of amorphous phenyldi(pyren-1-yl)phosphine oxide (POPy2). The 31P DNP-ssNMR spectra exhibited a sufficient signal-to-noise ratio to quantify the distribution of molecular orientations in amorphous films: the P=O axis of the vacuum-deposited and drop-cast POPy2 shows anisotropic and isotropic distribution, respectively. The different molecular orientations reflect the molecular origin of the different charge transport behaviors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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.

  17. 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.

  18. Simple non-fluorescent polarity labeling of microtubules for molecular motor assays.

    PubMed

    Soppina, Virupakshi; Rai, Arpan; Mallik, Roop

    2009-06-01

    Transport of intracellular organelles along the microtubule cytoskeleton occurs in a bidirectional manner due to opposing activity of microtubule-associated motor proteins of the kinesin and dynein families. Regulation of this opposing activity and the resultant motion is believed to generate a polarized distribution of many organelles within the cell. The bidirectional motion can be reconstituted on in vitro assembled microtubules using organelles extracted from cells. This provides an opportunity to understand the regulation of intracellular transport through quantitative analysis of the motion of organelles in a controlled environment. Such analysis requires the use of polarity-labeled microtubules to resolve the plus and minus components of bidirectional motion. However, existing methods of in vitro microtubule polarity labeling are unsuitable for high-resolution recording of motion. Here we present a simple and reliable method that uses avidin-coated magnetic beads to prepare microtubules labeled at the minus end. The microtubule polarity can be identified without any need for fluorescence excitation. We demonstrate video-rate high-resolution imaging of single cellular organelles moving along plus and minus directions on labeled microtubules. Quantitative analysis of this motion indicates that these organelles are likely to be driven by multiple dynein motors in vivo.

  19. 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.

  20. 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

  1. Atomistic evaluation of the stress concentration factor of graphene sheets having circular holes

    NASA Astrophysics Data System (ADS)

    Jalali, S. K.; Beigrezaee, M. J.; Pugno, N. M.

    2017-09-01

    Stress concentration factor concept has been developed for single-layered graphene sheets (SLGSs) with circular holes through an atomistic point of view by the application of molecular structural mechanics (MSM) approach. In this approach the response of SLGSs against unidirectional tensile loading is matched to the response of a frame-like macro structure containing beam elements by making an equivalence between strain energies of beam elements in MSM and potential energies of chemical bonds of SLGSs. Both chirality and size effects are considered and the atomistic evaluation of stress concentration factor is performed for different sizes of circular holes. Also, molecular dynamics simulations are implemented to verify the existence and location of the predicted stress concentration. The results reveal that size effects and the diameters of circular holes have a significant influence on the stress concentration factor of SLGSs and armchair SLGSs show a larger value of stress concentration than zigzag ones.

  2. 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.

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

    PubMed

    Zhou, Hua; Wang, Hui-Qiong; Liao, Xia-Xia; Zhang, Yufeng; Zheng, Jin-Cheng; Wang, Jia-Ou; Muhemmed, Emin; Qian, Hai-Jie; Ibrahim, Kurash; Chen, Xiaohang; Zhan, Huahan; Kang, Junyong

    2012-03-09

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

  4. Comprehensive molecular imaging of photolabile surface samples with synchronized dual-polarity time-of-flight mass spectrometry.

    PubMed

    Hsiao, Chih-Hao; Hong, Chia-Wei; Liu, Bo-Hong; Chen, Chiu Wen; Wu, Chih-Che; Wang, Yi-Sheng

    2011-04-15

    This work presents the unique features of a novel configuration of a synchronized dual-polarity time-of-flight mass spectrometer for comprehensive surface imaging. Mass spectrometry imaging of surface samples covering positive and negative ion modes is difficult due to rapid signal depletion. This limitation is overcome here by dual-polarity time-of-flight mass spectrometry (DP-TOFMS) via two separate TOF mass analyzers that are installed above a sample surface. The new instrument eliminates the polarity bias characteristic of most mass spectrometers, which is important for the analysis of samples with diverse physical and chemical properties. The experimental results show for the first time that the spatial distribution of positive and negative ions of various photolabile samples can be distinguished, including pigments and conventional matrix-assisted laser desorption/ionization samples. The different positive and negative ion distributions suggest that accurate quantitative information can only be obtained when the entire sample region is examined by DP-TOFMS, which was unfeasible in the past. Such a comprehensive diagnostic method is essential for the molecular imaging of trace compositions in delicate biological tissues, as demonstrated here with a Phyllanthus urinaria leaf that only produced ion signals in the first examination and not in the subsequent measurements. Copyright © 2011 John Wiley & Sons, Ltd.

  5. Molecular activation by surface coordination: New model for HCl reactivity on water-ice polar stratospheric clouds

    SciTech Connect

    MacTaylor, R.S.; Gilligan, J.J.; Moody, D.J.; Castleman, A.W. Jr.

    1999-05-27

    The annual depletion of the ozone layer in the polar stratosphere has received considerable scrutiny, particularly in the area of conversion chemistry involving chlorine. Numerous studies have implicated polar stratospheric clouds (PSCs) as playing a fundamental role in the conversion of reservoir chlorine species, such as HCl and ClONO{sub 2}, into active forms of chlorine such as Cl{sub 2} Results of studies of the uptake of HCl by the deuterated analogue of protonated water clusters are reported. The successive uptake of nHCl n = 1--4 is observed, n = 2--4 appearing in a stepwise manner with a ratio of 6:1 D{sub 2}O/HCl for the bimolecular reaction products. This primary uptake scheme is observed over a range of pressures and temperatures. However, for increased flows of HCl, enhanced uptake is observed at a lower ratio of D{sub 2}O/HCl, a trend that is effected by an increased buffer gas pressure. Two distinctly dominant mechanisms of HCl uptake are operative: the bimolecular uptake of HCl in a 6:1 ratio with water and a subsequent association mechanism of HCl binding to water in a 3:1 ratio. The atmospheric implications are discussed along with a proposed molecular activation by surface coordination (MASC) model for HCl uptake and subsequent reactivity on polar stratospheric clouds.

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

    PubMed Central

    Remko, Milan; Remková, Anna; Broer, Ria

    2016-01-01

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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Polar Side Chains Enhance Processability, Electrical Conductivity, and Thermal Stability of a Molecularly p-Doped Polythiophene.

    PubMed

    Kroon, Renee; Kiefer, David; Stegerer, Dominik; Yu, Liyang; Sommer, Michael; Müller, Christian

    2017-06-01

    Molecular doping of organic semiconductors is critical for optimizing a range of optoelectronic devices such as field-effect transistors, solar cells, and thermoelectric generators. However, many dopant:polymer pairs suffer from poor solubility in common organic solvents, which leads to a suboptimal solid-state nanostructure and hence low electrical conductivity. A further drawback is the poor thermal stability through sublimation of the dopant. The use of oligo ethylene glycol side chains is demonstrated to significantly improve the processability of the conjugated polymer p(g4 2T-T)-a polythiophene-in polar aprotic solvents, which facilitates coprocessing of dopant:polymer pairs from the same solution at room temperature. The use of common molecular dopants such as 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) is explored. Doping of p(g4 2T-T) with F4TCNQ results in an electrical conductivity of up to 100 S cm(-1) . Moreover, the increased compatibility of the polar dopant F4TCNQ with the oligo ethylene glycol functionalized polythiophene results in a high degree of thermal stability at up to 150 °C. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

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

    SciTech Connect

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

    2011-09-01

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

  20. 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.

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

    PubMed

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

    2016-07-28

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

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

    PubMed

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

    2015-09-11

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

  3. 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.

  4. Generalized molecular mechanics including quantum electronic structure variation of polar solvents. II. A molecular dynamics simulation study of water

    NASA Astrophysics Data System (ADS)

    Bursulaya, Badry D.; Jeon, Jonggu; Zichi, Dominic A.; Kim, Hyung J.

    1998-02-01

    By employing the truncated adiabatic basis set (TAB) description developed in the preceding article [B. D. Bursulaya and H. J. Kim, J. Chem. Phys. 108, 3277 (1998), preceding paper], solvent water under an ambient condition is studied via a molecular dynamics (MD) computer simulation method. The evolving charge distribution of each water molecule is described by the mixing of the TAB functions, which fluctuates with its local environment. The parametrization of these basis functions is couched in terms of the complete active space self-consistent field (CASSCF) ab initio calculations in vacuum. By using an interaction site representation for the diagonal and overlap charge distributions of the basis functions, electronic polarizability both in and out of the water molecular plane is accounted for. The ground-state charge distribution for the entire solvent system is determined at the self-consistent field (SCF) level with a numerical iteration method. Two different models, TAB/10 and TAB/10D, are studied. The average water dipole moment in liquid is found to be 2.58 D for the former and 2.65 D for the latter, while it is 1.85 D in vacuum for both models. The solution-phase electronic polarizability distributions, characterized by a narrow but finite width, show that nonlinear hyperpolarizability makes a non-negligible contribution to instantaneous electronic response of water even though its average response mainly falls in a linear regime. It is found that the TAB water predictions for structural, dynamic, spectroscopic, dielectric, and transport properties are in good agreement with corresponding experimental results.

  5. Darcy-Weisbach friction factor at the nanoscale: From atomistic calculations to continuum models

    NASA Astrophysics Data System (ADS)

    Liakopoulos, A.; Sofos, F.; Karakasidis, T. E.

    2017-05-01

    A modification of the Darcy-Weisbach friction factor applicable to nanoscale liquid transport processes is proposed. Non-equilibrium molecular dynamics simulations allow us to access the atomic behaviour of liquids moving in nanochannels, and by comparing atomistic simulation results with continuum Navier-Stokes solutions, we extend the applicability of continuum theory to nanoscale liquid flows. We find that classical continuum theory predictions of power dissipation do not apply in the case of nanochannels and have to be modified accordingly with input from atomistic simulations such as slip velocity and profiles of variable viscosity. The mathematical form of the friction factor expression persists for quite small nanochannel widths, i.e., the form of the relation for the friction factor f Re = const. is practically maintained even at the nanoscale, but the value of the constant significantly increases with increasing hydrophilicity.

  6. 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.

  7. 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).

  8. 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.

  9. 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.

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

    SciTech Connect

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

    2013-05-15

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

  11. 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.

  12. Atomistic Modeling of the Electrode–Electrolyte Interface in Li-Ion Energy Storage Systems: Electrolyte Structuring

    SciTech Connect

    Jorn, Ryan P.; Kumar, Revati; Abraham, Daniel P; Voth, Gregory A.

    2013-01-01

    The solid electrolyte interface (SEI) forms as a result of side reactions between the electrolyte and electrode surfaces in Li-ion batteries and can adversely impact performance by impeding Li-ion transport and diminishing the storage capacity of the battery. To gain a detailed understanding of the impact of the SEI on electrolyte structure, atomistic molecular dynamics simulations of the electrode/electrolyte interface were performed in the presence and absence of the SEI under applied voltages. The composition of the SEI was guided by a wealth of data from experiments and allowed to vary across the simulations. A novel computational approach was implemented that showed significant computational speedup compared to fully polarizable electrode simulations, yet, retained the correct qualitative physics for the electrolyte. A force-matching algorithm was used to construct a new force field for the pure electrolyte, LiPF6 in ethylene carbonate, which was developed from ab initio molecular dynamics simulations. The electrode/electrolyte interface was included using a simple, physically motivated model, which includes the polarization of the conducting graphitic electrode by the electrolyte and the application of an external voltage. Changes in the structure of the electrolyte at the interface as a function of applied voltage, the thickness of the SEI layer, and composition of the SEI provide molecular level insight into the species present at these interfaces and potential clues to the effect of the SEI on transport. It is noted that, with increasing SEI thickness and LiF content, lithium ions are drawn closer to the SEI surface, which implies that these interfaces favor desolvation and promote more rapid lithium transport.

  13. 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. © 2010 The Authors, Ophthalmic and Physiological Optics © 2010 The College of Optometrists.

  14. 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.

  15. 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

  16. 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.

  17. Molecular-level mechanisms of vibrational frequency shifts in a polar liquid.

    PubMed

    Morales, Christine M; Thompson, Ward H

    2011-06-16

    A molecular-level analysis of the origins of the vibrational frequency shifts of the CN stretching mode in neat liquid acetonitrile is presented. The frequency shifts and infrared spectrum are calculated using a perturbation theory approach within a molecular dynamics simulation and are in good agreement with measured values reported in the literature. The resulting instantaneous frequency of each nitrile group is decomposed into the contributions from each molecule in the liquid and by interaction type. This provides a detailed picture of the mechanisms of frequency shifts, including the number of surrounding molecules that contribute to the shift, the relationship between their position and relative contribution, and the roles of electrostatic and van der Waals interactions. These results provide insight into what information is contained in infrared (IR) and Raman spectra about the environment of the probed vibrational mode. © 2011 American Chemical Society

  18. 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.

  19. Addressing uncertainty in atomistic machine learning.

    PubMed

    Peterson, Andrew A; Christensen, Rune; Khorshidi, Alireza

    2017-05-10

    Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate of the uncertainty when the width is comparable to that in the training data. Intriguingly, we also show that the uncertainty can be localized to specific atoms in the simulation, which may offer hints for the generation of training data to strategically improve the machine-learned representation.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 2,4,6-Trimethylpyridinium perchlorate: Polar properties and correlations with molecular structure of organic-inorganic hybrid crystal

    SciTech Connect

    Wojtas, M.; Gagor, A.; Czupinski, O.; Pietraszko, A.; Jakubas, R.

    2009-11-15

    [(CH{sub 3}){sub 3}C{sub 5}H{sub 2}NH][ClO{sub 4}] has been synthesized and characterized by X-ray (at 344, 245, 180 and 115 K), calorimetric, dilatometric, dielectric and pyroelectric measurements. At room temperature the crystal structure is polar, space group Pmn2{sub 1}. It consists of discrete disordered [ClO{sub 4}]{sup -} anions and ordered trimethylpyridinium cations giving the 3D network of hydrogen bonds. The compound reveals a rich polymorphism in the solid state. It undergoes four solid-solid phase transitions: from phases I to II at 356/327 K (heating/cooling), II->III at 346/326, III->IV at 226 K and IV->V at 182/170 K. [(CH{sub 3}){sub 3}C{sub 5}H{sub 2}NH][ClO{sub 4}] reveals a strong pyroelectric response over a wide temperature region (phases III, IV and V) with the spontaneous polarization changes (DELTAP{sub s}) of the order of 1.5-8x10{sup -3}C/m{sup 2}. The spontaneous polarization is irreversible over all the polar phases, however, the magnitude of the DELTAP{sub s} in the vicinity of the phase transitions is characteristic of compounds with the ferroelectric order. The molecular mechanism of the successive phases transitions in the studied crystal is proposed. - A novel organic-inorganic hybrid material, simple ionic salt: 2,4,6-trimethylpyridinium perchlorate, [(CH{sub 3}){sub 3}C{sub 5}H{sub 2}NH][ClO{sub 4}] has been synthesized. In this paper we report singlecrystal X-ray, powder X-ray, calorimetric, dilatometric, dielectric and pyroelectric studies of this compound over a wide temperature range. A possible mechanism of the structural phase transitions in [(CH{sub 3}){sub 3}C{sub 5}H{sub 2}NH][ClO{sub 4}] is discussed with particular attention focused on unusually strong pyroelectric properties.

  5. 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.

  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. 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.

  8. Modeling of the mutual molecular polarization with an electronegativity equalization approach

    SciTech Connect

    Gerwens, H.; Jug, K.

    1995-12-05

    A model for the mutual polarization of two approaching molecules is proposed, exploiting the principle of electronegativity equalization. The deformation of the electronic density of one molecule is the response to the perturbation of its chemical potential due to the electrostatic potential of the other molecule. The electronic densities, the density deformations, and the electrostatic potentials of both molecules are described with a previously developed asymptotic density model (ADM). The ADM model allows a partitioning of all relevant properties in terms of atomic quantities. The perturbation of the chemical potential is given in atomic resolution, and the change of the electronic density is represented in terms of atomic charges. A hardness tensor, which determines the changes of the atomic chemical potentials due to the changes of the atomic charges, is modeled consistently with the ADM and earlier approaches. The results of the model, the changes of atomic charges within the molecules due to their mutual interaction, are compared with the changes of atomic charges obtained from population analysis of ab initio calculations. 31 refs., 7 figs., 3 tabs.

  9. 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

  10. 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.

  11. 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

  12. Slow Molecular Motions in Ionic Liquids Probed by Cross-Relaxation of Nuclear Spins During Overhauser Dynamic Nuclear Polarization.

    PubMed

    Banerjee, Abhishek; Dey, Arnab; Chandrakumar, Narayanan

    2016-11-14

    Solution-state Overhauser dynamic nuclear polarization (ODNP) at moderate fields, performed by saturating the electron spin resonance (ESR) of a free radical added to the sample of interest, is well known to lead to significant NMR signal enhancements in the steady state, owing to electron-nuclear cross-relaxation. Here it is shown that under conditions which limit radical access to the molecules of interest, the time course of establishment of ODNP can provide a unique window into internuclear cross-relaxation, and reflects relatively slow molecular motions. This behavior, modeled mathematically by a three-spin version of the Solomon equations (one unpaired electron and two nuclear spins), is demonstrated experimentally on the (19) F/(1) H system in ionic liquids. Bulky radicals in these viscous environments turn out to be just the right setting to exploit these effects. Compared to standard nuclear Overhauser effect (NOE) work, the present experiment offers significant improvement in dynamic range and sensitivity, retains usable chemical shift information, and reports on molecular motions in the sub-megahertz (MHz) to tens of MHz range-motions which are not accessed at high fields. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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

  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. 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.

  16. Filters for Improvement of Multiscale Data from Atomistic Simulations

    DOE PAGES

    Gardner, David J.; Reynolds, Daniel R.

    2017-01-05

    Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

  17. 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.

  18. 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.

  19. 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

  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. 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.

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

    SciTech Connect

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

    2013-11-21

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

  3. 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.

  4. ALMA Observations of Dust Polarization and Molecular Line Emission from the Class 0 Protostellar Source Serpens SMM1

    NASA Astrophysics Data System (ADS)

    Hull, Charles L. H.; Girart, Josep M.; Tychoniec, Łukasz; Rao, Ramprasad; Cortés, Paulo C.; Pokhrel, Riwaj; Zhang, Qizhou; Houde, Martin; Dunham, Michael M.; Kristensen, Lars E.; Lai, Shih-Ping; Li, Zhi-Yun; Plambeck, Richard L.

    2017-10-01

    We present high angular resolution dust polarization and molecular line observations carried out with the Atacama Large Millimeter/submillimeter Array (ALMA) toward the Class 0 protostar Serpens SMM1. By complementing these observations with new polarization observations from the Submillimeter Array (SMA) and archival data from the Combined Array for Research in Millimeter-wave Astronomy (CARMA) and the James Clerk Maxwell Telescopes (JCMT), we can compare the magnetic field orientations at different spatial scales. We find major changes in the magnetic field orientation between large (∼0.1 pc) scales—where the magnetic field is oriented E–W, perpendicular to the major axis of the dusty filament where SMM1 is embedded—and the intermediate and small scales probed by CARMA (∼1000 au resolution), the SMA (∼350 au resolution), and ALMA (∼140 au resolution). The ALMA maps reveal that the redshifted lobe of the bipolar outflow is shaping the magnetic field in SMM1 on the southeast side of the source; however, on the northwestern side and elsewhere in the source, low-velocity shocks may be causing the observed chaotic magnetic field pattern. High-spatial-resolution continuum and spectral-line observations also reveal a tight (∼130 au) protobinary system in SMM1-b, the eastern component of which is launching an extremely high-velocity, one-sided jet visible in both {CO}(J=2\\to 1) and {SiO}(J=5\\to 4); however, that jet does not appear to be shaping the magnetic field. These observations show that with the sensitivity and resolution of ALMA, we can now begin to understand the role that feedback (e.g., from protostellar outflows) plays in shaping the magnetic field in very young, star-forming sources like SMM1.

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  6. Surface Polarity and Self-Structured Nanogrooves Collaboratively Oriented Molecular Packing for High Crystallinity toward Efficient Charge Transport.

    PubMed

    Ji, Deyang; Xu, Xiaomin; Jiang, Longfeng; Amirjalayer, Saeed; Jiang, Lang; Zhen, Yonggang; Zou, Ye; Yao, Yifan; Dong, Huanli; Yu, Junsheng; Fuchs, Harald; Hu, Wenping

    2017-02-22

    Efficient charge transport in organic semiconductors is essential for construction of high performance optoelectronic devices. Herein, for the first time, we demonstrate that poly(amic acid) (PAA), a facilely deposited and annealing-free dielectric layer, can tailor the growth of organic semiconductor films with large area and high crystallinity toward efficient charge transport and high mobility in their thin film transistors. Pentacene is used as a model system to demonstrate the concept with mobility up to 30.6 cm(2) V(-1) s(-1), comparable to its high quality single crystal devices. The structure of PAA has corrugations with OH groups pointing out of the surface, and the presence of an amide bond further allows adjacent polymer strands to interact via hydrogen bonding, leading to a self-rippled surface perpendicular to the corrugation. On the other hand, the strong polar groups (-COOH/-CONH) of PAA could provide repulsive forces between PAA and pentacene, which results in the vertical orientation of pentacene on the dielectric surface. Indeed, in comparison with its imidized counterpart polyimide (PI), PAA dielectric significantly enhances the film crystallinity, drastically increases the domain size, and decreases the interface trap density, giving rise to superior device performance with high mobility. This concept can be extended to more organic semiconducting systems, e.g., 2,6-diphenylanthracene (DPA), tetracene, copper phthalocyanine (CuPc), and copper hexadecafluorophthalocyanine (F16CuPc), demonstrating the general applicability. The results show the importance of combining surface nanogrooves with the strong polarity in orienting the molecular arrangement for high crystallinity toward efficient charge transport in organic semiconductors.

  7. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Does quantum mechanics tell an atomistic spacetime?

    NASA Astrophysics Data System (ADS)

    Elze, Hans-Thomas

    2009-06-01

    The canonical answer to the question posed is "Yes." - tacitly assuming that quantum theory and the concept of spacetime are to be unified by 'quantizing' a theory of gravitation. Yet, instead, one may ponder: Could quantum mechanics arise as a coarse-grained reflection of the atomistic nature of spacetime? - We speculate that this may indeed be the case. We recall the similarity between evolution of classical and quantum mechanical ensembles, according to Liouville and von Neumann equation, respectively. The classical and quantum mechanical equations are indistinguishable for objects which are free or subject to spatially constant but possibly time dependent, or harmonic forces, if represented appropriately. This result suggests a way to incorporate anharmonic interactions, including fluctuations which are tentatively related to the underlying discreteness of spacetime. Being linear and local at the quantum mechanical level, the model offers a decoherence and natural localization mechanism. However, the relation to primordial deterministic degrees of freedom is nonlocal.

  9. 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.

  10. 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.

  11. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

    PubMed

    May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

    2014-02-01

    To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

  12. Molecular organization by head to tail recognition for polar liquid crystals

    NASA Astrophysics Data System (ADS)

    Yoshizawa, Atsushi; Narumi, Tsuyoshi; Dewa, Harutada; Hatai, Shinobu; Araake, Norihisa; Nishiyama, Isa; Yamamoto, Jun; Yokoyama, Hiroshi

    2003-12-01

    Novel non-symmetric dimeric liquid crystal, 1-(4-cyanobiphenyl-4'-yloxy)-11-[2-(4-octylphenyl)pyrimidine-5-yloxy]undecane (8YP11OCB), has been prepared and the physical properties investigated by means of optical microscopy, differential scanning calorimetry (DSC), X-ray diffraction and dielectric measurements. The crystal structure has been determined to understand microscopic behavior of the compound. Electro-optical properties for 8YP11OCB were compared to those for 1-(4-cyanobiphenyl-4'-yloxy)-11-[4-(5-octylpyrimidine-2-yl)phenyl-4''-oxy]undecane (8PY11OCB). 8YP11OCB with smaller dielectric anisotropy than 8PY11OCB was found to show lower threshold voltage in the intercalated smectic A phase than 8PY11OCB. Crystal structure of 8YP11OCB indicates that three types of core-core interactions exist and that the enthalpy gained by the specific interactions stabilizes the molecular packing with large free volume in the SmA phase.

  13. Molecular organization by head-to-tail recognition for polar liquid crystals

    NASA Astrophysics Data System (ADS)

    Yoshizawa, Atsushi; Narumi, Tsuyoshi; Dewa, Harutada; Hatai, Shinobu; Araake, Norihisa; Nishiyama, Isa; Yamamoto, Jun; Yokoyama, Hiroshi

    2004-01-01

    Novel non-symmetric dimeric liquid crystal, 1-(4-cyanobiphenyl-4'-yloxy)-11-[2-(4-octylphenyl)pyrimidine-5-yloxy]undecane (8YP11OCB), has been prepared and the physical properties investigated by means of optical microscopy, differential scanning calorimetry (DSC), X-ray diffraction and dielectric measurements. The crystal structure has been determined to understand microscopic behavior of the compound. Electro-optical properties for 8YP11OCB were compared to those for 1-(4-cyanobiphenyl-4'-yloxy)-11-[4-(5-octylpyrimidine-2-yl)phenyl-4"-oxy]undecane (8PY11OCB). 8YP11OCB with smaller dielectric anisotropy than 8PY11OCB was found to show a lower threshold voltage in the smectic A phase than 8PY11OCB. Crystal structure of 8YP11OCB indicates that three types of core-core interactions exist and that the enthalpy gained by the specific interactions stabilizes the molecular packing with large free volume in the SmA phase.

  14. 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

  15. 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.

  16. High molecular weight non-polar hydrocarbons as pure model substances and in motor oil samples can be ionized without fragmentation by atmospheric pressure chemical ionization mass spectrometry.

    PubMed

    Hourani, Nadim; Kuhnert, Nikolai

    2012-10-15

    High molecular weight non-polar hydrocarbons are still difficult to detect by mass spectrometry. Although several studies have targeted this problem, lack of good self-ionization has limited the ability of mass spectrometry to examine these hydrocarbons. Failure to control ion generation in the atmospheric pressure chemical ionization (APCI) source hampers the detection of intact stable gas-phase ions of non-polar hydrocarbon in mass spectrometry. Seventeen non-volatile non-polar hydrocarbons, reported to be difficult to ionize, were examined by an optimized APCI methodology using nitrogen as the reagent gas. All these analytes were successfully ionized as abundant and intact stable [M-H](+) ions without the use of any derivatization or adduct chemistry and without significant fragmentation. Application of the method to real-life hydrocarbon mixtures like light shredder waste and car motor oil was demonstrated. Despite numerous reports to the contrary, it is possible to ionize high molecular weight non-polar hydrocarbons by APCI, omitting the use of additives. This finding represents a significant step towards extending the applicability of mass spectrometry to non-polar hydrocarbon analyses in crude oil, petrochemical products, waste or food. Copyright © 2012 John Wiley & Sons, Ltd.

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

    SciTech Connect

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

    1986-01-01

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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  5. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

    Zhou, Xiaowang W.; Sills, Ryan B.; Ward, Donald 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 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:more » Ec = Asin2β + Bcos2β, 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. As a result, with our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.« less

  6. Statistical 3D 'Atomistic' Simulation of Decanano MOSFETs

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Slavcheva, G.; Brown, A. R.; Balasubramaniam, R.; Davies, J. H.

    2000-01-01

    A 3D statistical 'atomistic' simulation technique has been developed to study the effect of the random dopant induced parameter fluctuations in aggressively scaled MOSFETs. Efficient implementation of the 'atomistic' simulation approach has been used to investigate the threshold voltage standard deviation and lowering in the case of uniformly doped MOSFETs, and in fluctuation-resistant architectures utilising epitaxial-layers and delta-doping. The effect of the random doping in the polysilicon gate on the threshold voltage fluctuations has also been thoroughly investigated. The influence of a single-charge trapping on the channel conductivity in decanano MOSFETs is studied in the 'atomistic' framework as well. Quantum effects are taken into consideration in our 'atomistic' simulations using the density gradient formalism.

  7. 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.

  8. Electrocaloric effect in ferroelectric alloys from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Lisenkov, Sergey; Ponomareva, Inna

    2012-02-01

    Caloric effects, such as magnetocaloric and electrocaloric effects, have attracted a lot of attention recently in the context of increasing interest in energy conversion and renewable energy materials and devices. Here we develop and use accurate first-principles-based simulations to study electrocaloric effect (ECE) from an atomistic point of view. In particular, we develop a computational technique that allows both direct and indirect simulations of ECE within the same atomistic framework. We then use such a tool to provide first systematic comparison between ECE estimates obtained from direct and indirect approach which will allow us to bridge the macroscopic and atomistic description of ECE. The results of our direct atomistic simulations are then used to explore the intrinsic features of ECE in ferroelectrics with multiple transitions.

  9. ``Half-hydration'' at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hidekazu; Yamaguchi, Shoichi; Sen, Sobhan; Morita, Akihiro; Tahara, Tahei

    2010-04-01

    A solute-solvent interaction at the air/water interface was investigated both experimentally and theoretically, by studying a prototypical surface-active polarity indicator molecule, coumarin 110 (C110), adsorbed at the air/water interface with heterodyne-detected electronic sum frequency generation (HD-ESFG) spectroscopy, polarization second harmonic generation (SHG), and a molecular dynamics (MD) simulation. The second-order nonlinear optical susceptibility (χ(2)) tensor elements of C110 at the air/water interface were determined experimentally by HD-ESFG and polarization SHG, and information on "intermediate" polarity sensed by C110 at the interface was obtained by HD-ESFG. An MD simulation and a time-dependent density functional theory calculation were used to theoretically evaluate the χ(2) tensor elements, which were in good agreement with the experimental results of HD-ESFG and polarization SHG. The microscopic "half-hydration" structure around C110 at the water surface was visualized on the basis of the MD simulation data, with which we can intuitively understand the microscopic origin of the surface activity of C110 and the intermediate polarity sensed by C110 at the air/water interface.

  10. 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. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. 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.

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

    PubMed

    Katoh, Masaru

    2002-08-01

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

  13. Dynamic Nuclear Polarization Fast Field Cycling Method for the Selective Study of Molecular Dynamics in Block Copolymers.

    PubMed

    Gizatullin, Bulat; Neudert, Oliver; Stapf, Siegfried; Mattea, Carlos

    2017-09-06

    Dynamic nuclear polarization (DNP) is one of the most useful methods to increase sensitivity in NMR spectroscopy. It is based on the transfer of magnetization from an electron to the nuclear spin system. Based on previous work that demonstrated the feasibility of integrating DNP with fast field cycling (FFC) relaxometry and the possibility to distinguish between different mechanisms, such as the Overhauser effect (OE) and the solid effect (SE), the first FFC study of the differential relaxation properties of a copolymer is presented. For this purpose, concentrated solutions of the polystyrene-block-polybutadiene-block-polystyrene (SBS) triblock copolymer and the corresponding homopolymers were investigated. T1 -T2 relaxation data are discussed in terms of molecular mobility and the presence of radicals. The DNP selective data indicate a dominant SE contribution to the enhancement of the NMR signal for both blocks of the triblock copolymer and for the homopolymer solutions. The enhancement factors are different for both polymer types and in the copolymer, which is explained by the individual (1) H T1 relaxation times and different electron-nucleus coupling strength. The T1 relaxation dispersion measurements of the SE enhanced signal were performed, which led to improved signal-to-noise ratios that allowed the site-specific separation of relaxation times and their dependence on the Larmor frequency with a higher accuracy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 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

  15. Atomistic Cohesive Zone Models for Interface Decohesion in Metals

    NASA Technical Reports Server (NTRS)

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed

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

    2016-01-01

    Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. 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.

  1. Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2010-01-01

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

  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. 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

  5. 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.

  6. [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.

  7. 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

  8. 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.

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

    SciTech Connect

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

    1988-02-01

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

  10. 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.

  11. 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.

  12. 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.

  13. Strain Functionals for Characterizing Atomistic Geometries

    NASA Astrophysics Data System (ADS)

    Kober, Edward; Rudin, Sven

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

  14. 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.

  15. 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.

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

    PubMed

    Ribeiro, Mauro C C

    2010-04-07

    Thermodynamics, equilibrium structure, and dynamics of glass-forming liquids Ca(NO(3))(2) x nH(2)O, n=4, 6, and 8, have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H(2)O and NO(3)(-) on the basis of previous fluctuating charge models for pure water and the molten salt 2Ca(NO(3))(2) x 3 KNO(3). Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature, T(g), estimated from MD simulations was dependent on polarization, in particular the dependence of T(g) with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation, cation-anion, and water-water structures. Polarization increases the diffusion coefficient of H(2)O, but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization, but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

  17. The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors

    NASA Astrophysics Data System (ADS)

    Craig, E. M.; Dey, S.; Mogilner, A.

    2011-09-01

    We use linear stability analysis and numerical solutions of partial differential equations to investigate pattern formation in the one-dimensional system of short dynamic polymers and one (plus-end directed) or two (one is plus-end, another minus-end directed) molecular motors. If polymer sliding and motor gliding rates are slow and/or the polymer turnover rate is fast, then the polymer-motor bundle has mixed polarity and homogeneous motor distribution. However, if motor gliding is fast, a sarcomeric pattern with periodic bands of alternating polymer polarity separated by motor aggregates evolves. On the other hand, if polymer sliding is fast, a graded-polarity bundle with motors at the center emerges. In the presence of the second, minus-end directed motor, the sarcomeric pattern is more ubiquitous, while the graded-polarity pattern is destabilized. However, if the minus-end motor is weaker than the plus-end directed one, and/or polymer nucleation is autocatalytic, and/or long polymers are present in the bundle, then a spindle-like architecture with a sorted-out polarity emerges with the plus-end motors at the center and minus-end motors at the edges. We discuss modeling implications for actin-myosin fibers and in vitro and meiotic spindles.

  18. 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.

  19. In Search of an Imprint of Magnetization in the Balloon-Borne Observations of the Polarized Dust Emission From Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Soler, Juan Diego

    The observation of the polarization of thermal emission from dust grains is a key method in the study of the role of the magnetic fields in the star formation process. This dissertation introduces BLASTPol, a submillimeter telescope for polarization designed for mapping dust polarization in scales ranging from pre-stellar cores to sections of molecular clouds and the Histogram of Relative Orientations (HRO), a new statistical tool for the analysis of the polarization maps. The observations of BLASTPol were possible thanks to a novel light-weight carbon fibre sunshield structure and the detailed thermal modeling of the balloon-borne platform. The carbon fibre structure is based on the construction technique developed for the Spider gondola which integrates detailed Finite Element Analysis with the use of composite materials and adhesive joints. The thermal model uses 3D Computer Assisted Design allowing unprecedented control of the sun avoidance limits and detailed modeling of the gondola components. BLASTPol made observations of the Lupus I and Vela C molecular clouds, the Carina Nebula, and the Puppis Cloud Complex in two balloon-borne flights over Antarctica in 2010 and 2012. The construction of polarization maps from the BLASTPol10 observations was affected by multiple pathologies in the data. However, the preliminary maps indicate the need of a statistical tool which allows relating these observations to magnetohydrodynamics (MHD) simulations motivating the development of HRO. Most of the problems in the BLASTPol10 data were successfully addressed in BLASTPol12 and the construction of polarization maps of the observed regions is currently in progress. The HRO is a statistical tool which assesses the relative orientation between the magnetic field and the density structures. This tool was characterized by using simulated molecular clouds with different magnetization indicating that: 1. There is an imprint of the magnetization level in the relative orientation of

  20. 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

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

    SciTech Connect

    Sedlmeier, Felix; Netz, Roland R.

    2013-03-21

    The solvation thermodynamics and in particular the solvation heat capacity of polar and charged solutes in water is studied using atomistic molecular dynamics simulations. As ionic solutes we consider a F{sup -} and a Na{sup +} ion, as an example for a polar molecule with vanishing net charge we take a SPC/E water molecule. The partial charges of all three solutes are varied in a wide range by a scaling factor. Using a recently introduced method for the accurate determination of the solvation free energy of polar solutes, we determine the free energy, entropy, enthalpy, and heat capacity of the three different solutes as a function of temperature and partial solute charge. We find that the sum of the solvation heat capacities of the Na{sup +} and F{sup -} ions is negative, in agreement with experimental observations, but our results uncover a pronounced difference in the heat capacity between positively and negatively charged groups. While the solvation heat capacity {Delta}C{sub p} stays positive and even increases slightly upon charging the Na{sup +} ion, it decreases upon charging the F{sup -} ion and becomes negative beyond an ion charge of q=-0.3e. On the other hand, the heat capacity of the overall charge-neutral polar solute derived from a SPC/E water molecule is positive for all charge scaling factors considered by us. This means that the heat capacity of a wide class of polar solutes with vanishing net charge is positive. The common ascription of negative heat capacities to polar chemical groups might arise from the neglect of non-additive interaction effects between polar and apolar groups. The reason behind this non-additivity is suggested to be related to the second solvation shell that significantly affects the solvation thermodynamics and due to its large spatial extent induces quite long-ranged interactions between solvated molecular parts and groups.

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

    PubMed

    Sedlmeier, Felix; Netz, Roland R

    2013-03-21

    The solvation thermodynamics and in particular the solvation heat capacity of polar and charged solutes in water is studied using atomistic molecular dynamics simulations. As ionic solutes we consider a F(-) and a Na(+) ion, as an example for a polar molecule with vanishing net charge we take a SPC/E water molecule. The partial charges of all three solutes are varied in a wide range by a scaling factor. Using a recently introduced method for the accurate determination of the solvation free energy of polar solutes, we determine the free energy, entropy, enthalpy, and heat capacity of the three different solutes as a function of temperature and partial solute charge. We find that the sum of the solvation heat capacities of the Na(+) and F(-) ions is negative, in agreement with experimental observations, but our results uncover a pronounced difference in the heat capacity between positively and negatively charged groups. While the solvation heat capacity ΔC(p) stays positive and even increases slightly upon charging the Na(+) ion, it decreases upon charging the F(-) ion and becomes negative beyond an ion charge of q = -0.3e. On the other hand, the heat capacity of the overall charge-neutral polar solute derived from a SPC/E water molecule is positive for all charge scaling factors considered by us. This means that the heat capacity of a wide class of polar solutes with vanishing net charge is positive. The common ascription of negative heat capacities to polar chemical groups might arise from the neglect of non-additive interaction effects between polar and apolar groups. The reason behind this non-additivity is suggested to be related to the second solvation shell that significantly affects the solvation thermodynamics and due to its large spatial extent induces quite long-ranged interactions between solvated molecular parts and groups.

  3. 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.

  4. 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.

  5. 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.

  6. 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 act